0s autopkgtest [01:48:06]: starting date and time: 2024-03-25 01:48:06+0000
  0s autopkgtest [01:48:06]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps
  0s autopkgtest [01:48:06]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.q47hxol8/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=src:readline,src:asymptote --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=readline/8.2-4 asymptote/2.87+ds-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-44.secgroup --name adt-noble-arm64-cpptraj-20240325-014805-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-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://us.ports.ubuntu.com/ubuntu-ports/
117s autopkgtest [01:50:03]: testbed dpkg architecture: arm64
117s autopkgtest [01:50:03]: testbed apt version: 2.7.12
117s autopkgtest [01:50:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup
118s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
123s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB]
123s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B]
123s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.8 kB]
123s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3985 kB]
123s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [709 kB]
123s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B]
123s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB]
123s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B]
123s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB]
123s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B]
123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [71.0 kB]
123s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B]
127s Fetched 9851 kB in 3s (2987 kB/s)
128s Reading package lists...
133s Reading package lists...
134s Building dependency tree...
134s Reading state information...
135s Calculating upgrade...
136s The following packages will be upgraded:
136s   readline-common
137s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
137s Need to get 56.4 kB of archives.
137s After this operation, 0 B of additional disk space will be used.
137s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-4 [56.4 kB]
138s Fetched 56.4 kB in 0s (183 kB/s)
138s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75911 files and directories currently installed.)
138s Preparing to unpack .../readline-common_8.2-4_all.deb ...
138s Unpacking readline-common (8.2-4) over (8.2-3) ...
138s Setting up readline-common (8.2-4) ...
139s Processing triggers for install-info (7.1-3) ...
139s Processing triggers for man-db (2.12.0-3) ...
140s Reading package lists...
140s Building dependency tree...
140s Reading state information...
142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
144s sh: Attempting to set up Debian/Ubuntu apt sources automatically
144s sh: Distribution appears to be Ubuntu
146s Reading package lists...
147s Building dependency tree...
147s Reading state information...
148s eatmydata is already the newest version (131-1).
148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
148s Reading package lists...
149s Building dependency tree...
149s Reading state information...
150s dbus is already the newest version (1.14.10-4ubuntu1).
150s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
150s Reading package lists...
151s Building dependency tree...
151s Reading state information...
152s rng-tools-debian is already the newest version (2.4).
152s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
153s Reading package lists...
153s Building dependency tree...
153s Reading state information...
154s The following packages will be REMOVED:
154s   cloud-init* python3-configobj* python3-debconf*
155s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
155s After this operation, 3256 kB disk space will be freed.
155s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75911 files and directories currently installed.)
155s Removing cloud-init (24.1.2-0ubuntu1) ...
157s Removing python3-configobj (5.0.8-3) ...
157s Removing python3-debconf (1.5.86) ...
157s Processing triggers for man-db (2.12.0-3) ...
158s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75522 files and directories currently installed.)
158s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ...
160s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
160s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ...
160s invoke-rc.d: policy-rc.d denied execution of try-restart.
160s Reading package lists...
161s Building dependency tree...
161s Reading state information...
162s linux-generic is already the newest version (6.8.0-11.11+1).
162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
163s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
163s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
163s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
171s Reading package lists...
171s Reading package lists...
171s Building dependency tree...
171s Reading state information...
172s Calculating upgrade...
173s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
174s Reading package lists...
174s Building dependency tree...
174s Reading state information...
176s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
176s autopkgtest [01:51:02]: rebooting testbed after setup commands that affected boot
338s autopkgtest [01:53:44]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024
342s autopkgtest [01:53:48]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj
347s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B]
347s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB]
347s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B]
348s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC
348s gpgv:                using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D
348s gpgv: Can't check signature: No public key
348s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found
354s autopkgtest [01:53:59]: testing package cpptraj version 5.1.0+dfsg-3build1
354s autopkgtest [01:54:00]: build not needed
361s autopkgtest [01:54:07]: test command1: preparing testbed
363s Reading package lists...
364s Building dependency tree...
364s Reading state information...
365s Starting pkgProblemResolver with broken count: 0
365s Starting 2 pkgProblemResolver with broken count: 0
365s Done
366s The following additional packages will be installed:
366s   cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1
366s   libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2
366s   netcdf-bin
366s Suggested packages:
366s   libfftw3-bin libfftw3-dev
366s The following NEW packages will be installed:
366s   autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3
366s   libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19
366s   libopenmm8.0 libsz2 netcdf-bin
367s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded.
367s Need to get 7974 kB/7974 kB of archives.
367s After this operation, 23.7 MB of additional disk space will be used.
367s Get:1 /tmp/autopkgtest.BzKBgt/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B]
367s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB]
367s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB]
367s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB]
368s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libarpack2 arm64 3.9.1-1 [90.2 kB]
368s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB]
368s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu1 [380 kB]
368s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB]
368s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B]
368s Get:10 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB]
368s Get:11 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB]
368s Get:12 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf19 arm64 1:4.9.2-3ubuntu1 [470 kB]
368s Get:13 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmm8.0 arm64 8.0.0+dfsg-6ubuntu1 [948 kB]
369s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 cpptraj arm64 5.1.0+dfsg-3build1 [1641 kB]
369s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 netcdf-bin arm64 1:4.9.2-3ubuntu1 [200 kB]
370s Fetched 7974 kB in 2s (3438 kB/s)
370s Selecting previously unselected package libblas3:arm64.
370s (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 ... 75467 files and directories currently installed.)
370s Preparing to unpack .../00-libblas3_3.12.0-3_arm64.deb ...
370s Unpacking libblas3:arm64 (3.12.0-3) ...
370s Selecting previously unselected package libgfortran5:arm64.
370s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_arm64.deb ...
370s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ...
370s Selecting previously unselected package liblapack3:arm64.
370s Preparing to unpack .../02-liblapack3_3.12.0-3_arm64.deb ...
370s Unpacking liblapack3:arm64 (3.12.0-3) ...
