0s autopkgtest [00:40:04]: starting date and time: 2024-03-26 00:40:04+0000
  0s autopkgtest [00:40:04]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [00:40:04]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ozgctxx3/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 netcdf/1:4.9.2-5ubuntu3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@lcy02-17.secgroup --name adt-noble-amd64-cpptraj-20240326-004004-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
 84s autopkgtest [00:41:28]: testbed dpkg architecture: amd64
 84s autopkgtest [00:41:28]: testbed apt version: 2.7.12
 84s autopkgtest [00:41:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 84s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
 84s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [497 kB]
 84s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3976 kB]
 84s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [7592 B]
 84s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.0 kB]
 84s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [731 kB]
 84s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [484 kB]
 84s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B]
 84s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B]
 84s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [37.9 kB]
 84s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B]
 84s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4390 kB]
 84s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1260 kB]
 84s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B]
 84s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [28.6 kB]
 84s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.8 kB]
 84s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B]
 88s Fetched 11.7 MB in 2s (7587 kB/s)
 88s Reading package lists...
 90s Reading package lists...
 90s Building dependency tree...
 90s Reading state information...
 91s Calculating upgrade...
 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 91s Reading package lists...
 92s Building dependency tree...
 92s Reading state information...
 92s 0 upgraded, 0 newly installed, 0 to remove and 248 not upgraded.
 92s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 92s sh: Distribution appears to be Ubuntu
 93s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 94s eatmydata is already the newest version (131-1).
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 94s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 95s dbus is already the newest version (1.14.10-4ubuntu1).
 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 95s Reading package lists...
 95s Building dependency tree...
 95s Reading state information...
 96s rng-tools-debian is already the newest version (2.4).
 96s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 96s Reading package lists...
 96s Building dependency tree...
 96s Reading state information...
 96s The following packages will be REMOVED:
 96s   cloud-init* python3-configobj* python3-debconf*
 97s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
 97s After this operation, 3256 kB disk space will be freed.
 97s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
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(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 ... 71864 files and directories currently installed.)
 97s Removing cloud-init (24.1.2-0ubuntu1) ...
 98s Removing python3-configobj (5.0.8-3) ...
 98s Removing python3-debconf (1.5.86) ...
 98s Processing triggers for man-db (2.12.0-3) ...
 98s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 71475 files and directories currently installed.)
 98s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
 99s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 99s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
 99s invoke-rc.d: policy-rc.d denied execution of try-restart.
 99s Reading package lists...
100s Building dependency tree...
100s Reading state information...
100s linux-generic is already the newest version (6.8.0-11.11+1).
100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
100s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
100s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
100s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
103s Reading package lists...
103s Reading package lists...
103s Building dependency tree...
103s Reading state information...
103s Calculating upgrade...
103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
103s Reading package lists...
104s Building dependency tree...
104s Reading state information...
104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
104s autopkgtest [00:41:48]: rebooting testbed after setup commands that affected boot
389s autopkgtest [00:46:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024
389s autopkgtest [00:46:33]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj
393s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B]
393s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB]
393s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B]
393s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC
393s gpgv:                using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D
393s gpgv: Can't check signature: No public key
393s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found
394s autopkgtest [00:46:38]: testing package cpptraj version 5.1.0+dfsg-3build1
394s autopkgtest [00:46:38]: build not needed
395s autopkgtest [00:46:39]: test command1: preparing testbed
397s Reading package lists...
397s Building dependency tree...
397s Reading state information...
397s Starting pkgProblemResolver with broken count: 0
397s Starting 2 pkgProblemResolver with broken count: 0
397s Done
398s The following additional packages will be installed:
398s   cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1
398s   libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2
398s   netcdf-bin
398s Suggested packages:
398s   libfftw3-bin libfftw3-dev
398s The following NEW packages will be installed:
398s   autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3
398s   libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19
398s   libopenmm8.0 libsz2 netcdf-bin
398s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded.
398s Need to get 9826 kB/9826 kB of archives.
398s After this operation, 28.7 MB of additional disk space will be used.
398s Get:1 /tmp/autopkgtest.IcRMoi/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B]
398s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB]
398s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB]
398s Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB]
398s Get:5 http://ftpmaster.internal/ubuntu noble/universe amd64 libarpack2 amd64 3.9.1-1 [105 kB]
398s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB]
398s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu1 [835 kB]
398s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libaec0 amd64 1.1.2-1 [22.6 kB]
398s Get:9 http://ftpmaster.internal/ubuntu noble/universe amd64 libsz2 amd64 1.1.2-1 [5416 B]
398s Get:10 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-103-1 amd64 1.10.10+repack-3ubuntu1 [1327 kB]
398s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 libhdf5-hl-100 amd64 1.10.10+repack-3ubuntu1 [56.2 kB]
398s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 libnetcdf19 amd64 1:4.9.2-3ubuntu1 [472 kB]
398s Get:13 http://ftpmaster.internal/ubuntu noble/universe amd64 libopenmm8.0 amd64 8.0.0+dfsg-6ubuntu1 [1020 kB]
398s Get:14 http://ftpmaster.internal/ubuntu noble/universe amd64 cpptraj amd64 5.1.0+dfsg-3build1 [1818 kB]
398s Get:15 http://ftpmaster.internal/ubuntu noble/universe amd64 netcdf-bin amd64 1:4.9.2-3ubuntu1 [207 kB]
398s Fetched 9826 kB in 0s (42.5 MB/s)
398s Selecting previously unselected package libblas3:amd64.
399s (Reading database ... 
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(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(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 ... 71420 files and directories currently installed.)
399s Preparing to unpack .../00-libblas3_3.12.0-3_amd64.deb ...
399s Unpacking libblas3:amd64 (3.12.0-3) ...
399s Selecting previously unselected package libgfortran5:amd64.
399s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_amd64.deb ...
399s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ...
399s Selecting previously unselected package liblapack3:amd64.
399s Preparing to unpack .../02-liblapack3_3.12.0-3_amd64.deb ...
399s Unpacking liblapack3:amd64 (3.12.0-3) ...
399s Selecting previously unselected package libarpack2:amd64.
399s Preparing to unpack .../03-libarpack2_3.9.1-1_amd64.deb ...
399s Unpacking libarpack2:amd64 (3.9.1-1) ...
399s Selecting previously unselected package libgomp1:amd64.
399s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_amd64.deb ...
399s Unpacking libgomp1:amd64 (14-20240303-1ubuntu1) ...
399s Selecting previously unselected package libfftw3-double3:amd64.
399s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu1_amd64.deb ...
399s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu1) ...
399s Selecting previously unselected package libaec0:amd64.
399s Preparing to unpack .../06-libaec0_1.1.2-1_amd64.deb ...
399s Unpacking libaec0:amd64 (1.1.2-1) ...
