0s autopkgtest [19:37:46]: starting date and time: 2025-02-15 19:37:46+0000 0s autopkgtest [19:37:46]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [19:37:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e_65e81b/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc,src:iproute2,src:php-twig,src:postgresql-17,src:postgresql-common,src:roundcube --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu1 iproute2/6.13.0-1ubuntu1 php-twig/3.19.0-1 postgresql-17/17.3-2 postgresql-common/273 roundcube/1.6.10+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-11.secgroup --name adt-plucky-amd64-cpptraj-20250215-193746-juju-7f2275-prod-proposed-migration-environment-2-61e78bef-39fb-4f2b-9cdb-4d748f9edb5d --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 49s autopkgtest [19:38:35]: testbed dpkg architecture: amd64 49s autopkgtest [19:38:35]: testbed apt version: 2.9.28 50s autopkgtest [19:38:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [19:38:36]: testbed release detected to be: None 51s autopkgtest [19:38:37]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 51s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 51s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 51s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 52s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [62.8 kB] 52s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.7 kB] 52s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [822 kB] 52s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [82.9 kB] 52s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.0 kB] 52s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 52s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 52s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [823 kB] 52s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [287 kB] 52s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [10.6 kB] 52s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3520 B] 52s Fetched 2294 kB in 1s (2359 kB/s) 53s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 54s Calculating upgrade... 54s The following packages will be upgraded: 54s libtasn1-6 54s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 51.2 kB of archives. 54s After this operation, 22.5 kB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libtasn1-6 amd64 4.20.0-2 [51.2 kB] 54s Fetched 51.2 kB in 0s (181 kB/s) 55s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 55s Preparing to unpack .../libtasn1-6_4.20.0-2_amd64.deb ... 55s Unpacking libtasn1-6:amd64 (4.20.0-2) over (4.19.0-3build1) ... 55s Setting up libtasn1-6:amd64 (4.20.0-2) ... 55s Processing triggers for libc-bin (2.40-4ubuntu1) ... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. 55s autopkgtest [19:38:41]: upgrading testbed (apt dist-upgrade and autopurge) 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 56s Starting 2 pkgProblemResolver with broken count: 0 56s Done 57s Entering ResolveByKeep 57s 57s The following packages will be upgraded: 57s iproute2 libc-bin libc-dev-bin libc6 libc6-dev locales 57s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 11.8 MB of archives. 57s After this operation, 746 kB of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-dev-bin amd64 2.41-1ubuntu1 [24.7 kB] 57s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6-dev amd64 2.41-1ubuntu1 [2182 kB] 58s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 locales all 2.41-1ubuntu1 [4246 kB] 58s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc6 amd64 2.41-1ubuntu1 [3327 kB] 58s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libc-bin amd64 2.41-1ubuntu1 [701 kB] 58s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 58s Preconfiguring packages ... 58s Fetched 11.8 MB in 1s (13.4 MB/s) 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108914 files and directories currently installed.) 58s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu1_amd64.deb ... 58s Unpacking libc-dev-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 58s Preparing to unpack .../libc6-dev_2.41-1ubuntu1_amd64.deb ... 58s Unpacking libc6-dev:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 58s Preparing to unpack .../locales_2.41-1ubuntu1_all.deb ... 58s Unpacking locales (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 59s Preparing to unpack .../libc6_2.41-1ubuntu1_amd64.deb ... 59s Checking for services that may need to be restarted... 59s Checking init scripts... 59s Checking for services that may need to be restarted... 59s Checking init scripts... 59s Stopping some services possibly affected by the upgrade (will be restarted later): 59s cron: stopping...done. 59s 59s Unpacking libc6:amd64 (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 59s Setting up libc6:amd64 (2.41-1ubuntu1) ... 59s Checking for services that may need to be restarted... 59s Checking init scripts... 59s Restarting services possibly affected by the upgrade: 59s cron: restarting...done. 59s 59s Services restarted successfully. 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 59s Preparing to unpack .../libc-bin_2.41-1ubuntu1_amd64.deb ... 59s Unpacking libc-bin (2.41-1ubuntu1) over (2.40-4ubuntu1) ... 59s Setting up libc-bin (2.41-1ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108915 files and directories currently installed.) 59s Preparing to unpack .../iproute2_6.13.0-1ubuntu1_amd64.deb ... 60s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 60s Setting up iproute2 (6.13.0-1ubuntu1) ... 60s Setting up locales (2.41-1ubuntu1) ... 60s Installing new version of config file /etc/locale.alias ... 60s Generating locales (this might take a while)... 62s en_US.UTF-8... done 62s Generation complete. 62s Setting up libc-dev-bin (2.41-1ubuntu1) ... 62s Setting up libc6-dev:amd64 (2.41-1ubuntu1) ... 62s Processing triggers for man-db (2.13.0-1) ... 63s Processing triggers for systemd (257.2-3ubuntu1) ... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 64s Starting pkgProblemResolver with broken count: 0 64s Starting 2 pkgProblemResolver with broken count: 0 64s Done 64s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 67s autopkgtest [19:38:53]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 67s autopkgtest [19:38:53]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj 70s Get:1 http://ftpmaster.internal/ubuntu plucky/universe cpptraj 5.1.0+dfsg-4build1 (dsc) [2183 B] 70s Get:2 http://ftpmaster.internal/ubuntu plucky/universe cpptraj 5.1.0+dfsg-4build1 (tar) [28.4 MB] 70s Get:3 http://ftpmaster.internal/ubuntu plucky/universe cpptraj 5.1.0+dfsg-4build1 (diff) [6164 B] 70s gpgv: Signature made Mon Aug 5 15:58:41 2024 UTC 70s gpgv: using RSA key B8340990283D8D9BC1949AC74799A35146D12B35 70s gpgv: Can't check signature: No public key 70s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4build1.dsc: no acceptable signature found 72s autopkgtest [19:38:58]: testing package cpptraj version 5.1.0+dfsg-4build1 72s autopkgtest [19:38:58]: build not needed 79s autopkgtest [19:39:05]: test command1: preparing testbed 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Starting pkgProblemResolver with broken count: 0 80s Starting 2 pkgProblemResolver with broken count: 0 80s Done 80s The following NEW packages will be installed: 80s cpptraj libaec0 libarpack2t64 libblas3 libfftw3-double3 libgfortran5 80s libgomp1 libhdf5-310 libhdf5-hl-310 liblapack3 libnetcdf19t64 libopenmm8.1 80s libsz2 netcdf-bin 80s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 10.9 MB of archives. 