370s Selecting previously unselected package libarpack2:arm64.
370s Preparing to unpack .../03-libarpack2_3.9.1-1_arm64.deb ...
370s Unpacking libarpack2:arm64 (3.9.1-1) ...
370s Selecting previously unselected package libgomp1:arm64.
370s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_arm64.deb ...
370s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ...
370s Selecting previously unselected package libfftw3-double3:arm64.
370s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu1_arm64.deb ...
370s Unpacking libfftw3-double3:arm64 (3.3.10-1ubuntu1) ...
370s Selecting previously unselected package libaec0:arm64.
370s Preparing to unpack .../06-libaec0_1.1.2-1_arm64.deb ...
370s Unpacking libaec0:arm64 (1.1.2-1) ...
371s Selecting previously unselected package libsz2:arm64.
371s Preparing to unpack .../07-libsz2_1.1.2-1_arm64.deb ...
371s Unpacking libsz2:arm64 (1.1.2-1) ...
371s Selecting previously unselected package libhdf5-103-1:arm64.
371s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ...
371s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ...
371s Selecting previously unselected package libhdf5-hl-100:arm64.
371s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ...
371s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ...
371s Selecting previously unselected package libnetcdf19:arm64.
371s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_arm64.deb ...
371s Unpacking libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ...
371s Selecting previously unselected package libopenmm8.0.
371s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_arm64.deb ...
371s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
371s Selecting previously unselected package cpptraj.
371s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_arm64.deb ...
371s Unpacking cpptraj (5.1.0+dfsg-3build1) ...
371s Selecting previously unselected package netcdf-bin.
371s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_arm64.deb ...
371s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ...
371s Selecting previously unselected package autopkgtest-satdep.
371s Preparing to unpack .../14-1-autopkgtest-satdep.deb ...
371s Unpacking autopkgtest-satdep (0) ...
371s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ...
371s Setting up libaec0:arm64 (1.1.2-1) ...
371s Setting up libblas3:arm64 (3.12.0-3) ...
371s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
371s Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu1) ...
371s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ...
371s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
371s Setting up libsz2:arm64 (1.1.2-1) ...
371s Setting up liblapack3:arm64 (3.12.0-3) ...
371s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
371s Setting up libarpack2:arm64 (3.9.1-1) ...
371s Setting up libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ...
371s Setting up libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ...
371s Setting up libnetcdf19:arm64 (1:4.9.2-3ubuntu1) ...
371s Setting up cpptraj (5.1.0+dfsg-3build1) ...
371s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ...
371s Setting up autopkgtest-satdep (0) ...
371s Processing triggers for man-db (2.12.0-3) ...
372s Processing triggers for libc-bin (2.39-0ubuntu6) ...
378s (Reading database ... 75558 files and directories currently installed.)
378s Removing autopkgtest-satdep (0) ...
379s autopkgtest [01:54:25]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary
379s autopkgtest [01:54:25]: test command1: [-----------------------
380s make: Entering directory '/tmp/autopkgtest.BzKBgt/build.fVS/src/test'
380s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 25 01:54 ../bin/cpptraj -> /usr/bin/cpptraj
380s make[1]: Entering directory '/tmp/autopkgtest.BzKBgt/build.fVS/src/test'
380s ********************************************************************************
380s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_General
380s 
380s   CPPTRAJ: General tests
380s 
380s All 15 comparisons passed.
380s 
380s ********************************************************************************
380s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Parallel
380s 
380s   CPPTRAJ: Parallel tests.
380s 
380s   CPPTRAJ: Parallel test with trajectory offset
380s 
380s All 7 comparisons passed.
380s 
380s ********************************************************************************
380s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Strip
380s 
380s   CPPTRAJ: One frame strip command test
381s 
381s   CPPTRAJ: Unstrip (Lig/Rec/Complex) command test
381s 
381s   CPPTRAJ: Multi frame strip command test.
381s 
381s   CPPTRAJ: Strip topology with PDB info
381s 
381s All 11 comparisons passed.
381s 
381s ********************************************************************************
381s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_BrokenTraj
381s 
381s   CPPTRAJ: Broken Traj: Running good trajectory.
381s 
381s   CPPTRAJ: Broken Traj: Running broken trajectory.
381s 
381s   CPPTRAJ: Compressed broken trajectory test
381s 
381s All 2 comparisons passed.
381s 
381s ********************************************************************************
381s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_TrajinOffset
381s 
381s   CPPTRAJ: Normal trajectory read with offsets.
381s 
381s   CPPTRAJ: Gzipped trajectory read with offsets
381s 
381s   CPPTRAJ: Bzip2ed trajectory read with offsets
381s 
381s   CPPTRAJ: Start argument offset
381s 
381s All 4 comparisons passed.
381s 
381s ********************************************************************************
381s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_RemdTraj
381s 
381s   CPPTRAJ: CRD Replica Trajectory Run with offset
381s 
381s   CPPTRAJ: CRD Replica Trajectory Run
381s 
381s   CPPTRAJ: NetCDF Replica Trajectory Run test
381s 
381s   CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj
381s 
381s   CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj
382s 
382s   CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj
382s 
382s   CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj
382s 
382s   CPPTRAJ: CRD Replica Trajectory Run with remdout
382s 
382s All 8 comparisons passed.
382s 
382s ********************************************************************************
382s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_trajout_framerange
382s 
382s   CPPTRAJ: Trajout Frame Range [Amber Restart]
382s 
382s   CPPTRAJ: Trajout Frame Range [Amber Coordinates]
382s 
382s All 6 comparisons passed.
382s 
382s ********************************************************************************
382s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_PerResRMSD
382s 
382s   CPPTRAJ: Per-Residue RMSD Test.
382s 
382s   CPPTRAJ: Per-Residue RMSD Test with averaging
382s 
382s   CPPTRAJ: Per-Residue RMSD Test with residue centering.
382s 
382s All 3 comparisons passed.