399s Selecting previously unselected package libsz2:amd64.
399s Preparing to unpack .../07-libsz2_1.1.2-1_amd64.deb ...
399s Unpacking libsz2:amd64 (1.1.2-1) ...
399s Selecting previously unselected package libhdf5-103-1:amd64.
399s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_amd64.deb ...
399s Unpacking libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ...
399s Selecting previously unselected package libhdf5-hl-100:amd64.
399s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_amd64.deb ...
399s Unpacking libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ...
399s Selecting previously unselected package libnetcdf19:amd64.
399s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_amd64.deb ...
399s Unpacking libnetcdf19:amd64 (1:4.9.2-3ubuntu1) ...
399s Selecting previously unselected package libopenmm8.0.
399s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_amd64.deb ...
399s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
399s Selecting previously unselected package cpptraj.
399s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_amd64.deb ...
399s Unpacking cpptraj (5.1.0+dfsg-3build1) ...
399s Selecting previously unselected package netcdf-bin.
399s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_amd64.deb ...
399s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ...
399s Selecting previously unselected package autopkgtest-satdep.
399s Preparing to unpack .../14-1-autopkgtest-satdep.deb ...
399s Unpacking autopkgtest-satdep (0) ...
399s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ...
399s Setting up libaec0:amd64 (1.1.2-1) ...
399s Setting up libblas3:amd64 (3.12.0-3) ...
399s 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
399s Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu1) ...
399s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ...
399s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
399s Setting up libsz2:amd64 (1.1.2-1) ...
399s Setting up liblapack3:amd64 (3.12.0-3) ...
399s 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
399s Setting up libarpack2:amd64 (3.9.1-1) ...
399s Setting up libhdf5-103-1:amd64 (1.10.10+repack-3ubuntu1) ...
399s Setting up libhdf5-hl-100:amd64 (1.10.10+repack-3ubuntu1) ...
399s Setting up libnetcdf19:amd64 (1:4.9.2-3ubuntu1) ...
399s Setting up cpptraj (5.1.0+dfsg-3build1) ...
399s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ...
399s Setting up autopkgtest-satdep (0) ...
399s Processing triggers for man-db (2.12.0-3) ...
400s Processing triggers for libc-bin (2.39-0ubuntu6) ...
402s (Reading database ... 71511 files and directories currently installed.)
402s Removing autopkgtest-satdep (0) ...
402s autopkgtest [00:46:46]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary
402s autopkgtest [00:46:46]: test command1: [-----------------------
402s make: Entering directory '/tmp/autopkgtest.IcRMoi/build.0GL/src/test'
402s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 26 00:46 ../bin/cpptraj -> /usr/bin/cpptraj
402s make[1]: Entering directory '/tmp/autopkgtest.IcRMoi/build.0GL/src/test'
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_General
402s 
402s   CPPTRAJ: General tests
402s 
402s All 15 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Parallel
402s 
402s   CPPTRAJ: Parallel tests.
403s 
403s   CPPTRAJ: Parallel test with trajectory offset
403s 
403s All 7 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Strip
403s 
403s   CPPTRAJ: One frame strip command test
403s 
403s   CPPTRAJ: Unstrip (Lig/Rec/Complex) command test
403s 
403s   CPPTRAJ: Multi frame strip command test.
403s 
403s   CPPTRAJ: Strip topology with PDB info
403s 
403s All 11 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_BrokenTraj
403s 
403s   CPPTRAJ: Broken Traj: Running good trajectory.
403s 
403s   CPPTRAJ: Broken Traj: Running broken trajectory.
403s 
403s   CPPTRAJ: Compressed broken trajectory test
403s 
403s All 2 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_TrajinOffset
403s 
403s   CPPTRAJ: Normal trajectory read with offsets.
403s 
403s   CPPTRAJ: Gzipped trajectory read with offsets
403s 
403s   CPPTRAJ: Bzip2ed trajectory read with offsets
403s 
403s   CPPTRAJ: Start argument offset
403s 
403s All 4 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_RemdTraj
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run with offset
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run
403s 
403s   CPPTRAJ: NetCDF Replica Trajectory Run test
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj
403s 
403s   CPPTRAJ: CRD Replica Trajectory Run with remdout
403s 
403s All 8 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_trajout_framerange
403s 
403s   CPPTRAJ: Trajout Frame Range [Amber Restart]
403s 
403s   CPPTRAJ: Trajout Frame Range [Amber Coordinates]
403s 
403s All 6 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_PerResRMSD
403s 
403s   CPPTRAJ: Per-Residue RMSD Test.
403s 
403s   CPPTRAJ: Per-Residue RMSD Test with averaging
403s 
403s   CPPTRAJ: Per-Residue RMSD Test with residue centering.
403s 
403s All 3 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DSSP
403s 
403s   CPPTRAJ: Secstruct (DSSP) command test.
403s 
403s   CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format.
403s 
403s   CPPTRAJ: Secstruct (DSSP) command with changing number of residues.
403s 
403s   CPPTRAJ: Secstruct (DSSP): SS assign output test
403s 
403s   CPPTRAJ: FtuFabI Assignment test
404s 
404s All 10 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Center
404s 
404s   CPPTRAJ: Center command test.
404s 
404s   CPPTRAJ: Center origin command test.
404s 
404s   CPPTRAJ: Center origin mass command test.
404s 
404s   CPPTRAJ: Center reference command test.
404s 
404s   CPPTRAJ: Center point test.
404s 
404s All 5 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Hbond
404s 
404s   CPPTRAJ: Solute Hbond test
404s 
404s   CPPTRAJ: Solute Hbond test with disk caching
404s 
404s   CPPTRAJ: Solute-solvent hbond test
404s 
404s   CPPTRAJ: Hbond, no intramolecular hydrogen bonds test
404s 
404s   CPPTRAJ: Hbond, specified solute masks
404s 
404s   CPPTRAJ: Hbond, no angle cutoff test
404s 
404s   CPPTRAJ: Hbond, Bridge nointramol test
404s 
404s   CPPTRAJ: Hbond with imaging
404s 
404s   CPPTRAJ: Hbond, orthogonal imaging
404s 
404s All 23 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_NCrestart
404s 
404s   CPPTRAJ: NetCDF Restart Test - TXT->NetCDF
404s 
404s   CPPTRAJ: NetCDF Restart Test - NetCDF->TXT
404s 
404s   CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF
404s 
404s   CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt
404s 
404s All 2 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Image
404s 
404s   CPPTRAJ: Orthorhombic imaged distance test.
404s 
404s   CPPTRAJ: Non-orthorhombic imaged distance test.