80s After this operation, 31.9 MB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-17ubuntu1 [910 kB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 81s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libarpack2t64 amd64 3.9.1-4 [120 kB] 81s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-17ubuntu1 [148 kB] 81s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1build1 [839 kB] 81s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 81s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 81s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 81s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 81s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnetcdf19t64 amd64 1:4.9.2-6ubuntu2 [531 kB] 81s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-3 [1120 kB] 81s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 cpptraj amd64 5.1.0+dfsg-4build1 [1872 kB] 81s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 netcdf-bin amd64 1:4.9.2-6ubuntu2 [226 kB] 81s Fetched 10.9 MB in 1s (12.8 MB/s) 81s Selecting previously unselected package libblas3:amd64. 81s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 108916 files and directories currently installed.) 81s Preparing to unpack .../00-libblas3_3.12.1-2_amd64.deb ... 81s Unpacking libblas3:amd64 (3.12.1-2) ... 82s Selecting previously unselected package libgfortran5:amd64. 82s Preparing to unpack .../01-libgfortran5_14.2.0-17ubuntu1_amd64.deb ... 82s Unpacking libgfortran5:amd64 (14.2.0-17ubuntu1) ... 82s Selecting previously unselected package liblapack3:amd64. 82s Preparing to unpack .../02-liblapack3_3.12.1-2_amd64.deb ... 82s Unpacking liblapack3:amd64 (3.12.1-2) ... 82s Selecting previously unselected package libarpack2t64:amd64. 82s Preparing to unpack .../03-libarpack2t64_3.9.1-4_amd64.deb ... 82s Unpacking libarpack2t64:amd64 (3.9.1-4) ... 82s Selecting previously unselected package libgomp1:amd64. 82s Preparing to unpack .../04-libgomp1_14.2.0-17ubuntu1_amd64.deb ... 82s Unpacking libgomp1:amd64 (14.2.0-17ubuntu1) ... 82s Selecting previously unselected package libfftw3-double3:amd64. 82s Preparing to unpack .../05-libfftw3-double3_3.3.10-2fakesync1build1_amd64.deb ... 82s Unpacking libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 82s Selecting previously unselected package libaec0:amd64. 82s Preparing to unpack .../06-libaec0_1.1.3-1_amd64.deb ... 82s Unpacking libaec0:amd64 (1.1.3-1) ... 82s Selecting previously unselected package libsz2:amd64. 82s Preparing to unpack .../07-libsz2_1.1.3-1_amd64.deb ... 82s Unpacking libsz2:amd64 (1.1.3-1) ... 82s Selecting previously unselected package libhdf5-310:amd64. 82s Preparing to unpack .../08-libhdf5-310_1.14.5+repack-3_amd64.deb ... 82s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 82s Selecting previously unselected package libhdf5-hl-310:amd64. 82s Preparing to unpack .../09-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 82s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 82s Selecting previously unselected package libnetcdf19t64:amd64. 82s Preparing to unpack .../10-libnetcdf19t64_1%3a4.9.2-6ubuntu2_amd64.deb ... 82s Unpacking libnetcdf19t64:amd64 (1:4.9.2-6ubuntu2) ... 82s Selecting previously unselected package libopenmm8.1. 82s Preparing to unpack .../11-libopenmm8.1_8.1.2+dfsg-3_amd64.deb ... 82s Unpacking libopenmm8.1 (8.1.2+dfsg-3) ... 82s Selecting previously unselected package cpptraj. 82s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-4build1_amd64.deb ... 82s Unpacking cpptraj (5.1.0+dfsg-4build1) ... 82s Selecting previously unselected package netcdf-bin. 82s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-6ubuntu2_amd64.deb ... 82s Unpacking netcdf-bin (1:4.9.2-6ubuntu2) ... 82s Setting up libgomp1:amd64 (14.2.0-17ubuntu1) ... 82s Setting up libaec0:amd64 (1.1.3-1) ... 82s Setting up libblas3:amd64 (3.12.1-2) ... 82s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 82s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1build1) ... 82s Setting up libgfortran5:amd64 (14.2.0-17ubuntu1) ... 82s Setting up libopenmm8.1 (8.1.2+dfsg-3) ... 82s Setting up libsz2:amd64 (1.1.3-1) ... 82s Setting up liblapack3:amd64 (3.12.1-2) ... 82s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 82s Setting up libarpack2t64:amd64 (3.9.1-4) ... 82s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 82s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 82s Setting up libnetcdf19t64:amd64 (1:4.9.2-6ubuntu2) ... 82s Setting up netcdf-bin (1:4.9.2-6ubuntu2) ... 82s Setting up cpptraj (5.1.0+dfsg-4build1) ... 82s Processing triggers for man-db (2.13.0-1) ... 82s Processing triggers for libc-bin (2.41-1ubuntu1) ... 83s autopkgtest [19:39:09]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary 83s autopkgtest [19:39:09]: test command1: [----------------------- 84s make: Entering directory '/tmp/autopkgtest.gaswEJ/build.Psr/src/test' 84s lrwxrwxrwx 1 ubuntu ubuntu 16 Feb 15 19:39 ../bin/cpptraj -> /usr/bin/cpptraj 84s make[1]: Entering directory '/tmp/autopkgtest.gaswEJ/build.Psr/src/test' 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_General 84s 84s CPPTRAJ: General tests 84s 84s All 15 comparisons passed. 84s 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Parallel 84s 84s CPPTRAJ: Parallel tests. 84s 84s CPPTRAJ: Parallel test with trajectory offset 84s 84s All 7 comparisons passed. 84s 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Strip 84s 84s CPPTRAJ: One frame strip command test 84s 84s CPPTRAJ: Unstrip (Lig/Rec/Complex) command test 84s 84s CPPTRAJ: Multi frame strip command test. 84s 84s CPPTRAJ: Strip topology with PDB info 84s 84s All 11 comparisons passed. 84s 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_BrokenTraj 84s 84s CPPTRAJ: Broken Traj: Running good trajectory. 84s 84s CPPTRAJ: Broken Traj: Running broken trajectory. 84s 84s CPPTRAJ: Compressed broken trajectory test 84s 84s All 2 comparisons passed. 84s 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_TrajinOffset 84s 84s CPPTRAJ: Normal trajectory read with offsets. 84s 84s CPPTRAJ: Gzipped trajectory read with offsets 84s 84s CPPTRAJ: Bzip2ed trajectory read with offsets 84s 84s CPPTRAJ: Start argument offset 84s 84s All 4 comparisons passed. 84s 84s ******************************************************************************** 84s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_RemdTraj 84s 84s CPPTRAJ: CRD Replica Trajectory Run with offset 84s 84s CPPTRAJ: CRD Replica Trajectory Run 84s 84s CPPTRAJ: NetCDF Replica Trajectory Run test 84s 84s CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj 84s 84s CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj 84s 84s CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj 84s 84s CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj 84s 84s CPPTRAJ: CRD Replica Trajectory Run with remdout 85s 85s All 8 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_trajout_framerange 85s 85s CPPTRAJ: Trajout Frame Range [Amber Restart] 85s 85s CPPTRAJ: Trajout Frame Range [Amber Coordinates] 85s 85s All 6 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_PerResRMSD 85s 85s CPPTRAJ: Per-Residue RMSD Test. 85s 85s CPPTRAJ: Per-Residue RMSD Test with averaging 85s 85s CPPTRAJ: Per-Residue RMSD Test with residue centering. 