382s 
382s ********************************************************************************
382s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DSSP
382s 
382s   CPPTRAJ: Secstruct (DSSP) command test.
382s 
382s   CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format.
382s 
382s   CPPTRAJ: Secstruct (DSSP) command with changing number of residues.
382s 
382s   CPPTRAJ: Secstruct (DSSP): SS assign output test
382s 
382s   CPPTRAJ: FtuFabI Assignment test
382s 
382s All 10 comparisons passed.
382s 
382s ********************************************************************************
382s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Center
382s 
382s   CPPTRAJ: Center command test.
382s 
382s   CPPTRAJ: Center origin command test.
383s 
383s   CPPTRAJ: Center origin mass command test.
383s 
383s   CPPTRAJ: Center reference command test.
383s 
383s   CPPTRAJ: Center point test.
383s 
383s All 5 comparisons passed.
383s 
383s ********************************************************************************
383s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Hbond
383s 
383s   CPPTRAJ: Solute Hbond test
383s 
383s   CPPTRAJ: Solute Hbond test with disk caching
383s 
383s   CPPTRAJ: Solute-solvent hbond test
383s 
383s   CPPTRAJ: Hbond, no intramolecular hydrogen bonds test
383s 
383s   CPPTRAJ: Hbond, specified solute masks
383s 
383s   CPPTRAJ: Hbond, no angle cutoff test
383s 
383s   CPPTRAJ: Hbond, Bridge nointramol test
384s 
384s   CPPTRAJ: Hbond with imaging
384s 
384s   CPPTRAJ: Hbond, orthogonal imaging
384s 
384s All 23 comparisons passed.
384s 
384s ********************************************************************************
384s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_NCrestart
384s 
384s   CPPTRAJ: NetCDF Restart Test - TXT->NetCDF
384s 
384s   CPPTRAJ: NetCDF Restart Test - NetCDF->TXT
384s 
384s   CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF
384s 
384s   CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt
384s 
384s All 2 comparisons passed.
384s 
384s ********************************************************************************
384s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Image
384s 
384s   CPPTRAJ: Orthorhombic imaged distance test.
384s 
384s   CPPTRAJ: Non-orthorhombic imaged distance test.
384s 
384s   CPPTRAJ: Orthorhombic coordinate imaging test
385s 
385s   CPPTRAJ: Nonorthorhombic coordinate imaging test
385s 
385s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar
385s 
385s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM
385s 
385s All 6 comparisons passed.
385s 
385s ********************************************************************************
385s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Surf
385s 
385s   CPPTRAJ: Surface calculation test
385s 
385s   CPPTRAJ: Partial Surface calculation test
386s 
386s   CPPTRAJ: LCPO test with GAFF atom types
386s 
386s All 3 comparisons passed.
386s 
386s ********************************************************************************
386s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Radgyr
386s 
386s   CPPTRAJ: Radius of gyration command test
386s 
386s All 2 comparisons passed.
386s 
386s ********************************************************************************
386s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Mask
386s 
386s   CPPTRAJ: Mask single frame test
386s 
386s   CPPTRAJ: Mask longer command test.
386s 
386s All 5 comparisons passed.
386s 
386s ********************************************************************************
386s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Jcoupling
386s 
386s   CPPTRAJ: J-Coupling single frame test
386s   J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set.
386s   Skipped test: J-Coupling extended test
386s 
386s All 1 comparisons passed.
386s 1 comparisons skipped.
386s 
386s ********************************************************************************
386s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Diffusion
386s 
386s   CPPTRAJ: Diffusion test, no imaging.
386s 
386s   CPPTRAJ: Diffusion test, old syntax.
386s 
386s   CPPTRAJ: Diffusion test, new syntax.
386s 
386s   CPPTRAJ: Diffusion test, nonorthogonal box
386s 
386s   CPPTRAJ: STFC Diffusion Test
386s 
386s   CPPTRAJ: STFC Diffusion Test with individual distances
387s 
387s   CPPTRAJ: STFC Diffusion Test with COM
387s 
387s   CPPTRAJ: STFC Diffusion Test with second mask
387s 
387s All 16 comparisons passed.
387s 
387s ********************************************************************************
387s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Outtraj
387s 
387s   CPPTRAJ: RMSD Test with outtraj.
387s 
387s   CPPTRAJ: Outtraj Test with maxmin.
387s 
387s All 4 comparisons passed.
387s 
387s ********************************************************************************
387s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Charmm
387s 
387s   CPPTRAJ: CHARMM PSF/DCD test
388s 
388s   CPPTRAJ: CHARMM DCD Write, step 1.
388s 
388s   CPPTRAJ: CHARMM DCD Write, step 2.
388s 
388s   CPPTRAJ: CHAMBER topology read/strip test.
388s 
388s   CPPTRAJ: Read CHARMM restart
388s 
388s   CPPTRAJ: CHARMM PSF write
388s 
388s   CPPTRAJ: CHARMM COORdinates test
388s 
388s All 6 comparisons passed.
388s 
388s ********************************************************************************
388s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CharmmParams
388s 
388s   CPPTRAJ: Test updating topology with Charmm parameters (single residue)
388s 
388s All 2 comparisons passed.
388s 
388s ********************************************************************************
388s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Rotdif
388s 
388s   CPPTRAJ: Rotational diffusion calculation test
388s 
388s All 4 comparisons passed.
388s 
388s ********************************************************************************
388s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_NetcdfTraj
388s 
388s   CPPTRAJ: Convert mdcrd -> NetCDF
388s 
388s   CPPTRAJ: Convert NetCDF -> mdcrd
388s 
388s All 1 comparisons passed.
388s 
388s ********************************************************************************
388s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Runavg
388s 
388s   CPPTRAJ: Coordinate Running Average test.
388s 
388s   CPPTRAJ: Coordinate Running Average Traj Write
388s 
388s All 2 comparisons passed.