404s 
404s   CPPTRAJ: Orthorhombic coordinate imaging test
404s 
404s   CPPTRAJ: Nonorthorhombic coordinate imaging test
404s 
404s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar
405s 
405s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM
405s 
405s All 6 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Surf
405s 
405s   CPPTRAJ: Surface calculation test
405s 
405s   CPPTRAJ: Partial Surface calculation test
405s 
405s   CPPTRAJ: LCPO test with GAFF atom types
405s 
405s All 3 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Radgyr
405s 
405s   CPPTRAJ: Radius of gyration command test
405s 
405s All 2 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Mask
405s 
405s   CPPTRAJ: Mask single frame test
405s 
405s   CPPTRAJ: Mask longer command test.
405s 
405s All 5 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Jcoupling
405s 
405s   CPPTRAJ: J-Coupling single frame test
405s   J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set.
405s   Skipped test: J-Coupling extended test
405s 
405s All 1 comparisons passed.
405s 1 comparisons skipped.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Diffusion
405s 
405s   CPPTRAJ: Diffusion test, no imaging.
405s 
405s   CPPTRAJ: Diffusion test, old syntax.
405s 
405s   CPPTRAJ: Diffusion test, new syntax.
405s 
405s   CPPTRAJ: Diffusion test, nonorthogonal box
405s 
405s   CPPTRAJ: STFC Diffusion Test
405s 
405s   CPPTRAJ: STFC Diffusion Test with individual distances
405s 
405s   CPPTRAJ: STFC Diffusion Test with COM
405s 
405s   CPPTRAJ: STFC Diffusion Test with second mask
405s 
405s All 16 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Outtraj
405s 
405s   CPPTRAJ: RMSD Test with outtraj.
406s 
406s   CPPTRAJ: Outtraj Test with maxmin.
406s 
406s All 4 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Charmm
406s 
406s   CPPTRAJ: CHARMM PSF/DCD test
406s 
406s   CPPTRAJ: CHARMM DCD Write, step 1.
406s 
406s   CPPTRAJ: CHARMM DCD Write, step 2.
406s 
406s   CPPTRAJ: CHAMBER topology read/strip test.
406s 
406s   CPPTRAJ: Read CHARMM restart
406s 
406s   CPPTRAJ: CHARMM PSF write
406s 
406s   CPPTRAJ: CHARMM COORdinates test
406s 
406s All 6 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CharmmParams
406s 
406s   CPPTRAJ: Test updating topology with Charmm parameters (single residue)
406s 
406s All 2 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Rotdif
406s 
406s   CPPTRAJ: Rotational diffusion calculation test
406s 
406s All 4 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_NetcdfTraj
406s 
406s   CPPTRAJ: Convert mdcrd -> NetCDF
406s 
406s   CPPTRAJ: Convert NetCDF -> mdcrd
406s 
406s All 1 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Runavg
406s 
406s   CPPTRAJ: Coordinate Running Average test.
406s 
406s   CPPTRAJ: Coordinate Running Average Traj Write
406s 
406s All 2 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_RMSD
406s 
406s   CPPTRAJ: Basic RMSD tests
406s 
406s   CPPTRAJ: RMS coordinate rotation/rotation matrices test
406s 
406s   CPPTRAJ: RMS fit with no coordinates modification test.
406s 
406s   CPPTRAJ: RMS fit to previous test
406s 
406s   CPPTRAJ: RMS: imaging after unit cell rotation
406s 
406s All 12 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_2DRMS
406s 
406s   CPPTRAJ: 2D RMSD Test.
406s 
406s   CPPTRAJ: 2D RMSD Test, mass-weighted.
406s 
406s   CPPTRAJ: 2D RMSD Test with reference trajectory
406s 
406s   CPPTRAJ: 2D DME Test.
406s 
406s   CPPTRAJ: 2D RMSD with reference mask test.
406s 
406s   CPPTRAJ: 2D RMSD test, no fitting.
406s 
406s All 6 comparisons passed.
406s 
406s ********************************************************************************
406s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Mol2
406s 
406s   CPPTRAJ: Mol2 Parm/Traj Read/Write Test.
406s 
406s   CPPTRAJ: PDB => Mol2
407s 
407s   CPPTRAJ: Amber Top/Rst => Mol2
407s   Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set.
407s   Skipped test: Amber Top/Rst => Mol2, SYBYL atom types
407s 
407s All 4 comparisons passed.
407s 1 comparisons skipped.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_NAstruct
407s 
407s   CPPTRAJ: NAstruct command test.
407s 
407s   CPPTRAJ: NAstruct command test, single strand
407s 
407s All 11 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_NAstruct_8OG
407s 
407s   CPPTRAJ: NA test (8OG)
407s 
407s All 3 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Average
407s 
407s   CPPTRAJ: Average Test.
407s 
407s All 2 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Pucker
407s 
407s   CPPTRAJ: Pucker command test
407s 
407s   CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test
407s 
407s   CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test.
407s 
407s All 3 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AtomMap
407s 
407s   CPPTRAJ: AtomMap Test
407s 
407s   CPPTRAJ: AtomMap with 'rmsfit'
407s 
407s   CPPTRAJ: Atom map charmm->amber atom order
407s 
407s   CPPTRAJ: Atom map charmm->amber atom order, by residue
407s 
407s All 9 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Datafile
407s 
407s   CPPTRAJ: Data file output precision test
407s 
407s   CPPTRAJ: Standard -> Grace Data
407s 
407s   CPPTRAJ: Grace -> Standard Data
407s 
407s   CPPTRAJ: X column format/precision test.
407s 
407s   CPPTRAJ: Data file group by name test
407s 
407s   CPPTRAJ: Data file group by aspect test
407s 
407s All 6 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Radial
407s 
407s   CPPTRAJ: Radial test, non-orthogonal imaging
407s 
407s   CPPTRAJ: Radial test, orthogonal and no imaging
407s 
407s All 9 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Hist
407s 
407s   CPPTRAJ: 1D/2D Histogram Analysis test
407s 
407s   CPPTRAJ: 3D histogram test.
407s 
407s All 7 comparisons passed.
407s 
408s ********************************************************************************
408s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Closest
408s 
408s   CPPTRAJ: Closest command test using first solvent atom.
408s 
408s   CPPTRAJ: Closest command test using all solvent atoms.
408s 
408s   CPPTRAJ: Closest command test, using mask center
408s 
408s   CPPTRAJ: Closest command test, using mask center and solvent mask
408s 
408s   CPPTRAJ: Closest command test, solvent mask, water oxygen only
408s 
408s All 8 comparisons passed.
408s 
408s ********************************************************************************
408s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DRMSD
408s 
408s   CPPTRAJ: Distance RMSD test
408s 
408s All 1 comparisons passed.
408s 
408s ********************************************************************************
408s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster
408s 
408s   CPPTRAJ: Cluster command test, in-memory pairwise distances.
408s 
408s   CPPTRAJ: Cluster command test, read pairwise distances.
408s 
408s   CPPTRAJ: Cluster command test, read NetCDF pairwise distances.