85s 85s All 3 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DSSP 85s 85s CPPTRAJ: Secstruct (DSSP) command test. 85s 85s CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. 85s 85s CPPTRAJ: Secstruct (DSSP) command with changing number of residues. 85s 85s CPPTRAJ: Secstruct (DSSP): SS assign output test 85s 85s CPPTRAJ: FtuFabI Assignment test 85s 85s All 10 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Center 85s 85s CPPTRAJ: Center command test. 85s 85s CPPTRAJ: Center origin command test. 85s 85s CPPTRAJ: Center origin mass command test. 85s 85s CPPTRAJ: Center reference command test. 85s 85s CPPTRAJ: Center point test. 85s 85s All 5 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Hbond 85s 85s CPPTRAJ: Solute Hbond test 85s 85s CPPTRAJ: Solute Hbond test with disk caching 85s 85s CPPTRAJ: Solute-solvent hbond test 85s 85s CPPTRAJ: Hbond, no intramolecular hydrogen bonds test 85s 85s CPPTRAJ: Hbond, specified solute masks 85s 85s CPPTRAJ: Hbond, no angle cutoff test 85s 85s CPPTRAJ: Hbond, Bridge nointramol test 85s 85s CPPTRAJ: Hbond with imaging 85s 85s CPPTRAJ: Hbond, orthogonal imaging 85s 85s All 23 comparisons passed. 85s 85s ******************************************************************************** 85s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_NCrestart 85s 85s CPPTRAJ: NetCDF Restart Test - TXT->NetCDF 85s 85s CPPTRAJ: NetCDF Restart Test - NetCDF->TXT 85s 85s CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF 85s 85s CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt 86s 86s All 2 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Image 86s 86s CPPTRAJ: Orthorhombic imaged distance test. 86s 86s CPPTRAJ: Non-orthorhombic imaged distance test. 86s 86s CPPTRAJ: Orthorhombic coordinate imaging test 86s 86s CPPTRAJ: Nonorthorhombic coordinate imaging test 86s 86s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar 86s 86s CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM 86s 86s All 6 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Surf 86s 86s CPPTRAJ: Surface calculation test 86s 86s CPPTRAJ: Partial Surface calculation test 86s 86s CPPTRAJ: LCPO test with GAFF atom types 86s 86s All 3 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Radgyr 86s 86s CPPTRAJ: Radius of gyration command test 86s 86s All 2 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Mask 86s 86s CPPTRAJ: Mask single frame test 86s 86s CPPTRAJ: Mask longer command test. 86s 86s All 5 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Jcoupling 86s 86s CPPTRAJ: J-Coupling single frame test 86s J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. 86s Skipped test: J-Coupling extended test 86s 86s All 1 comparisons passed. 86s 1 comparisons skipped. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Diffusion 86s 86s CPPTRAJ: Diffusion test, no imaging. 86s 86s CPPTRAJ: Diffusion test, old syntax. 86s 86s CPPTRAJ: Diffusion test, new syntax. 86s 86s CPPTRAJ: Diffusion test, nonorthogonal box 86s 86s CPPTRAJ: STFC Diffusion Test 86s 86s CPPTRAJ: STFC Diffusion Test with individual distances 86s 86s CPPTRAJ: STFC Diffusion Test with COM 86s 86s CPPTRAJ: STFC Diffusion Test with second mask 86s 86s All 16 comparisons passed. 86s 86s ******************************************************************************** 86s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Outtraj 86s 86s CPPTRAJ: RMSD Test with outtraj. 87s 87s CPPTRAJ: Outtraj Test with maxmin. 87s 87s All 4 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Charmm 87s 87s CPPTRAJ: CHARMM PSF/DCD test 87s 87s CPPTRAJ: CHARMM DCD Write, step 1. 87s 87s CPPTRAJ: CHARMM DCD Write, step 2. 87s 87s CPPTRAJ: CHAMBER topology read/strip test. 87s 87s CPPTRAJ: Read CHARMM restart 87s 87s CPPTRAJ: CHARMM PSF write 87s 87s CPPTRAJ: CHARMM COORdinates test 87s 87s All 6 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CharmmParams 87s 87s CPPTRAJ: Test updating topology with Charmm parameters (single residue) 87s 87s All 2 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Rotdif 87s 87s CPPTRAJ: Rotational diffusion calculation test 87s 87s All 4 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_NetcdfTraj 87s 87s CPPTRAJ: Convert mdcrd -> NetCDF 87s 87s CPPTRAJ: Convert NetCDF -> mdcrd 87s 87s All 1 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Runavg 87s 87s CPPTRAJ: Coordinate Running Average test. 87s 87s CPPTRAJ: Coordinate Running Average Traj Write 87s 87s All 2 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_RMSD 87s 87s CPPTRAJ: Basic RMSD tests 87s 87s CPPTRAJ: RMS coordinate rotation/rotation matrices test 87s 87s CPPTRAJ: RMS fit with no coordinates modification test. 87s 87s CPPTRAJ: RMS fit to previous test 87s 87s CPPTRAJ: RMS: imaging after unit cell rotation 87s 87s All 12 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_2DRMS 87s 87s CPPTRAJ: 2D RMSD Test. 87s 87s CPPTRAJ: 2D RMSD Test, mass-weighted. 87s 87s CPPTRAJ: 2D RMSD Test with reference trajectory 87s 87s CPPTRAJ: 2D DME Test. 87s 87s CPPTRAJ: 2D RMSD with reference mask test. 87s 87s CPPTRAJ: 2D RMSD test, no fitting. 87s 87s All 6 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Mol2 87s 87s CPPTRAJ: Mol2 Parm/Traj Read/Write Test. 87s 87s CPPTRAJ: PDB => Mol2 87s 87s CPPTRAJ: Amber Top/Rst => Mol2 87s Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. 87s Skipped test: Amber Top/Rst => Mol2, SYBYL atom types 87s 87s All 4 comparisons passed. 87s 1 comparisons skipped. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_NAstruct 87s 87s CPPTRAJ: NAstruct command test. 87s 87s CPPTRAJ: NAstruct command test, single strand 87s 87s All 11 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_NAstruct_8OG 87s 87s CPPTRAJ: NA test (8OG) 87s 87s All 3 comparisons passed. 87s 87s ******************************************************************************** 87s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Average 87s 87s CPPTRAJ: Average Test. 87s 87s All 2 comparisons passed. 87s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Pucker 88s 88s CPPTRAJ: Pucker command test 88s 88s CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test 88s 88s CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. 88s 88s All 3 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AtomMap 88s 88s CPPTRAJ: AtomMap Test 88s 88s CPPTRAJ: AtomMap with 'rmsfit' 88s 88s CPPTRAJ: Atom map charmm->amber atom order 88s 88s CPPTRAJ: Atom map charmm->amber atom order, by residue 88s 88s All 9 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Datafile 88s 88s CPPTRAJ: Data file output precision test 88s 88s CPPTRAJ: Standard -> Grace Data 88s 88s CPPTRAJ: Grace -> Standard Data 88s 88s CPPTRAJ: X column format/precision test. 88s 88s CPPTRAJ: Data file group by name test 88s 88s CPPTRAJ: Data file group by aspect test 88s 88s All 6 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Radial 88s 88s CPPTRAJ: Radial test, non-orthogonal imaging 88s 88s CPPTRAJ: Radial test, orthogonal and no imaging 88s 88s All 9 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Hist 88s 88s CPPTRAJ: 1D/2D Histogram Analysis test 88s 88s CPPTRAJ: 3D histogram test. 88s 88s All 7 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Closest 88s 88s CPPTRAJ: Closest command test using first solvent atom. 88s 88s CPPTRAJ: Closest command test using all solvent atoms. 