388s 
388s ********************************************************************************
388s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_RMSD
388s 
388s   CPPTRAJ: Basic RMSD tests
388s 
388s   CPPTRAJ: RMS coordinate rotation/rotation matrices test
389s 
389s   CPPTRAJ: RMS fit with no coordinates modification test.
389s 
389s   CPPTRAJ: RMS fit to previous test
389s 
389s   CPPTRAJ: RMS: imaging after unit cell rotation
389s 
389s All 12 comparisons passed.
389s 
389s ********************************************************************************
389s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_2DRMS
389s 
389s   CPPTRAJ: 2D RMSD Test.
389s 
389s   CPPTRAJ: 2D RMSD Test, mass-weighted.
389s 
389s   CPPTRAJ: 2D RMSD Test with reference trajectory
389s 
389s   CPPTRAJ: 2D DME Test.
389s 
389s   CPPTRAJ: 2D RMSD with reference mask test.
389s 
389s   CPPTRAJ: 2D RMSD test, no fitting.
389s 
389s All 6 comparisons passed.
389s 
389s ********************************************************************************
389s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Mol2
389s 
389s   CPPTRAJ: Mol2 Parm/Traj Read/Write Test.
389s 
389s   CPPTRAJ: PDB => Mol2
389s 
389s   CPPTRAJ: Amber Top/Rst => Mol2
389s   Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set.
389s   Skipped test: Amber Top/Rst => Mol2, SYBYL atom types
389s 
389s All 4 comparisons passed.
389s 1 comparisons skipped.
389s 
389s ********************************************************************************
389s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_NAstruct
389s 
389s   CPPTRAJ: NAstruct command test.
389s 
389s   CPPTRAJ: NAstruct command test, single strand
389s 
389s All 11 comparisons passed.
389s 
389s ********************************************************************************
389s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_NAstruct_8OG
389s 
389s   CPPTRAJ: NA test (8OG)
390s 
390s All 3 comparisons passed.
390s 
390s ********************************************************************************
390s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Average
390s 
390s   CPPTRAJ: Average Test.
390s 
390s All 2 comparisons passed.
390s 
390s ********************************************************************************
390s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Pucker
390s 
390s   CPPTRAJ: Pucker command test
390s 
390s   CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test
390s 
390s   CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test.
390s 
390s All 3 comparisons passed.
390s 
390s ********************************************************************************
390s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AtomMap
390s 
390s   CPPTRAJ: AtomMap Test
390s 
390s   CPPTRAJ: AtomMap with 'rmsfit'
390s 
390s   CPPTRAJ: Atom map charmm->amber atom order
390s 
390s   CPPTRAJ: Atom map charmm->amber atom order, by residue
390s 
390s All 9 comparisons passed.
390s 
390s ********************************************************************************
390s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Datafile
390s 
390s   CPPTRAJ: Data file output precision test
390s 
390s   CPPTRAJ: Standard -> Grace Data
390s 
390s   CPPTRAJ: Grace -> Standard Data
390s 
390s   CPPTRAJ: X column format/precision test.
390s 
390s   CPPTRAJ: Data file group by name test
390s 
390s   CPPTRAJ: Data file group by aspect test
390s 
390s All 6 comparisons passed.
390s 
390s ********************************************************************************
390s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Radial
390s 
390s   CPPTRAJ: Radial test, non-orthogonal imaging
391s 
391s   CPPTRAJ: Radial test, orthogonal and no imaging
391s 
391s All 9 comparisons passed.
391s 
391s ********************************************************************************
391s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Hist
391s 
391s   CPPTRAJ: 1D/2D Histogram Analysis test
391s 
391s   CPPTRAJ: 3D histogram test.
391s 
391s All 7 comparisons passed.
391s 
391s ********************************************************************************
391s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Closest
391s 
391s   CPPTRAJ: Closest command test using first solvent atom.
391s 
391s   CPPTRAJ: Closest command test using all solvent atoms.
392s 
392s   CPPTRAJ: Closest command test, using mask center
392s 
392s   CPPTRAJ: Closest command test, using mask center and solvent mask
392s 
392s   CPPTRAJ: Closest command test, solvent mask, water oxygen only
394s 
394s All 8 comparisons passed.
394s 
394s ********************************************************************************
394s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DRMSD
394s 
394s   CPPTRAJ: Distance RMSD test
394s 
394s All 1 comparisons passed.
394s 
394s ********************************************************************************
394s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster
394s 
394s   CPPTRAJ: Cluster command test, in-memory pairwise distances.
394s 
394s   CPPTRAJ: Cluster command test, read pairwise distances.
394s 
394s   CPPTRAJ: Cluster command test, read NetCDF pairwise distances.
394s 
394s   CPPTRAJ: Cluster command test, write ASCII pairwise distances.
394s 
394s   CPPTRAJ: Cluster command test, read ASCII pairwise distances.
394s 
394s All 9 comparisons passed.
394s 
394s ********************************************************************************
394s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_Sieve
394s 
394s   CPPTRAJ: Cluster, nosieve 
394s 
394s   CPPTRAJ: Cluster, sieve5 
394s 
394s   CPPTRAJ: Cluster, nosieve savepairdist
394s 
394s   CPPTRAJ: Cluster, nosieve loadpairdist
394s 
394s   CPPTRAJ: Cluster, sieve5 savepairdist
395s 
395s   CPPTRAJ: Cluster, sieve5 loadpairdist
395s 
395s   CPPTRAJ: Cluster, nosieve pairwisecache none
395s 
395s   CPPTRAJ: Cluster, sieve5 pairwisecache none
395s 
395s   CPPTRAJ: Cluster, random 
395s 
395s All 28 comparisons passed.
395s 
395s ********************************************************************************
395s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_RandomSieve
395s 
395s   CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances).
395s 
395s   CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances).
395s 
395s All 4 comparisons passed.