408s 
408s   CPPTRAJ: Cluster command test, write ASCII pairwise distances.
408s 
408s   CPPTRAJ: Cluster command test, read ASCII pairwise distances.
408s 
408s All 9 comparisons passed.
408s 
408s ********************************************************************************
408s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_Sieve
408s 
408s   CPPTRAJ: Cluster, nosieve 
408s 
408s   CPPTRAJ: Cluster, sieve5 
408s 
408s   CPPTRAJ: Cluster, nosieve savepairdist
408s 
408s   CPPTRAJ: Cluster, nosieve loadpairdist
408s 
408s   CPPTRAJ: Cluster, sieve5 savepairdist
408s 
408s   CPPTRAJ: Cluster, sieve5 loadpairdist
408s 
408s   CPPTRAJ: Cluster, nosieve pairwisecache none
409s 
409s   CPPTRAJ: Cluster, sieve5 pairwisecache none
409s 
409s   CPPTRAJ: Cluster, random 
409s 
409s All 28 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_RandomSieve
409s 
409s   CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances).
409s 
409s   CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances).
409s 
409s All 4 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_DataSet
409s 
409s   CPPTRAJ: Clustering, One DataSet
409s 
409s   CPPTRAJ: Clustering, Two DataSets
409s 
409s   CPPTRAJ: Clustering, dihedral DataSet
409s 
409s   CPPTRAJ: Clustering, two dihedral DataSets
409s 
409s   CPPTRAJ: Clustering, dihedral DataSet, K-means
409s 
409s   CPPTRAJ: Clustering, two dihedral DataSets, K-means
409s 
409s All 8 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_DBSCAN
409s 
409s   CPPTRAJ: DBSCAN test
409s 
409s   CPPTRAJ: DBSCAN automatic parameter determination test.
409s 
409s   CPPTRAJ: DBSCAN kdist map test
409s 
409s   CPPTRAJ: DBSCAN with sieve
409s 
409s All 4 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_Kmeans
409s 
409s   CPPTRAJ: Cpptraj Kmeans
409s 
409s   CPPTRAJ: Cpptraj Kmeans random
409s 
409s All 6 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_SymmRMSD
409s 
409s   CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD)
409s 
409s All 5 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_TrajWrites
409s 
409s   CPPTRAJ: Cluster command test, coordinate writes.
409s 
409s   CPPTRAJ: Cluster command test, coordinate writes using info file.
409s 
409s All 8 comparisons passed.
409s 
409s ********************************************************************************
409s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_Dpeaks
409s 
409s   CPPTRAJ: Density peaks clustering test
410s 
410s All 3 comparisons passed.
410s 
410s ********************************************************************************
410s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cluster_Nreps
410s 
410s   CPPTRAJ: Clustering with specified # reps
410s 
410s All 2 comparisons passed.
410s 
410s ********************************************************************************
410s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_IRED
410s 
410s   CPPTRAJ: IRED vector/matrix test
410s 
410s 
410s ********************************************************************************
410s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_RandomizeIons
410s 
410s   CPPTRAJ: randomizeions test (original algorithm)
410s 
410s   CPPTRAJ: Randomize (around, overlap)
411s 
411s   CPPTRAJ: Randomize (around)
411s 
411s   CPPTRAJ: Randomize (overlap)
411s 
411s   CPPTRAJ: Randomize (no restrictions)
411s 
411s All 5 comparisons passed.
411s 
411s ********************************************************************************
411s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Molsurf
411s 
411s   CPPTRAJ: Molsurf test
411s 
411s All 1 comparisons passed.
411s 
411s ********************************************************************************
411s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Corr
411s 
411s   CPPTRAJ: Correlation test
411s 
411s All 2 comparisons passed.
411s 
411s ********************************************************************************
411s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CheckStructure
411s 
411s   CPPTRAJ: Structure Check
411s 
411s   CPPTRAJ: Structure Check with Around and Skip
411s 
411s   CPPTRAJ: Structure Check with PBC
412s 
412s   CPPTRAJ: Structure Check with Around
412s 
412s All 8 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_RmsAvgCorr
412s 
412s   CPPTRAJ: RmsAvgCorr Reference
412s 
412s   CPPTRAJ: RmsAvgCorr First
412s 
412s All 3 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Contacts
412s 
412s   CPPTRAJ: Contacts test.
412s 
412s All 3 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Principal
412s 
412s   CPPTRAJ: Principal Test
412s 
412s All 3 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_ClusterDihedral
412s 
412s   CPPTRAJ: clusterdihedral test
412s 
412s All 4 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Vector
412s 
412s   CPPTRAJ: Basic vector tests
412s 
412s   CPPTRAJ: Test vector center with magnitude
412s 
412s   CPPTRAJ: Momentum/velocity vector test.
412s 
412s   CPPTRAJ: Force vector test.
412s 
412s All 14 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Matrix
412s 
412s   CPPTRAJ: Matrix Tests
412s 
412s   CPPTRAJ: Generate matrix with trajectory start/stop/offset
412s 
412s   CPPTRAJ: Generate matrix with action stop/start/offset
412s 
412s All 15 comparisons passed.
412s 
412s ********************************************************************************
412s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AtomicFluct
412s 
412s   CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor].
412s 
412s   CPPTRAJ: Atomic fluctuations test [:2-12 byatom].
412s 
412s   CPPTRAJ: Atomic fluctuations test [bymask :3,4,5].
412s 
412s   CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor].
412s 
412s   CPPTRAJ: Atomicfluct test with ADP output
412s 
412s   CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output.
413s 
413s All 13 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Grid
413s 
413s   CPPTRAJ: Dipole test
413s 
413s   CPPTRAJ: Grid test
413s 
413s   CPPTRAJ: OpenDX Grid read test
413s 
413s   CPPTRAJ: Grid with specified center test.
413s 
413s   CPPTRAJ: Grid with box center offset test.
413s 
413s   CPPTRAJ: Grid with mask center offset test.
413s 
413s   CPPTRAJ: Non-orthogonal grid test.
413s 
413s   CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test
413s 
413s   CPPTRAJ: Grid generation from 'bounds' test.
413s 
413s All 13 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Unwrap
413s 
413s   CPPTRAJ: Unwrap non-orthogonal test
413s 
413s   CPPTRAJ: Unwrap orthogonal test
413s 
413s All 2 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Project
413s 
413s   CPPTRAJ: Projection
413s 
413s All 1 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Analyze_Modes
413s 
413s   CPPTRAJ: Modes analysis, RMS fluctuations
413s 
413s   CPPTRAJ: Modes analysis, displacements
413s 
413s   CPPTRAJ: Modes analysis, dipole correlation
413s 
413s   CPPTRAJ: Modes analysis, pseudo trajectory creation test
413s 
413s   CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test
413s 
413s All 6 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Watershell
413s 
413s   CPPTRAJ: Watershell Test, non-orthorhombic imaging.