88s 88s CPPTRAJ: Closest command test, using mask center 88s 88s CPPTRAJ: Closest command test, using mask center and solvent mask 88s 88s CPPTRAJ: Closest command test, solvent mask, water oxygen only 88s 88s All 8 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DRMSD 88s 88s CPPTRAJ: Distance RMSD test 88s 88s All 1 comparisons passed. 88s 88s ******************************************************************************** 88s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster 88s 88s CPPTRAJ: Cluster command test, in-memory pairwise distances. 89s 89s CPPTRAJ: Cluster command test, read pairwise distances. 89s 89s CPPTRAJ: Cluster command test, read NetCDF pairwise distances. 89s 89s CPPTRAJ: Cluster command test, write ASCII pairwise distances. 89s 89s CPPTRAJ: Cluster command test, read ASCII pairwise distances. 89s 89s All 9 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_Sieve 89s 89s CPPTRAJ: Cluster, nosieve 89s 89s CPPTRAJ: Cluster, sieve5 89s 89s CPPTRAJ: Cluster, nosieve savepairdist 89s 89s CPPTRAJ: Cluster, nosieve loadpairdist 89s 89s CPPTRAJ: Cluster, sieve5 savepairdist 89s 89s CPPTRAJ: Cluster, sieve5 loadpairdist 89s 89s CPPTRAJ: Cluster, nosieve pairwisecache none 89s 89s CPPTRAJ: Cluster, sieve5 pairwisecache none 89s 89s CPPTRAJ: Cluster, random 89s 89s All 28 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_RandomSieve 89s 89s CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). 89s 89s CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 89s 89s All 4 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_DataSet 89s 89s CPPTRAJ: Clustering, One DataSet 89s 89s CPPTRAJ: Clustering, Two DataSets 89s 89s CPPTRAJ: Clustering, dihedral DataSet 89s 89s CPPTRAJ: Clustering, two dihedral DataSets 89s 89s CPPTRAJ: Clustering, dihedral DataSet, K-means 89s 89s CPPTRAJ: Clustering, two dihedral DataSets, K-means 89s 89s All 8 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_DBSCAN 89s 89s CPPTRAJ: DBSCAN test 89s 89s CPPTRAJ: DBSCAN automatic parameter determination test. 89s 89s CPPTRAJ: DBSCAN kdist map test 89s 89s CPPTRAJ: DBSCAN with sieve 89s 89s All 4 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_Kmeans 89s 89s CPPTRAJ: Cpptraj Kmeans 89s 89s CPPTRAJ: Cpptraj Kmeans random 89s 89s All 6 comparisons passed. 89s 89s ******************************************************************************** 89s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_SymmRMSD 89s 89s CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) 90s 90s All 5 comparisons passed. 90s 90s ******************************************************************************** 90s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_TrajWrites 90s 90s CPPTRAJ: Cluster command test, coordinate writes. 90s 90s CPPTRAJ: Cluster command test, coordinate writes using info file. 90s 90s All 8 comparisons passed. 90s 90s ******************************************************************************** 90s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_Dpeaks 90s 90s CPPTRAJ: Density peaks clustering test 90s 90s All 3 comparisons passed. 90s 90s ******************************************************************************** 90s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cluster_Nreps 90s 90s CPPTRAJ: Clustering with specified # reps 90s 90s All 2 comparisons passed. 90s 90s ******************************************************************************** 90s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_IRED 90s 90s CPPTRAJ: IRED vector/matrix test 90s 90s 90s ******************************************************************************** 90s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_RandomizeIons 90s 90s CPPTRAJ: randomizeions test (original algorithm) 90s 90s CPPTRAJ: Randomize (around, overlap) 90s 90s CPPTRAJ: Randomize (around) 91s 91s CPPTRAJ: Randomize (overlap) 91s 91s CPPTRAJ: Randomize (no restrictions) 91s 91s All 5 comparisons passed. 91s 91s ******************************************************************************** 91s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Molsurf 91s 91s CPPTRAJ: Molsurf test 91s 91s All 1 comparisons passed. 91s 91s ******************************************************************************** 91s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Corr 91s 91s CPPTRAJ: Correlation test 91s 91s All 2 comparisons passed. 91s 91s ******************************************************************************** 91s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CheckStructure 91s 91s CPPTRAJ: Structure Check 91s 91s CPPTRAJ: Structure Check with Around and Skip 91s 91s CPPTRAJ: Structure Check with PBC 91s 91s CPPTRAJ: Structure Check with Around 91s 91s All 8 comparisons passed. 91s 91s ******************************************************************************** 91s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_RmsAvgCorr 91s 91s CPPTRAJ: RmsAvgCorr Reference 91s 91s CPPTRAJ: RmsAvgCorr First 91s 91s All 3 comparisons passed. 91s 91s ******************************************************************************** 91s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Contacts 91s 91s CPPTRAJ: Contacts test. 92s 92s All 3 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Principal 92s 92s CPPTRAJ: Principal Test 92s 92s All 3 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_ClusterDihedral 92s 92s CPPTRAJ: clusterdihedral test 92s 92s All 4 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Vector 92s 92s CPPTRAJ: Basic vector tests 92s 92s CPPTRAJ: Test vector center with magnitude 92s 92s CPPTRAJ: Momentum/velocity vector test. 92s 92s CPPTRAJ: Force vector test. 92s 92s All 14 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Matrix 92s 92s CPPTRAJ: Matrix Tests 92s 92s CPPTRAJ: Generate matrix with trajectory start/stop/offset 92s 92s CPPTRAJ: Generate matrix with action stop/start/offset 92s 92s All 15 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AtomicFluct 92s 92s CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. 92s 92s CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. 92s 92s CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. 92s 92s CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. 92s 92s CPPTRAJ: Atomicfluct test with ADP output 92s 92s CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. 92s 92s All 13 comparisons passed. 