395s 
395s ********************************************************************************
395s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_DataSet
395s 
395s   CPPTRAJ: Clustering, One DataSet
395s 
395s   CPPTRAJ: Clustering, Two DataSets
396s 
396s   CPPTRAJ: Clustering, dihedral DataSet
396s 
396s   CPPTRAJ: Clustering, two dihedral DataSets
396s 
396s   CPPTRAJ: Clustering, dihedral DataSet, K-means
396s 
396s   CPPTRAJ: Clustering, two dihedral DataSets, K-means
396s 
396s All 8 comparisons passed.
396s 
396s ********************************************************************************
396s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_DBSCAN
396s 
396s   CPPTRAJ: DBSCAN test
396s 
396s   CPPTRAJ: DBSCAN automatic parameter determination test.
396s 
396s   CPPTRAJ: DBSCAN kdist map test
396s 
396s   CPPTRAJ: DBSCAN with sieve
396s 
396s All 4 comparisons passed.
396s 
396s ********************************************************************************
396s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_Kmeans
396s 
396s   CPPTRAJ: Cpptraj Kmeans
396s 
396s   CPPTRAJ: Cpptraj Kmeans random
396s 
396s All 6 comparisons passed.
396s 
396s ********************************************************************************
396s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_SymmRMSD
396s 
396s   CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD)
396s 
396s All 5 comparisons passed.
396s 
396s ********************************************************************************
396s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_TrajWrites
397s 
397s   CPPTRAJ: Cluster command test, coordinate writes.
397s 
397s   CPPTRAJ: Cluster command test, coordinate writes using info file.
397s 
397s All 8 comparisons passed.
397s 
397s ********************************************************************************
397s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_Dpeaks
397s 
397s   CPPTRAJ: Density peaks clustering test
397s 
397s All 3 comparisons passed.
397s 
397s ********************************************************************************
397s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cluster_Nreps
397s 
397s   CPPTRAJ: Clustering with specified # reps
397s 
397s All 2 comparisons passed.
397s 
397s ********************************************************************************
397s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_IRED
397s 
397s   CPPTRAJ: IRED vector/matrix test
398s 
398s 
398s ********************************************************************************
398s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_RandomizeIons
398s 
398s   CPPTRAJ: randomizeions test (original algorithm)
398s 
398s   CPPTRAJ: Randomize (around, overlap)
399s 
399s   CPPTRAJ: Randomize (around)
399s 
399s   CPPTRAJ: Randomize (overlap)
400s 
400s   CPPTRAJ: Randomize (no restrictions)
400s 
400s All 5 comparisons passed.
400s 
400s ********************************************************************************
400s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Molsurf
400s 
400s   CPPTRAJ: Molsurf test
400s 
400s All 1 comparisons passed.
400s 
400s ********************************************************************************
400s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Corr
400s 
400s   CPPTRAJ: Correlation test
400s 
400s All 2 comparisons passed.
400s 
400s ********************************************************************************
400s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CheckStructure
400s 
400s   CPPTRAJ: Structure Check
400s 
400s   CPPTRAJ: Structure Check with Around and Skip
401s 
401s   CPPTRAJ: Structure Check with PBC
401s 
401s   CPPTRAJ: Structure Check with Around
402s 
402s All 8 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_RmsAvgCorr
402s 
402s   CPPTRAJ: RmsAvgCorr Reference
402s 
402s   CPPTRAJ: RmsAvgCorr First
402s 
402s All 3 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Contacts
402s 
402s   CPPTRAJ: Contacts test.
402s 
402s All 3 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Principal
402s 
402s   CPPTRAJ: Principal Test
402s 
402s All 3 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_ClusterDihedral
402s 
402s   CPPTRAJ: clusterdihedral test
402s 
402s All 4 comparisons passed.
402s 
402s ********************************************************************************
402s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Vector
402s 
402s   CPPTRAJ: Basic vector tests
402s 
402s   CPPTRAJ: Test vector center with magnitude
402s 
402s   CPPTRAJ: Momentum/velocity vector test.
402s 
402s   CPPTRAJ: Force vector test.
403s 
403s All 14 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Matrix
403s 
403s   CPPTRAJ: Matrix Tests
403s 
403s   CPPTRAJ: Generate matrix with trajectory start/stop/offset
403s 
403s   CPPTRAJ: Generate matrix with action stop/start/offset
403s 
403s All 15 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AtomicFluct
403s 
403s   CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor].
403s 
403s   CPPTRAJ: Atomic fluctuations test [:2-12 byatom].
403s 
403s   CPPTRAJ: Atomic fluctuations test [bymask :3,4,5].
403s 
403s   CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor].
403s 
403s   CPPTRAJ: Atomicfluct test with ADP output
403s 
403s   CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output.
403s 
403s All 13 comparisons passed.
403s 
403s ********************************************************************************
403s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Grid
403s 
403s   CPPTRAJ: Dipole test
403s 
403s   CPPTRAJ: Grid test
403s 
403s   CPPTRAJ: OpenDX Grid read test
404s 
404s   CPPTRAJ: Grid with specified center test.
404s 
404s   CPPTRAJ: Grid with box center offset test.
404s 
404s   CPPTRAJ: Grid with mask center offset test.
404s 
404s   CPPTRAJ: Non-orthogonal grid test.
404s 
404s   CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test
404s 
404s   CPPTRAJ: Grid generation from 'bounds' test.
404s 
404s All 13 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Unwrap
404s 
404s   CPPTRAJ: Unwrap non-orthogonal test
404s 
404s   CPPTRAJ: Unwrap orthogonal test
404s 
404s All 2 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Project
404s 
404s   CPPTRAJ: Projection
404s 
404s All 1 comparisons passed.
404s 
404s ********************************************************************************
404s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Analyze_Modes
404s 
404s   CPPTRAJ: Modes analysis, RMS fluctuations
404s 
404s   CPPTRAJ: Modes analysis, displacements
404s 
404s   CPPTRAJ: Modes analysis, dipole correlation
404s 
404s   CPPTRAJ: Modes analysis, pseudo trajectory creation test
405s 
405s   CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test
405s 
405s All 6 comparisons passed.