414s 
414s   CPPTRAJ: Watershell Test, orthorhombic imaging.
414s 
414s   CPPTRAJ: Watershell Test, no imaging.
414s 
414s All 3 comparisons passed.
414s 
414s ********************************************************************************
414s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AnalysisRunAvg
414s 
414s   CPPTRAJ: Analysis Running Average
414s 
414s All 2 comparisons passed.
414s 
414s ********************************************************************************
414s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Volmap
414s 
414s   CPPTRAJ: VMD VolMap Algorithm test
414s   VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run.
414s   Skipped test: VMD VolMap Algorithm longer tests
414s 
414s All 2 comparisons passed.
414s 1 comparisons skipped.
414s 
414s ********************************************************************************
414s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_SPAM
414s 
414s   CPPTRAJ: SPAM Test
414s 
414s   CPPTRAJ: SPAM Pure Solvent Test
416s 
416s All 5 comparisons passed.
416s 
416s ********************************************************************************
416s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LIE
416s 
416s   CPPTRAJ: LIE test
416s 
416s All 1 comparisons passed.
416s 
416s ********************************************************************************
416s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Density
416s 
416s   CPPTRAJ: Density along axis tests
416s 
416s   CPPTRAJ: Multi-frame density along axis test
416s 
416s   CPPTRAJ: Total system density test
416s 
416s All 7 comparisons passed.
416s 
416s ********************************************************************************
416s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LipidOrder
416s 
416s   CPPTRAJ: Lipid Order Parameter Test.
416s 
416s All 6 comparisons passed.
416s 
416s ********************************************************************************
416s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LipidSCD
416s 
416s   CPPTRAJ: Basic lipid order parameter test
416s 
416s   CPPTRAJ: New Lipid Order Parameter Test, DOPC.
416s 
416s All 4 comparisons passed.
416s 
416s ********************************************************************************
416s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_PairDist
416s 
416s   CPPTRAJ: PairDist Test.
416s 
416s   CPPTRAJ: Pairdist test, orthogonal imaging.
417s 
417s   CPPTRAJ: Pairdist test, nonorthogonal imaging.
417s 
417s   CPPTRAJ: Pairdist test, 2 masks.
417s 
417s All 4 comparisons passed.
417s 
418s ********************************************************************************
418s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_ReadData
418s 
418s   CPPTRAJ: Read vector data test (no origins, origins)
418s 
418s   CPPTRAJ: Read vector data set (origins, no origins)
418s 
418s   CPPTRAJ: Read Amber output test
418s 
418s   CPPTRAJ: Read CHARMM output test
418s 
418s   CPPTRAJ: 3D data read/write test
418s 
418s   CPPTRAJ: Standard 3D data write test
418s 
418s   CPPTRAJ: Standard 3D data read test
418s 
418s   CPPTRAJ: Standard 3D data read/append test
418s 
418s   CPPTRAJ: Standard 3D data, sparse
418s 
418s   CPPTRAJ: Nonorthogonal grid standard write/read tests.
418s 
418s   CPPTRAJ: Read specific columns test.
418s 
418s   CPPTRAJ: Write non-square matrix
418s 
418s   CPPTRAJ: Read non-square matrix
418s 
418s   CPPTRAJ: Read square matrix
418s 
418s All 15 comparisons passed.
418s 
418s ********************************************************************************
418s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_GIST
418s 
418s   CPPTRAJ: GIST water-water interaction test
419s 
419s   CPPTRAJ: GIST test, orthogonal cell
421s 
421s   CPPTRAJ: GIST test, nonorthogonal cell
424s 
424s All 11 comparisons passed.
424s 
424s ********************************************************************************
424s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_GIST_Order
424s 
424s   CPPTRAJ: TIP3P water cluster test
424s 
424s   CPPTRAJ: TIP4P water cluster test
424s 
424s   CPPTRAJ: TIP5P water cluster test
424s 
424s All 4 comparisons passed.
424s 
424s ********************************************************************************
424s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_systemVF
424s 
424s   CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test
425s 
425s All 1 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AtomicCorr
425s 
425s   CPPTRAJ: Atomic Correlation test
425s 
425s All 1 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AutoCorr
425s 
425s   CPPTRAJ: AutoCorr test.
425s 
425s All 1 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Box
425s 
425s   CPPTRAJ: Box Test (Add box info)
425s 
425s   CPPTRAJ: Box test (remove box info)
425s 
425s   CPPTRAJ: Box test (Modify box length)
425s 
425s   CPPTRAJ: Box test (auto orthogonal box, no radii)
425s 
425s   CPPTRAJ: Box test (auto orthogonal box, VDW radii)
425s 
425s All 7 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AtomTypeSelect
425s 
425s   CPPTRAJ: Selection by atom type test.
425s 
425s All 1 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AvgRef
425s 
425s   CPPTRAJ: RMSD Test with averaged reference coordinates.
425s 
425s All 1 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Crank_Stat
425s 
425s   CPPTRAJ: Crankshaft test
425s 
425s All 3 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CreateCrd
425s 
425s   CPPTRAJ: COORDS data set creation and CRDFLUCT test.
425s 
425s   CPPTRAJ: COORDS data set creation with velocities test
425s 
425s   CPPTRAJ: TRAJ data set creation and CRDFLUCT test.
425s 
425s   CPPTRAJ: TRAJ data set creation with velocities test.
425s 
425s   CPPTRAJ: COORDS data set append test
425s 
425s   CPPTRAJ: COORDS test storing frame metadata
425s 
425s   CPPTRAJ: TRAJ test storing frame metadata
425s 
425s All 8 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AutoImage
425s 
425s   CPPTRAJ: AutoImage test (split DNA duplex)
425s 
425s   CPPTRAJ: AutoImage test, use anchor mask
425s 
425s All 2 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LoadCrd
425s 
425s   CPPTRAJ: LoadCrd test.
425s 
425s   CPPTRAJ: LoadTraj test.
425s 
425s   CPPTRAJ: LoadTraj from trajin test.
425s 
425s   CPPTRAJ: LoadCrd append from multiple files test
425s 
425s All 4 comparisons passed.
425s 
425s ********************************************************************************
425s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_MultiVector
425s 
425s   CPPTRAJ: Multivector test
425s 
425s All 1 comparisons passed.
425s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Lifetime
426s 
426s   CPPTRAJ: Lifetime test.
426s 
426s   CPPTRAJ: Lifetime test with data set caching.
426s 
426s   CPPTRAJ: Lifetime average and cumulative average test.
426s 
426s All 12 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_FFT
426s 
426s   CPPTRAJ: FFT test.
426s 
426s All 5 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Timecorr
426s 
426s   CPPTRAJ: Timecorr test.