92s 92s ******************************************************************************** 92s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Grid 92s 92s CPPTRAJ: Dipole test 92s 92s CPPTRAJ: Grid test 92s 92s CPPTRAJ: OpenDX Grid read test 92s 92s CPPTRAJ: Grid with specified center test. 92s 92s CPPTRAJ: Grid with box center offset test. 92s 92s CPPTRAJ: Grid with mask center offset test. 92s 92s CPPTRAJ: Non-orthogonal grid test. 93s 93s CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test 93s 93s CPPTRAJ: Grid generation from 'bounds' test. 93s 93s All 13 comparisons passed. 93s 93s ******************************************************************************** 93s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Unwrap 93s 93s CPPTRAJ: Unwrap non-orthogonal test 93s 93s CPPTRAJ: Unwrap orthogonal test 93s 93s All 2 comparisons passed. 93s 93s ******************************************************************************** 93s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Project 93s 93s CPPTRAJ: Projection 93s 93s All 1 comparisons passed. 93s 93s ******************************************************************************** 93s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Analyze_Modes 93s 93s CPPTRAJ: Modes analysis, RMS fluctuations 93s 93s CPPTRAJ: Modes analysis, displacements 93s 93s CPPTRAJ: Modes analysis, dipole correlation 93s 93s CPPTRAJ: Modes analysis, pseudo trajectory creation test 93s 93s CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test 93s 93s All 6 comparisons passed. 93s 93s ******************************************************************************** 93s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Watershell 93s 93s CPPTRAJ: Watershell Test, non-orthorhombic imaging. 93s 93s CPPTRAJ: Watershell Test, orthorhombic imaging. 94s 94s CPPTRAJ: Watershell Test, no imaging. 94s 94s All 3 comparisons passed. 94s 94s ******************************************************************************** 94s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AnalysisRunAvg 94s 94s CPPTRAJ: Analysis Running Average 94s 94s All 2 comparisons passed. 94s 94s ******************************************************************************** 94s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Volmap 94s 94s CPPTRAJ: VMD VolMap Algorithm test 94s VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. 94s Skipped test: VMD VolMap Algorithm longer tests 94s 94s All 2 comparisons passed. 94s 1 comparisons skipped. 94s 94s ******************************************************************************** 94s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_SPAM 94s 94s CPPTRAJ: SPAM Test 94s 94s CPPTRAJ: SPAM Pure Solvent Test 95s 95s All 5 comparisons passed. 95s 95s ******************************************************************************** 95s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LIE 95s 95s CPPTRAJ: LIE test 95s 95s All 1 comparisons passed. 95s 95s ******************************************************************************** 95s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Density 95s 95s CPPTRAJ: Density along axis tests 95s 95s CPPTRAJ: Multi-frame density along axis test 95s 95s CPPTRAJ: Total system density test 95s 95s All 7 comparisons passed. 95s 95s ******************************************************************************** 95s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LipidOrder 95s 95s CPPTRAJ: Lipid Order Parameter Test. 95s 95s All 6 comparisons passed. 95s 95s ******************************************************************************** 95s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LipidSCD 95s 95s CPPTRAJ: Basic lipid order parameter test 95s 95s CPPTRAJ: New Lipid Order Parameter Test, DOPC. 95s 95s All 4 comparisons passed. 95s 95s ******************************************************************************** 95s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_PairDist 95s 95s CPPTRAJ: PairDist Test. 96s 96s CPPTRAJ: Pairdist test, orthogonal imaging. 96s 96s CPPTRAJ: Pairdist test, nonorthogonal imaging. 96s 96s CPPTRAJ: Pairdist test, 2 masks. 96s 96s All 4 comparisons passed. 96s 96s ******************************************************************************** 96s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_ReadData 96s 96s CPPTRAJ: Read vector data test (no origins, origins) 96s 96s CPPTRAJ: Read vector data set (origins, no origins) 96s 96s CPPTRAJ: Read Amber output test 96s 96s CPPTRAJ: Read CHARMM output test 96s 96s CPPTRAJ: 3D data read/write test 96s 96s CPPTRAJ: Standard 3D data write test 96s 96s CPPTRAJ: Standard 3D data read test 96s 96s CPPTRAJ: Standard 3D data read/append test 96s 96s CPPTRAJ: Standard 3D data, sparse 96s 96s CPPTRAJ: Nonorthogonal grid standard write/read tests. 97s 97s CPPTRAJ: Read specific columns test. 97s 97s CPPTRAJ: Write non-square matrix 97s 97s CPPTRAJ: Read non-square matrix 97s 97s CPPTRAJ: Read square matrix 97s 97s All 15 comparisons passed. 97s 97s ******************************************************************************** 97s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_GIST 97s 97s CPPTRAJ: GIST water-water interaction test 97s 97s CPPTRAJ: GIST test, orthogonal cell 99s 99s CPPTRAJ: GIST test, nonorthogonal cell 101s 101s All 11 comparisons passed. 101s 101s ******************************************************************************** 101s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_GIST_Order 101s 101s CPPTRAJ: TIP3P water cluster test 101s 101s CPPTRAJ: TIP4P water cluster test 101s 101s CPPTRAJ: TIP5P water cluster test 101s 101s All 4 comparisons passed. 101s 101s ******************************************************************************** 101s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_systemVF 101s 101s CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test 101s 101s All 1 comparisons passed. 101s 101s ******************************************************************************** 101s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AtomicCorr 101s 101s CPPTRAJ: Atomic Correlation test 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AutoCorr 102s 102s CPPTRAJ: AutoCorr test. 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Box 102s 102s CPPTRAJ: Box Test (Add box info) 102s 102s CPPTRAJ: Box test (remove box info) 102s 102s CPPTRAJ: Box test (Modify box length) 102s 102s CPPTRAJ: Box test (auto orthogonal box, no radii) 102s 102s CPPTRAJ: Box test (auto orthogonal box, VDW radii) 102s 102s All 7 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AtomTypeSelect 102s 102s CPPTRAJ: Selection by atom type test. 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AvgRef 102s 102s CPPTRAJ: RMSD Test with averaged reference coordinates. 