405s 
405s ********************************************************************************
405s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Watershell
405s 
405s   CPPTRAJ: Watershell Test, non-orthorhombic imaging.
406s 
406s   CPPTRAJ: Watershell Test, orthorhombic imaging.
407s 
407s   CPPTRAJ: Watershell Test, no imaging.
407s 
407s All 3 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AnalysisRunAvg
407s 
407s   CPPTRAJ: Analysis Running Average
407s 
407s All 2 comparisons passed.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Volmap
407s 
407s   CPPTRAJ: VMD VolMap Algorithm test
407s   VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run.
407s   Skipped test: VMD VolMap Algorithm longer tests
407s 
407s All 2 comparisons passed.
407s 1 comparisons skipped.
407s 
407s ********************************************************************************
407s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_SPAM
407s 
407s   CPPTRAJ: SPAM Test
408s 
408s   CPPTRAJ: SPAM Pure Solvent Test
413s 
413s   1 out of 5 comparisons failed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LIE
413s 
413s   CPPTRAJ: LIE test
413s 
413s All 1 comparisons passed.
413s 
413s ********************************************************************************
413s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Density
413s 
413s   CPPTRAJ: Density along axis tests
413s 
413s   CPPTRAJ: Multi-frame density along axis test
414s 
414s   CPPTRAJ: Total system density test
414s 
414s All 7 comparisons passed.
414s 
414s ********************************************************************************
414s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LipidOrder
414s 
414s   CPPTRAJ: Lipid Order Parameter Test.
414s 
414s All 6 comparisons passed.
414s 
414s ********************************************************************************
414s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LipidSCD
414s 
414s   CPPTRAJ: Basic lipid order parameter test
414s 
414s   CPPTRAJ: New Lipid Order Parameter Test, DOPC.
415s 
415s All 4 comparisons passed.
415s 
415s ********************************************************************************
415s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_PairDist
415s 
415s   CPPTRAJ: PairDist Test.
415s 
415s   CPPTRAJ: Pairdist test, orthogonal imaging.
416s 
416s   CPPTRAJ: Pairdist test, nonorthogonal imaging.
416s 
416s   CPPTRAJ: Pairdist test, 2 masks.
417s 
417s All 4 comparisons passed.
417s 
417s ********************************************************************************
417s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_ReadData
417s 
417s   CPPTRAJ: Read vector data test (no origins, origins)
417s 
417s   CPPTRAJ: Read vector data set (origins, no origins)
417s 
417s   CPPTRAJ: Read Amber output test
417s 
417s   CPPTRAJ: Read CHARMM output test
417s 
417s   CPPTRAJ: 3D data read/write test
417s 
417s   CPPTRAJ: Standard 3D data write test
417s 
417s   CPPTRAJ: Standard 3D data read test
417s 
417s   CPPTRAJ: Standard 3D data read/append test
417s 
417s   CPPTRAJ: Standard 3D data, sparse
417s 
417s   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.BzKBgt/build.fVS/src/test/Test_GIST
418s 
418s   CPPTRAJ: GIST water-water interaction test
421s 
421s   CPPTRAJ: GIST test, orthogonal cell
426s 
426s   CPPTRAJ: GIST test, nonorthogonal cell
437s 
437s All 11 comparisons passed.
437s 
437s ********************************************************************************
437s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_GIST_Order
437s 
437s   CPPTRAJ: TIP3P water cluster test
437s 
437s   CPPTRAJ: TIP4P water cluster test
439s 
439s   CPPTRAJ: TIP5P water cluster test
439s 
439s All 4 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_systemVF
439s 
439s   CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AtomicCorr
439s 
439s   CPPTRAJ: Atomic Correlation test
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AutoCorr
439s 
439s   CPPTRAJ: AutoCorr test.
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Box
439s 
439s   CPPTRAJ: Box Test (Add box info)
439s 
439s   CPPTRAJ: Box test (remove box info)
439s 
439s   CPPTRAJ: Box test (Modify box length)
439s 
439s   CPPTRAJ: Box test (auto orthogonal box, no radii)
439s 
439s   CPPTRAJ: Box test (auto orthogonal box, VDW radii)
439s 
439s All 7 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AtomTypeSelect
439s 
439s   CPPTRAJ: Selection by atom type test.
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AvgRef
439s 
439s   CPPTRAJ: RMSD Test with averaged reference coordinates.
439s 
439s All 1 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Crank_Stat
439s 
439s   CPPTRAJ: Crankshaft test
439s 
439s All 3 comparisons passed.
439s 
439s ********************************************************************************
439s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CreateCrd
439s 
439s   CPPTRAJ: COORDS data set creation and CRDFLUCT test.
439s 
439s   CPPTRAJ: COORDS data set creation with velocities test
439s 
439s   CPPTRAJ: TRAJ data set creation and CRDFLUCT test.
439s 
439s   CPPTRAJ: TRAJ data set creation with velocities test.
439s 
439s   CPPTRAJ: COORDS data set append test
439s 
439s   CPPTRAJ: COORDS test storing frame metadata
439s 
439s   CPPTRAJ: TRAJ test storing frame metadata
440s 
440s All 8 comparisons passed.
440s 
440s ********************************************************************************
440s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AutoImage
440s 
440s   CPPTRAJ: AutoImage test (split DNA duplex)
440s 
440s   CPPTRAJ: AutoImage test, use anchor mask
440s 
440s All 2 comparisons passed.
440s 
440s ********************************************************************************
440s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LoadCrd
440s 
440s   CPPTRAJ: LoadCrd test.
440s 
440s   CPPTRAJ: LoadTraj test.
440s 
440s   CPPTRAJ: LoadTraj from trajin test.
440s 
440s   CPPTRAJ: LoadCrd append from multiple files test
440s 
440s All 4 comparisons passed.
440s 
440s ********************************************************************************
440s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_MultiVector
440s 
440s   CPPTRAJ: Multivector test
440s 
440s All 1 comparisons passed.