426s 
426s All 7 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CrossCorr
426s 
426s   CPPTRAJ: CrossCorr test
426s 
426s All 1 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_SymmRmsd
426s 
426s   CPPTRAJ: SymmRmsd
426s 
426s   CPPTRAJ: ASP symmetry-corrected RMSD test
426s 
426s   CPPTRAJ: GLU symmetry-corrected RMSD test
426s 
426s   CPPTRAJ: TYR symmetry-corrected RMSD test
426s 
426s   CPPTRAJ: Longer symmetry-corrected RMSD test.
426s 
426s All 8 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Multidihedral
426s 
426s   CPPTRAJ: Multidihedral test
426s 
426s   CPPTRAJ: Multidihedral Nucleotide CHI test
426s 
426s   CPPTRAJ: Multidihedral protein dihedrals test
426s 
426s   CPPTRAJ: Multidihedral cyclic molecule test
426s 
426s All 6 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Ensemble_MREMD
426s 
426s   CPPTRAJ: M-REMD sort test.
426s 
426s   CPPTRAJ: M-REMD actions test.
426s 
426s   CPPTRAJ: M-REMD ensemble outtraj test.
426s 
426s   CPPTRAJ: M-REMD no sort, running average test
426s 
426s   CPPTRAJ: M-REMD, generate RMS data
426s 
426s   CPPTRAJ: M-REMD, meltcurve analysis
426s 
426s All 17 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_MakeStructure
426s 
426s   CPPTRAJ: Basic makestructure test
426s 
426s   CPPTRAJ: Makestructure test with reference.
426s 
426s All 5 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Rotate
426s 
426s   CPPTRAJ: Rotation (and inverse) of coords from matrices
426s 
426s   CPPTRAJ: Rotate with defined axis
426s 
426s All 3 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Integrate
426s 
426s   CPPTRAJ: Integration test.
426s 
426s All 2 comparisons passed.
426s 
426s ********************************************************************************
426s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_NativeContacts
426s 
426s   CPPTRAJ: NativeContacts test.
426s 
426s   CPPTRAJ: NativeContacts test, save non-native contacts, residue time series
427s 
427s   CPPTRAJ: NativeContacts test, orthorhombic imaging.
427s 
427s All 17 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CheckChiral
427s 
427s   CPPTRAJ: Check chirality test
427s 
427s All 1 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Energy
427s 
427s   CPPTRAJ: Simple energy tests
427s 
427s   CPPTRAJ: Test kinetic energy calculation
427s 
427s   CPPTRAJ: Test total energy calculation
427s 
427s   CPPTRAJ: Test partial energy calculation
427s 
427s All 6 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LESsplit
427s 
427s   CPPTRAJ: LES split/average test
427s 
427s All 2 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_PermuteDihedrals
427s 
427s   CPPTRAJ: PermuteDihedrals interval -120, phi psi
427s 
427s   CPPTRAJ: PermuteDihedrals, random rotations
427s 
427s All 4 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CCP4
427s 
427s   CPPTRAJ: CCP4 read/write and DX conversion test.
427s 
427s All 2 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DihCovar
427s 
427s   CPPTRAJ: Dihedral Covariance Matrix Test
427s 
427s All 3 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CurveFit
427s 
427s   CPPTRAJ: Curve fitting test.
427s 
427s   CPPTRAJ: Curve fitting multi-exponential tests.
427s 
427s   CPPTRAJ: Curve fitting, custom output range.
427s 
427s All 6 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Multicurve
427s 
427s   CPPTRAJ: Multicurve test
427s 
427s All 1 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DataSetAverage
427s 
427s   CPPTRAJ: Data set averaging and averaging over all sets test.
427s 
427s All 2 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_VectorMath
427s 
427s   CPPTRAJ: Vector dot/cross product test
427s 
427s All 2 comparisons passed.
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Esander
427s   SANDER energy tests (long) requires SANDER API from AmberTools.
427s   Cpptraj was compiled without SANDER API from AmberTools support.
427s   SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run.
427s   SKIP: SANDER energy tests (long)
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Esander_Short
427s   Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools.
427s   Cpptraj was compiled without SANDER API from AmberTools support.
427s   SKIP: Energy via sander API short tests (GB/PME)
427s 
427s ********************************************************************************
427s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Temperature
427s 
427s   CPPTRAJ: Temperature test.
427s 
427s   CPPTRAJ: Temperature with SHAKE on hydrogens.
427s 
427s   CPPTRAJ: Temperature with SHAKE on all atoms.
427s 
427s   CPPTRAJ: Temperature calc with extra points.
428s 
428s All 5 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Spline
428s 
428s   CPPTRAJ: Spline test
428s 
428s All 1 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_KDE
428s 
428s   CPPTRAJ: KDE test.
428s 
428s   CPPTRAJ: KDE with Kullback-Leibler divergence test
428s 
428s All 4 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Wavelet
428s 
428s   CPPTRAJ: Wavelet analysis test
428s 
428s   CPPTRAJ: Wavelet WAFEX test
428s 
428s All 3 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CIF
428s 
428s   CPPTRAJ: CIF read test
428s 
428s   CPPTRAJ: Generate offset traj from PDB
428s 
428s   CPPTRAJ: Generate offset traj from CIF
428s 
428s All 2 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_PDB
428s 
428s   CPPTRAJ: PDB format read/write test
428s 
428s   CPPTRAJ: PQR file write with various radii
428s 
428s   CPPTRAJ: PDB filter alternate atom location IDs test
428s 
428s   CPPTRAJ: Adding PDB info to topology
428s 
428s All 10 comparisons passed.
428s 
428s ********************************************************************************
428s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Align
428s 
428s   CPPTRAJ: Align Tests.
428s 
428s   CPPTRAJ: Align, unit cell rotation/imaging test.
429s 
429s All 4 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_VelocityAutoCorr
429s 
429s   CPPTRAJ: Velocity autocorrelation test
429s 
429s All 3 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_VelFrc
429s 
429s   CPPTRAJ: Test combining coordinates, velocities, and forces.
429s 
429s   CPPTRAJ: Test using velocities as coordinates.
429s 
429s   CPPTRAJ: Test writing velocities (MDVEL)
429s 
429s   CPPTRAJ: Test using forces as coordinates.
429s 
429s   CPPTRAJ: Test writing forces (MDFRC)
429s 
429s   CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart.
429s 
429s   CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart.
429s 
429s All 5 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_RotateDihedral
429s 
429s   CPPTRAJ: Rotate dihedral to target value.