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Crank_Stat 102s 102s CPPTRAJ: Crankshaft test 102s 102s All 3 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CreateCrd 102s 102s CPPTRAJ: COORDS data set creation and CRDFLUCT test. 102s 102s CPPTRAJ: COORDS data set creation with velocities test 102s 102s CPPTRAJ: TRAJ data set creation and CRDFLUCT test. 102s 102s CPPTRAJ: TRAJ data set creation with velocities test. 102s 102s CPPTRAJ: COORDS data set append test 102s 102s CPPTRAJ: COORDS test storing frame metadata 102s 102s CPPTRAJ: TRAJ test storing frame metadata 102s 102s All 8 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AutoImage 102s 102s CPPTRAJ: AutoImage test (split DNA duplex) 102s 102s CPPTRAJ: AutoImage test, use anchor mask 102s 102s All 2 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LoadCrd 102s 102s CPPTRAJ: LoadCrd test. 102s 102s CPPTRAJ: LoadTraj test. 102s 102s CPPTRAJ: LoadTraj from trajin test. 102s 102s CPPTRAJ: LoadCrd append from multiple files test 102s 102s All 4 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_MultiVector 102s 102s CPPTRAJ: Multivector test 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Lifetime 102s 102s CPPTRAJ: Lifetime test. 102s 102s CPPTRAJ: Lifetime test with data set caching. 102s 102s CPPTRAJ: Lifetime average and cumulative average test. 102s 102s All 12 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_FFT 102s 102s CPPTRAJ: FFT test. 102s 102s All 5 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Timecorr 102s 102s CPPTRAJ: Timecorr test. 102s 102s All 7 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CrossCorr 102s 102s CPPTRAJ: CrossCorr test 102s 102s All 1 comparisons passed. 102s 102s ******************************************************************************** 102s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_SymmRmsd 102s 102s CPPTRAJ: SymmRmsd 103s 103s CPPTRAJ: ASP symmetry-corrected RMSD test 103s 103s CPPTRAJ: GLU symmetry-corrected RMSD test 103s 103s CPPTRAJ: TYR symmetry-corrected RMSD test 103s 103s CPPTRAJ: Longer symmetry-corrected RMSD test. 103s 103s All 8 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Multidihedral 103s 103s CPPTRAJ: Multidihedral test 103s 103s CPPTRAJ: Multidihedral Nucleotide CHI test 103s 103s CPPTRAJ: Multidihedral protein dihedrals test 103s 103s CPPTRAJ: Multidihedral cyclic molecule test 103s 103s All 6 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Ensemble_MREMD 103s 103s CPPTRAJ: M-REMD sort test. 103s 103s CPPTRAJ: M-REMD actions test. 103s 103s CPPTRAJ: M-REMD ensemble outtraj test. 103s 103s CPPTRAJ: M-REMD no sort, running average test 103s 103s CPPTRAJ: M-REMD, generate RMS data 103s 103s CPPTRAJ: M-REMD, meltcurve analysis 103s 103s All 17 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_MakeStructure 103s 103s CPPTRAJ: Basic makestructure test 103s 103s CPPTRAJ: Makestructure test with reference. 103s 103s All 5 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Rotate 103s 103s CPPTRAJ: Rotation (and inverse) of coords from matrices 103s 103s CPPTRAJ: Rotate with defined axis 103s 103s All 3 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Integrate 103s 103s CPPTRAJ: Integration test. 103s 103s All 2 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_NativeContacts 103s 103s CPPTRAJ: NativeContacts test. 103s 103s CPPTRAJ: NativeContacts test, save non-native contacts, residue time series 103s 103s CPPTRAJ: NativeContacts test, orthorhombic imaging. 103s 103s All 17 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CheckChiral 103s 103s CPPTRAJ: Check chirality test 103s 103s All 1 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Energy 103s 103s CPPTRAJ: Simple energy tests 103s 103s CPPTRAJ: Test kinetic energy calculation 103s 103s CPPTRAJ: Test total energy calculation 103s 103s CPPTRAJ: Test partial energy calculation 103s 103s All 6 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LESsplit 103s 103s CPPTRAJ: LES split/average test 103s 103s All 2 comparisons passed. 103s 103s ******************************************************************************** 103s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_PermuteDihedrals 103s 103s CPPTRAJ: PermuteDihedrals interval -120, phi psi 104s 104s CPPTRAJ: PermuteDihedrals, random rotations 104s 104s All 4 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CCP4 104s 104s CPPTRAJ: CCP4 read/write and DX conversion test. 104s 104s All 2 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DihCovar 104s 104s CPPTRAJ: Dihedral Covariance Matrix Test 104s 104s All 3 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CurveFit 104s 104s CPPTRAJ: Curve fitting test. 104s 104s CPPTRAJ: Curve fitting multi-exponential tests. 104s 104s CPPTRAJ: Curve fitting, custom output range. 104s 104s All 6 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Multicurve 104s 104s CPPTRAJ: Multicurve test 104s 104s All 1 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DataSetAverage 104s 104s CPPTRAJ: Data set averaging and averaging over all sets test. 104s 104s All 2 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_VectorMath 104s 104s CPPTRAJ: Vector dot/cross product test 104s 104s All 2 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Esander 104s SANDER energy tests (long) requires SANDER API from AmberTools. 104s Cpptraj was compiled without SANDER API from AmberTools support. 104s SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. 104s SKIP: SANDER energy tests (long) 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Esander_Short 104s Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. 104s Cpptraj was compiled without SANDER API from AmberTools support. 104s SKIP: Energy via sander API short tests (GB/PME) 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Temperature 104s 104s CPPTRAJ: Temperature test. 104s 104s CPPTRAJ: Temperature with SHAKE on hydrogens. 104s 104s CPPTRAJ: Temperature with SHAKE on all atoms. 104s 104s CPPTRAJ: Temperature calc with extra points. 104s 104s All 5 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Spline 104s 104s CPPTRAJ: Spline test 104s 104s All 1 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_KDE 104s 104s CPPTRAJ: KDE test. 104s 104s CPPTRAJ: KDE with Kullback-Leibler divergence test 104s 104s All 4 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Wavelet 104s 104s CPPTRAJ: Wavelet analysis test 104s 104s CPPTRAJ: Wavelet WAFEX test 104s 104s All 3 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CIF 104s 104s CPPTRAJ: CIF read test 104s 104s CPPTRAJ: Generate offset traj from PDB 104s 104s CPPTRAJ: Generate offset traj from CIF 104s 104s All 2 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_PDB 104s 104s CPPTRAJ: PDB format read/write test 104s 104s CPPTRAJ: PQR file write with various radii 104s 104s CPPTRAJ: PDB filter alternate atom location IDs test 104s 104s CPPTRAJ: Adding PDB info to topology 104s 104s All 10 comparisons passed. 104s 104s ******************************************************************************** 104s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Align 104s 104s CPPTRAJ: Align Tests. 104s 104s CPPTRAJ: Align, unit cell rotation/imaging test. 105s 105s All 4 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_VelocityAutoCorr 105s 105s CPPTRAJ: Velocity autocorrelation test 105s 105s All 3 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_VelFrc 105s 105s CPPTRAJ: Test combining coordinates, velocities, and forces. 105s 105s CPPTRAJ: Test using velocities as coordinates. 105s 105s CPPTRAJ: Test writing velocities (MDVEL) 105s 105s CPPTRAJ: Test using forces as coordinates. 105s 105s CPPTRAJ: Test writing forces (MDFRC) 105s 105s CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. 