440s 
440s ********************************************************************************
440s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Lifetime
440s 
440s   CPPTRAJ: Lifetime test.
440s 
440s   CPPTRAJ: Lifetime test with data set caching.
440s 
440s   CPPTRAJ: Lifetime average and cumulative average test.
440s 
440s All 12 comparisons passed.
440s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_FFT
441s 
441s   CPPTRAJ: FFT test.
441s 
441s All 5 comparisons passed.
441s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Timecorr
441s 
441s   CPPTRAJ: Timecorr test.
441s 
441s All 7 comparisons passed.
441s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CrossCorr
441s 
441s   CPPTRAJ: CrossCorr test
441s 
441s All 1 comparisons passed.
441s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_SymmRmsd
441s 
441s   CPPTRAJ: SymmRmsd
441s 
441s   CPPTRAJ: ASP symmetry-corrected RMSD test
441s 
441s   CPPTRAJ: GLU symmetry-corrected RMSD test
441s 
441s   CPPTRAJ: TYR symmetry-corrected RMSD test
441s 
441s   CPPTRAJ: Longer symmetry-corrected RMSD test.
441s 
441s All 8 comparisons passed.
441s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Multidihedral
441s 
441s   CPPTRAJ: Multidihedral test
441s 
441s   CPPTRAJ: Multidihedral Nucleotide CHI test
441s 
441s   CPPTRAJ: Multidihedral protein dihedrals test
441s 
441s   CPPTRAJ: Multidihedral cyclic molecule test
441s 
441s All 6 comparisons passed.
441s 
441s ********************************************************************************
441s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Ensemble_MREMD
441s 
441s   CPPTRAJ: M-REMD sort test.
441s 
441s   CPPTRAJ: M-REMD actions test.
441s 
441s   CPPTRAJ: M-REMD ensemble outtraj test.
441s 
441s   CPPTRAJ: M-REMD no sort, running average test
442s 
442s   CPPTRAJ: M-REMD, generate RMS data
442s 
442s   CPPTRAJ: M-REMD, meltcurve analysis
442s 
442s All 17 comparisons passed.
442s 
442s ********************************************************************************
442s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_MakeStructure
442s 
442s   CPPTRAJ: Basic makestructure test
442s 
442s   CPPTRAJ: Makestructure test with reference.
443s 
443s All 5 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Rotate
443s 
443s   CPPTRAJ: Rotation (and inverse) of coords from matrices
443s 
443s   CPPTRAJ: Rotate with defined axis
443s 
443s All 3 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Integrate
443s 
443s   CPPTRAJ: Integration test.
443s 
443s All 2 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_NativeContacts
443s 
443s   CPPTRAJ: NativeContacts test.
443s 
443s   CPPTRAJ: NativeContacts test, save non-native contacts, residue time series
443s 
443s   CPPTRAJ: NativeContacts test, orthorhombic imaging.
443s 
443s All 17 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CheckChiral
443s 
443s   CPPTRAJ: Check chirality test
443s 
443s All 1 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Energy
443s 
443s   CPPTRAJ: Simple energy tests
443s 
443s   CPPTRAJ: Test kinetic energy calculation
443s 
443s   CPPTRAJ: Test total energy calculation
443s 
443s   CPPTRAJ: Test partial energy calculation
443s 
443s All 6 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LESsplit
443s 
443s   CPPTRAJ: LES split/average test
443s 
443s All 2 comparisons passed.
443s 
443s ********************************************************************************
443s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_PermuteDihedrals
443s 
443s   CPPTRAJ: PermuteDihedrals interval -120, phi psi
444s 
444s   CPPTRAJ: PermuteDihedrals, random rotations
444s 
444s All 4 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CCP4
444s 
444s   CPPTRAJ: CCP4 read/write and DX conversion test.
444s 
444s All 2 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DihCovar
444s 
444s   CPPTRAJ: Dihedral Covariance Matrix Test
444s 
444s All 3 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CurveFit
444s 
444s   CPPTRAJ: Curve fitting test.
444s 
444s   CPPTRAJ: Curve fitting multi-exponential tests.
444s 
444s   CPPTRAJ: Curve fitting, custom output range.
444s 
444s All 6 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Multicurve
444s 
444s   CPPTRAJ: Multicurve test
444s 
444s All 1 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DataSetAverage
444s 
444s   CPPTRAJ: Data set averaging and averaging over all sets test.
444s 
444s All 2 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_VectorMath
444s 
444s   CPPTRAJ: Vector dot/cross product test
444s 
444s All 2 comparisons passed.
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Esander
444s   SANDER energy tests (long) requires SANDER API from AmberTools.
444s   Cpptraj was compiled without SANDER API from AmberTools support.
444s   SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run.
444s   SKIP: SANDER energy tests (long)
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Esander_Short
444s   Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools.
444s   Cpptraj was compiled without SANDER API from AmberTools support.
444s   SKIP: Energy via sander API short tests (GB/PME)
444s 
444s ********************************************************************************
444s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Temperature
444s 
444s   CPPTRAJ: Temperature test.
444s 
444s   CPPTRAJ: Temperature with SHAKE on hydrogens.
445s 
445s   CPPTRAJ: Temperature with SHAKE on all atoms.
445s 
445s   CPPTRAJ: Temperature calc with extra points.
445s 
445s All 5 comparisons passed.
445s 
445s ********************************************************************************
445s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Spline
445s 
445s   CPPTRAJ: Spline test
445s 
445s All 1 comparisons passed.
445s 
445s ********************************************************************************
445s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_KDE
445s 
445s   CPPTRAJ: KDE test.
445s 
445s   CPPTRAJ: KDE with Kullback-Leibler divergence test
445s 
445s All 4 comparisons passed.
445s 
445s ********************************************************************************
445s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Wavelet
445s 
445s   CPPTRAJ: Wavelet analysis test
445s 
445s   CPPTRAJ: Wavelet WAFEX test
445s 
445s All 3 comparisons passed.