429s 
429s   CPPTRAJ: Rotate dihedral by increment
429s 
429s   CPPTRAJ: Rotate dihedral in TRAJ data set
429s 
429s All 3 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DataSetCmd
429s 
429s   CPPTRAJ: Data Set commands test
429s 
429s All 10 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Remap
429s 
429s   CPPTRAJ: Remap Test
429s 
429s All 1 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CompareTop
429s 
429s   CPPTRAJ: Compare topology test
429s 
429s All 1 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Filter
429s 
429s   CPPTRAJ: Basic filter test
429s 
429s   CPPTRAJ: Data filter test.
429s 
429s   CPPTRAJ: Filter matrix test.
429s 
429s All 5 comparisons passed.
429s 
429s ********************************************************************************
429s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CombineCrd
429s 
429s   CPPTRAJ: Combine COORDS test.
429s 
429s   CPPTRAJ: Combine COORDS test with box info.
429s 
429s   CPPTRAJ: Split coords and recombine test.
430s 
430s All 5 comparisons passed.
430s 
430s ********************************************************************************
430s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_TopInfo
430s 
430s   CPPTRAJ: Topology info print test.
430s 
430s   CPPTRAJ: Topology info with reference coords test
430s 
430s All 12 comparisons passed.
430s 
430s ********************************************************************************
430s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_GromacsTrr
430s 
430s   CPPTRAJ: TRR force/velocity read -> NetCDF write test
430s 
430s   CPPTRAJ: TRR force/velocity read -> TRR write test
430s 
430s   CPPTRAJ: CRD => TRR
430s 
430s   CPPTRAJ: TRR => CRD
430s 
430s   CPPTRAJ: CRD(1-5) => TRR
430s 
430s   CPPTRAJ: CRD(6-10) => TRR
430s 
430s   CPPTRAJ: TRR (appended) => CRD
430s 
430s   CPPTRAJ: GMX: CRD with offset
430s 
430s   CPPTRAJ: GMX: TRR with offset
430s 
430s All 5 comparisons passed.
430s 
430s ********************************************************************************
430s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_GromacsXtc
430s 
430s   CPPTRAJ: XTC read test
430s 
430s   CPPTRAJ: CRD => XTC
430s 
430s   CPPTRAJ: XTC => CRD
431s 
431s   CPPTRAJ: CRD(1-5) => XTC
431s 
431s   CPPTRAJ: CRD(6-10) => XTC
431s 
431s   CPPTRAJ: XTC (appended) => CRD
431s 
431s   CPPTRAJ: GMX: CRD with offset
431s 
431s   CPPTRAJ: GMX: XTC with offset
431s 
431s All 4 comparisons passed.
431s 
431s ********************************************************************************
431s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_GromacsTNG
431s 
431s   CPPTRAJ: TNG read test
431s 
431s   CPPTRAJ: TNG read test (with offset)
431s 
431s All 6 comparisons passed.
431s 
431s ********************************************************************************
431s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Ewald
431s 
431s   CPPTRAJ: Direct sum test
431s 
431s   CPPTRAJ: Ewald test (NaCl crystal)
431s 
431s   CPPTRAJ: Ewald test (trunc. oct)
432s 
432s   CPPTRAJ: Ewald test (partial system, trunc. oct)
432s   Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
432s   Skipped test: Ewald test (trunc. oct), 10 frames
432s   Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run.
432s   Skipped test: Ewald test (ortho), 10 frames
432s 
432s All 4 comparisons passed.
432s 2 comparisons skipped.
432s 
432s ********************************************************************************
432s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LibPME
432s 
432s   CPPTRAJ: Particle mesh Ewald test (NaCl crystal)
432s 
432s   CPPTRAJ: Particle mesh Ewald test (trunc. oct)
432s 
432s   CPPTRAJ: Particle mesh Ewald test (ortho)
432s 
432s   CPPTRAJ: Particle mesh Ewald test (ortho, with mask)
432s 
432s   CPPTRAJ: PME test (partial system, trunc. oct)
432s   PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
432s   Skipped test: PME test (trunc. oct), 10 frames
432s 
432s All 5 comparisons passed.
432s 1 comparisons skipped.
432s 
432s ********************************************************************************
432s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LJ_PME
432s 
432s   CPPTRAJ: LJ PME test.
432s 
432s   CPPTRAJ: LJ PME kappa sweep test, 0.25
432s 
432s   CPPTRAJ: LJ PME kappa sweep test, 0.35
432s 
432s   CPPTRAJ: LJ PME kappa sweep test, 0.45
432s 
432s   CPPTRAJ: LJ PME kappa sweep test, 0.5
432s 
432s   CPPTRAJ: LJ with switch function test
433s 
433s All 5 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_TI
433s 
433s   CPPTRAJ: TI analysis test.
433s 
433s All 5 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_FixImagedBonds
433s 
433s   CPPTRAJ: Fix imaged bonds test (Ortho.)
433s 
433s   CPPTRAJ: Fix imaged bonds test (Non-ortho.)
433s 
433s All 2 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Distance
433s 
433s   CPPTRAJ: Distance tests
433s 
433s   CPPTRAJ: Orthogonal imaged distance
433s 
433s   CPPTRAJ: Non-orthogonal imaged distance
433s 
433s All 3 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Volume
433s 
433s   CPPTRAJ: Volume tests
433s 
433s All 1 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_SetVelocity
433s 
433s   CPPTRAJ: Set Velocity test
433s 
433s   CPPTRAJ: Scale velocity test
433s 
433s All 3 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Remlog
433s 
433s   CPPTRAJ: Replica log read/analyze test.
433s 
433s All 7 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_AreaPerMol
433s 
433s   CPPTRAJ: Area per molecule test
433s 
433s All 6 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DistBasedMask
433s 
433s   CPPTRAJ: Distance-based atom mask tests (atom, residue)
433s 
433s   CPPTRAJ: Distance-based atom mask tests (molecule)
433s 
433s All 6 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Calc
433s 
433s   CPPTRAJ: Calc test
433s 
433s   CPPTRAJ: Calc test with data sets
433s 
433s   CPPTRAJ: Test math functions
433s 
433s All 4 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CalcState
433s 
433s   CPPTRAJ: Calcstate test
433s 
433s All 4 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Change
433s 
433s   CPPTRAJ: Change atom and residue name tests
433s 
433s   CPPTRAJ: Change chain ID test
433s 
433s   CPPTRAJ: Change chain ID of COORDS set test
433s 
433s All 3 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CreateReservoir
433s 
433s   CPPTRAJ: Create RREMD NetCDF reservoir test
433s 
433s All 1 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_FixAtomOrder
433s 
433s   CPPTRAJ: Out of order molecules test
433s 
433s All 2 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_LowestCurve
433s 
433s   CPPTRAJ: LowestCurve test
433s 
433s All 1 comparisons passed.
433s 
433s ********************************************************************************
433s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_MinImage
433s 
433s   CPPTRAJ: Minimum Image test.
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Regress
434s 
434s   CPPTRAJ: Linear regression test.