105s 105s CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. 105s 105s All 5 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_RotateDihedral 105s 105s CPPTRAJ: Rotate dihedral to target value. 105s 105s CPPTRAJ: Rotate dihedral by increment 105s 105s CPPTRAJ: Rotate dihedral in TRAJ data set 105s 105s All 3 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DataSetCmd 105s 105s CPPTRAJ: Data Set commands test 105s 105s All 10 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Remap 105s 105s CPPTRAJ: Remap Test 105s 105s All 1 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CompareTop 105s 105s CPPTRAJ: Compare topology test 105s 105s All 1 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Filter 105s 105s CPPTRAJ: Basic filter test 105s 105s CPPTRAJ: Data filter test. 105s 105s CPPTRAJ: Filter matrix test. 105s 105s All 5 comparisons passed. 105s 105s ******************************************************************************** 105s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CombineCrd 105s 105s CPPTRAJ: Combine COORDS test. 105s 105s CPPTRAJ: Combine COORDS test with box info. 105s 105s CPPTRAJ: Split coords and recombine test. 106s 106s All 5 comparisons passed. 106s 106s ******************************************************************************** 106s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_TopInfo 106s 106s CPPTRAJ: Topology info print test. 106s 106s CPPTRAJ: Topology info with reference coords test 106s 106s All 12 comparisons passed. 106s 106s ******************************************************************************** 106s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_GromacsTrr 106s 106s CPPTRAJ: TRR force/velocity read -> NetCDF write test 106s 106s CPPTRAJ: TRR force/velocity read -> TRR write test 106s 106s CPPTRAJ: CRD => TRR 106s 106s CPPTRAJ: TRR => CRD 106s 106s CPPTRAJ: CRD(1-5) => TRR 106s 106s CPPTRAJ: CRD(6-10) => TRR 106s 106s CPPTRAJ: TRR (appended) => CRD 106s 106s CPPTRAJ: GMX: CRD with offset 106s 106s CPPTRAJ: GMX: TRR with offset 106s 106s All 5 comparisons passed. 106s 106s ******************************************************************************** 106s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_GromacsXtc 106s 106s CPPTRAJ: XTC read test 106s 106s CPPTRAJ: CRD => XTC 106s 106s CPPTRAJ: XTC => CRD 106s 106s CPPTRAJ: CRD(1-5) => XTC 106s 106s CPPTRAJ: CRD(6-10) => XTC 106s 106s CPPTRAJ: XTC (appended) => CRD 106s 106s CPPTRAJ: GMX: CRD with offset 107s 107s CPPTRAJ: GMX: XTC with offset 107s 107s All 4 comparisons passed. 107s 107s ******************************************************************************** 107s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_GromacsTNG 107s 107s CPPTRAJ: TNG read test 107s 107s CPPTRAJ: TNG read test (with offset) 107s 107s All 6 comparisons passed. 107s 107s ******************************************************************************** 107s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Ewald 107s 107s CPPTRAJ: Direct sum test 107s 107s CPPTRAJ: Ewald test (NaCl crystal) 107s 107s CPPTRAJ: Ewald test (trunc. oct) 107s 107s CPPTRAJ: Ewald test (partial system, trunc. oct) 107s Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 107s Skipped test: Ewald test (trunc. oct), 10 frames 107s Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. 107s Skipped test: Ewald test (ortho), 10 frames 107s 107s All 4 comparisons passed. 107s 2 comparisons skipped. 107s 107s ******************************************************************************** 107s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LibPME 107s 107s CPPTRAJ: Particle mesh Ewald test (NaCl crystal) 107s 107s CPPTRAJ: Particle mesh Ewald test (trunc. oct) 107s 107s CPPTRAJ: Particle mesh Ewald test (ortho) 108s 108s CPPTRAJ: Particle mesh Ewald test (ortho, with mask) 108s 108s CPPTRAJ: PME test (partial system, trunc. oct) 108s PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. 108s Skipped test: PME test (trunc. oct), 10 frames 108s 108s All 5 comparisons passed. 108s 1 comparisons skipped. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LJ_PME 108s 108s CPPTRAJ: LJ PME test. 108s 108s CPPTRAJ: LJ PME kappa sweep test, 0.25 108s 108s CPPTRAJ: LJ PME kappa sweep test, 0.35 108s 108s CPPTRAJ: LJ PME kappa sweep test, 0.45 108s 108s CPPTRAJ: LJ PME kappa sweep test, 0.5 108s 108s CPPTRAJ: LJ with switch function test 108s 108s All 5 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_TI 108s 108s CPPTRAJ: TI analysis test. 108s 108s All 5 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_FixImagedBonds 108s 108s CPPTRAJ: Fix imaged bonds test (Ortho.) 108s 108s CPPTRAJ: Fix imaged bonds test (Non-ortho.) 108s 108s All 2 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Distance 108s 108s CPPTRAJ: Distance tests 108s 108s CPPTRAJ: Orthogonal imaged distance 108s 108s CPPTRAJ: Non-orthogonal imaged distance 108s 108s All 3 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Volume 108s 108s CPPTRAJ: Volume tests 108s 108s All 1 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_SetVelocity 108s 108s CPPTRAJ: Set Velocity test 108s 108s CPPTRAJ: Scale velocity test 108s 108s All 3 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Remlog 108s 108s CPPTRAJ: Replica log read/analyze test. 108s 108s All 7 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_AreaPerMol 108s 108s CPPTRAJ: Area per molecule test 108s 108s All 6 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DistBasedMask 108s 108s CPPTRAJ: Distance-based atom mask tests (atom, residue) 108s 108s CPPTRAJ: Distance-based atom mask tests (molecule) 108s 108s All 6 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Calc 108s 108s CPPTRAJ: Calc test 108s 108s CPPTRAJ: Calc test with data sets 108s 108s CPPTRAJ: Test math functions 108s 108s All 4 comparisons passed. 108s 108s ******************************************************************************** 108s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CalcState 108s 108s CPPTRAJ: Calcstate test 109s 109s All 4 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Change 109s 109s CPPTRAJ: Change atom and residue name tests 109s 109s CPPTRAJ: Change chain ID test 109s 109s CPPTRAJ: Change chain ID of COORDS set test 109s 109s All 3 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CreateReservoir 109s 109s CPPTRAJ: Create RREMD NetCDF reservoir test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_FixAtomOrder 109s 109s CPPTRAJ: Out of order molecules test 109s 109s All 2 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_LowestCurve 109s 109s CPPTRAJ: LowestCurve test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_MinImage 109s 109s CPPTRAJ: Minimum Image test. 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Regress 109s 109s CPPTRAJ: Linear regression test. 109s 109s All 3 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Rst 109s 109s CPPTRAJ: Generate restraints (rst) test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Pairwise 109s 109s CPPTRAJ: Pairwise tests 109s 109s CPPTRAJ: Pairwise test, partial system 109s 109s All 10 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_ParmBox 109s 109s CPPTRAJ: Parmbox test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Solvent 109s 109s CPPTRAJ: Test solvent command with closest 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Translate 109s 109s CPPTRAJ: Translate test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_ReplicateCell 109s 109s CPPTRAJ: Replicate cell test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_ScaleDihedralK 109s 109s CPPTRAJ: Scale dihedral force constant test 109s 109s CPPTRAJ: Scale dihedral force constant with 'useall' 109s 109s All 2 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_PhiPsi 109s 109s CPPTRAJ: Phipsi test 109s 109s All 1 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Control 109s 109s CPPTRAJ: Loop tests 109s 109s CPPTRAJ: Test set command 109s 109s CPPTRAJ: Test reading comma-separated list of strings 109s 109s CPPTRAJ: Test nested loops and variables in loops 109s 109s CPPTRAJ: Test loop over data set blocks 109s 109s CPPTRAJ: Test for filename wildcards and oversets 109s 109s All 13 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_InfraredSpec 109s 109s CPPTRAJ: Infrared spectrum calculation test 109s 109s All 2 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Cphstats 109s 109s CPPTRAJ: Explicit pH REMD ensemble data read / sort 109s 109s CPPTRAJ: Constant pH stats test 109s 109s CPPTRAJ: Sorted implicit constant pH stats test 109s 109s CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats 109s 109s CPPTRAJ: Unsorted pH read/write test 109s 109s All 16 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CmdLine 109s 109s CPPTRAJ: Command line trajectory args test, part 1 109s 109s CPPTRAJ: Command line test trajectory args test, part 2 109s 109s CPPTRAJ: Command line wildcard test, part 1 109s 109s CPPTRAJ: Command line wildcard test, part 2 109s 109s All 2 comparisons passed. 109s 109s ******************************************************************************** 109s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_XYZformat 109s 109s CPPTRAJ: XYZ format write 109s 109s CPPTRAJ: Atom XYZ format read, test 1 110s 110s CPPTRAJ: Atom XYZ format read, test 2 110s 110s CPPTRAJ: Atom XYZ format read, test 3 110s 110s CPPTRAJ: Atom XYZ format read, test 4 110s 110s CPPTRAJ: Atom XYZ format read, test 5 110s 110s CPPTRAJ: Atom XYZ format read, test 6 110s 110s All 6 comparisons passed. 110s 110s ******************************************************************************** 110s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Hausdorff 110s 110s CPPTRAJ: Simple Hausdorff distance test. 110s 110s CPPTRAJ: Hausdorff distance of 2D rms output test. 110s 110s CPPTRAJ: Hausdorff distance of 2D rms output test. 110s 110s All 3 comparisons passed. 110s 110s ******************************************************************************** 110s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_CatCrd 110s 110s CPPTRAJ: Concatenate COORDS data set test 110s 110s All 1 comparisons passed. 110s 110s ******************************************************************************** 110s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_XtalSymm 110s 110s CPPTRAJ: XtalSymm Reference 110s 110s CPPTRAJ: XtalSymm Reimaging by Atom 111s 111s CPPTRAJ: XtalSymm Reimaging by Molecule 112s 112s All 3 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Time 112s 112s CPPTRAJ: Add time to restart test 112s 112s CPPTRAJ: Remove time from restart test 112s 112s CPPTRAJ: Add time to trajectory test 112s 112s CPPTRAJ: Modify time info test. 112s 112s All 4 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_SplitCoords 112s 112s CPPTRAJ: SplitCoords test 112s 112s All 1 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_DihedralRMS 112s 112s CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) 112s 112s CPPTRAJ: Dihedral RMSD test (to previous) 112s 112s CPPTRAJ: Dihedral RMS fluctuation test. 112s 112s All 5 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Slope 112s 112s CPPTRAJ: Finite difference test. 112s 112s All 1 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Diagmatrix 112s 112s CPPTRAJ: MW covariance matrix thermo analysis test 112s 112s All 1 comparisons passed. 112s 112s ******************************************************************************** 112s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Emin 112s 112s CPPTRAJ: Basic energy minimization test. 112s 112s CPPTRAJ: Energy minimization with angle term test. 112s 112s CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. 112s 112s CPPTRAJ: Energy minimization with nonbond term test. 112s 112s CPPTRAJ: OpenMM basic energy minimization tests (bonds) 112s 112s CPPTRAJ: OpenMM basic energy minimization tests (angles) 112s 112s CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) 112s 112s CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) 112s 112s CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) 113s 113s All 9 comparisons passed. 113s 113s ******************************************************************************** 113s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_EvalPlateau 113s 113s CPPTRAJ: Evalulate plateau test 113s 113s All 2 comparisons passed. 113s 113s ******************************************************************************** 113s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Graft 113s 113s CPPTRAJ: Graft test 113s 113s All 1 comparisons passed. 113s 113s ******************************************************************************** 113s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Flatten 113s 113s CPPTRAJ: Flatten test. 113s 113s All 1 comparisons passed. 113s 113s ******************************************************************************** 113s TEST: /tmp/autopkgtest.gaswEJ/build.Psr/src/test/Test_Random 113s 113s CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs 113s 113s CPPTRAJ: PCG32 RNG test. 113s 113s CPPTRAJ: Test Stdlib RNG 113s 113s CPPTRAJ: Test Mersenne Twister RNG 113s 113s All 4 comparisons passed. 113s 113s make[1]: Leaving directory '/tmp/autopkgtest.gaswEJ/build.Psr/src/test' 113s lrwxrwxrwx 1 ubuntu ubuntu 16 Feb 15 19:39 ../bin/cpptraj -> /usr/bin/cpptraj 113s ===================== TEST SUMMARY ====================== 113s 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 113s 480 out of 480 program executions completed. 113s 170 out of 173 tests completed with no issues. 113s 2 tests skipped. 113s ========================================================= 113s make: Leaving directory '/tmp/autopkgtest.gaswEJ/build.Psr/src/test' 113s autopkgtest [19:39:39]: test command1: -----------------------] 114s autopkgtest [19:39:40]: test command1: - - - - - - - - - - results - - - - - - - - - - 114s command1 PASS 114s autopkgtest [19:39:40]: @@@@@@@@@@@@@@@@@@@@ summary 114s command1 PASS 121s nova [W] Skipping flock for amd64 121s Creating nova instance adt-plucky-amd64-cpptraj-20250215-193746-juju-7f2275-prod-proposed-migration-environment-2-61e78bef-39fb-4f2b-9cdb-4d748f9edb5d from image adt/ubuntu-plucky-amd64-server-20250215.img (UUID d1f7bb98-7df8-4026-816e-9f6798166d8b)... 121s nova [W] Timed out waiting for c0774610-d737-4357-8780-6b1b8484ad97 to get deleted.