434s 
434s All 3 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Rst
434s 
434s   CPPTRAJ: Generate restraints (rst) test
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Pairwise
434s 
434s   CPPTRAJ: Pairwise tests
434s 
434s   CPPTRAJ: Pairwise test, partial system
434s 
434s All 10 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_ParmBox
434s 
434s   CPPTRAJ: Parmbox test
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Solvent
434s 
434s   CPPTRAJ: Test solvent command with closest
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Translate
434s 
434s   CPPTRAJ: Translate test
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_ReplicateCell
434s 
434s   CPPTRAJ: Replicate cell test
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_ScaleDihedralK
434s 
434s   CPPTRAJ: Scale dihedral force constant test
434s 
434s   CPPTRAJ: Scale dihedral force constant with 'useall'
434s 
434s All 2 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_PhiPsi
434s 
434s   CPPTRAJ: Phipsi test
434s 
434s All 1 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Control
434s 
434s   CPPTRAJ: Loop tests
434s 
434s   CPPTRAJ: Test set command
434s 
434s   CPPTRAJ: Test reading comma-separated list of strings
434s 
434s   CPPTRAJ: Test nested loops and variables in loops
434s 
434s   CPPTRAJ: Test loop over data set blocks
434s 
434s   CPPTRAJ: Test for filename wildcards and oversets
434s 
434s All 13 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_InfraredSpec
434s 
434s   CPPTRAJ: Infrared spectrum calculation test
434s 
434s All 2 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Cphstats
434s 
434s   CPPTRAJ: Explicit pH REMD ensemble data read / sort
434s 
434s   CPPTRAJ: Constant pH stats test
434s 
434s   CPPTRAJ: Sorted implicit constant pH stats test
434s 
434s   CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats
434s 
434s   CPPTRAJ: Unsorted pH read/write test
434s 
434s All 16 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CmdLine
434s 
434s   CPPTRAJ: Command line trajectory args test, part 1
434s 
434s   CPPTRAJ: Command line test trajectory args test, part 2
434s 
434s   CPPTRAJ: Command line wildcard test, part 1
434s 
434s   CPPTRAJ: Command line wildcard test, part 2
434s 
434s All 2 comparisons passed.
434s 
434s ********************************************************************************
434s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_XYZformat
434s 
434s   CPPTRAJ: XYZ format write
434s 
434s   CPPTRAJ: Atom XYZ format read, test 1
435s 
435s   CPPTRAJ: Atom XYZ format read, test 2
435s 
435s   CPPTRAJ: Atom XYZ format read, test 3
435s 
435s   CPPTRAJ: Atom XYZ format read, test 4
435s 
435s   CPPTRAJ: Atom XYZ format read, test 5
435s 
435s   CPPTRAJ: Atom XYZ format read, test 6
435s 
435s All 6 comparisons passed.
435s 
435s ********************************************************************************
435s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Hausdorff
435s 
435s   CPPTRAJ: Simple Hausdorff distance test.
435s 
435s   CPPTRAJ: Hausdorff distance of 2D rms output test.
435s 
435s   CPPTRAJ: Hausdorff distance of 2D rms output test.
435s 
435s All 3 comparisons passed.
435s 
435s ********************************************************************************
435s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_CatCrd
435s 
435s   CPPTRAJ: Concatenate COORDS data set test
435s 
435s All 1 comparisons passed.
435s 
435s ********************************************************************************
435s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_XtalSymm
435s 
435s   CPPTRAJ: XtalSymm Reference
435s 
435s   CPPTRAJ: XtalSymm Reimaging by Atom
436s 
436s   CPPTRAJ: XtalSymm Reimaging by Molecule
437s 
437s All 3 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Time
437s 
437s   CPPTRAJ: Add time to restart test
437s 
437s   CPPTRAJ: Remove time from restart test
437s 
437s   CPPTRAJ: Add time to trajectory test
437s 
437s   CPPTRAJ: Modify time info test.
437s 
437s All 4 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_SplitCoords
437s 
437s   CPPTRAJ: SplitCoords test
437s 
437s All 1 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_DihedralRMS
437s 
437s   CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.)
437s 
437s   CPPTRAJ: Dihedral RMSD test (to previous)
437s 
437s   CPPTRAJ: Dihedral RMS fluctuation test.
437s 
437s All 5 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Slope
437s 
437s   CPPTRAJ: Finite difference test.
437s 
437s All 1 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Diagmatrix
437s 
437s   CPPTRAJ: MW covariance matrix thermo analysis test
437s 
437s All 1 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Emin
437s 
437s   CPPTRAJ: Basic energy minimization test.
437s 
437s   CPPTRAJ: Energy minimization with angle term test.
437s 
437s   CPPTRAJ: Energy minimization with dihedral and 1-4 terms test.
437s 
437s   CPPTRAJ: Energy minimization with nonbond term test.
438s 
438s   CPPTRAJ: OpenMM basic energy minimization tests (bonds)
438s 
438s   CPPTRAJ: OpenMM basic energy minimization tests (angles)
438s 
438s   CPPTRAJ: OpenMM basic energy minimization tests (dihedrals)
438s 
438s   CPPTRAJ: OpenMM basic energy minimization tests (nonbonds)
438s 
438s   CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME)
439s 
439s All 9 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_EvalPlateau
439s 
439s   CPPTRAJ: Evalulate plateau test
439s 
439s All 2 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Graft
439s 
439s   CPPTRAJ: Graft test
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Flatten
439s 
439s   CPPTRAJ: Flatten test.
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.IcRMoi/build.0GL/src/test/Test_Random
439s 
439s   CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs
439s 
439s   CPPTRAJ: PCG32 RNG test.
439s 
439s   CPPTRAJ: Test Stdlib RNG
439s 
439s   CPPTRAJ: Test Mersenne Twister RNG
439s 
439s All 4 comparisons passed.
439s 
439s make[1]: Leaving directory '/tmp/autopkgtest.IcRMoi/build.0GL/src/test'
439s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 26 00:46 ../bin/cpptraj -> /usr/bin/cpptraj
439s ===================== TEST SUMMARY ======================
439s   853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped).
439s   480 out of 480 program executions completed.
439s   170 out of 173 tests completed with no issues.
439s   2 tests skipped.
439s =========================================================
439s make: Leaving directory '/tmp/autopkgtest.IcRMoi/build.0GL/src/test'
439s autopkgtest [00:47:23]: test command1: -----------------------]
439s command1             PASS
439s autopkgtest [00:47:23]: test command1:  - - - - - - - - - - results - - - - - - - - - -
440s autopkgtest [00:47:24]: @@@@@@@@@@@@@@@@@@@@ summary
440s command1             PASS
450s Creating nova instance adt-noble-amd64-cpptraj-20240326-004004-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-amd64-server-20240325.img (UUID ba43860b-557a-4db2-b3f0-378a99bca08c)...