445s 
445s ********************************************************************************
445s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CIF
445s 
445s   CPPTRAJ: CIF read test
446s 
446s   CPPTRAJ: Generate offset traj from PDB
446s 
446s   CPPTRAJ: Generate offset traj from CIF
446s 
446s All 2 comparisons passed.
446s 
446s ********************************************************************************
446s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_PDB
446s 
446s   CPPTRAJ: PDB format read/write test
446s 
446s   CPPTRAJ: PQR file write with various radii
446s 
446s   CPPTRAJ: PDB filter alternate atom location IDs test
446s 
446s   CPPTRAJ: Adding PDB info to topology
446s 
446s All 10 comparisons passed.
446s 
446s ********************************************************************************
446s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Align
446s 
446s   CPPTRAJ: Align Tests.
446s 
446s   CPPTRAJ: Align, unit cell rotation/imaging test.
447s 
447s All 4 comparisons passed.
447s 
447s ********************************************************************************
447s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_VelocityAutoCorr
447s 
447s   CPPTRAJ: Velocity autocorrelation test
447s 
447s All 3 comparisons passed.
447s 
447s ********************************************************************************
447s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_VelFrc
447s 
447s   CPPTRAJ: Test combining coordinates, velocities, and forces.
447s 
447s   CPPTRAJ: Test using velocities as coordinates.
447s 
447s   CPPTRAJ: Test writing velocities (MDVEL)
447s 
447s   CPPTRAJ: Test using forces as coordinates.
447s 
447s   CPPTRAJ: Test writing forces (MDFRC)
447s 
447s   CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart.
447s 
447s   CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart.
448s 
448s All 5 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_RotateDihedral
448s 
448s   CPPTRAJ: Rotate dihedral to target value.
448s 
448s   CPPTRAJ: Rotate dihedral by increment
448s 
448s   CPPTRAJ: Rotate dihedral in TRAJ data set
448s 
448s All 3 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DataSetCmd
448s 
448s   CPPTRAJ: Data Set commands test
448s 
448s All 10 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Remap
448s 
448s   CPPTRAJ: Remap Test
448s 
448s All 1 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CompareTop
448s 
448s   CPPTRAJ: Compare topology test
448s 
448s All 1 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Filter
448s 
448s   CPPTRAJ: Basic filter test
448s 
448s   CPPTRAJ: Data filter test.
448s 
448s   CPPTRAJ: Filter matrix test.
448s 
448s All 5 comparisons passed.
448s 
448s ********************************************************************************
448s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CombineCrd
448s 
448s   CPPTRAJ: Combine COORDS test.
448s 
448s   CPPTRAJ: Combine COORDS test with box info.
448s 
448s   CPPTRAJ: Split coords and recombine test.
450s 
450s All 5 comparisons passed.
450s 
450s ********************************************************************************
450s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_TopInfo
450s 
450s   CPPTRAJ: Topology info print test.
451s 
451s   CPPTRAJ: Topology info with reference coords test
451s 
451s All 12 comparisons passed.
451s 
451s ********************************************************************************
451s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_GromacsTrr
451s 
451s   CPPTRAJ: TRR force/velocity read -> NetCDF write test
451s 
451s   CPPTRAJ: TRR force/velocity read -> TRR write test
451s 
451s   CPPTRAJ: CRD => TRR
451s 
451s   CPPTRAJ: TRR => CRD
451s 
451s   CPPTRAJ: CRD(1-5) => TRR
451s 
451s   CPPTRAJ: CRD(6-10) => TRR
451s 
451s   CPPTRAJ: TRR (appended) => CRD
452s 
452s   CPPTRAJ: GMX: CRD with offset
452s 
452s   CPPTRAJ: GMX: TRR with offset
452s 
452s All 5 comparisons passed.
452s 
452s ********************************************************************************
452s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_GromacsXtc
452s 
452s   CPPTRAJ: XTC read test
452s 
452s   CPPTRAJ: CRD => XTC
452s 
452s   CPPTRAJ: XTC => CRD
452s 
452s   CPPTRAJ: CRD(1-5) => XTC
452s 
452s   CPPTRAJ: CRD(6-10) => XTC
452s 
452s   CPPTRAJ: XTC (appended) => CRD
453s 
453s   CPPTRAJ: GMX: CRD with offset
453s 
453s   CPPTRAJ: GMX: XTC with offset
453s 
453s All 4 comparisons passed.
453s 
453s ********************************************************************************
453s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_GromacsTNG
453s 
453s   CPPTRAJ: TNG read test
453s 
453s   CPPTRAJ: TNG read test (with offset)
453s 
453s All 6 comparisons passed.
453s 
453s ********************************************************************************
453s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Ewald
453s 
453s   CPPTRAJ: Direct sum test
455s 
455s   CPPTRAJ: Ewald test (NaCl crystal)
455s 
455s   CPPTRAJ: Ewald test (trunc. oct)
455s 
455s   CPPTRAJ: Ewald test (partial system, trunc. oct)
455s   Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
455s   Skipped test: Ewald test (trunc. oct), 10 frames
455s   Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run.
455s   Skipped test: Ewald test (ortho), 10 frames
455s 
455s All 4 comparisons passed.
455s 2 comparisons skipped.
455s 
455s ********************************************************************************
455s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LibPME
455s 
455s   CPPTRAJ: Particle mesh Ewald test (NaCl crystal)
455s 
455s   CPPTRAJ: Particle mesh Ewald test (trunc. oct)
456s 
456s   CPPTRAJ: Particle mesh Ewald test (ortho)
456s 
456s   CPPTRAJ: Particle mesh Ewald test (ortho, with mask)
456s 
456s   CPPTRAJ: PME test (partial system, trunc. oct)
456s   PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
456s   Skipped test: PME test (trunc. oct), 10 frames
456s 
456s All 5 comparisons passed.
456s 1 comparisons skipped.
456s 
456s ********************************************************************************
456s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LJ_PME
456s 
456s   CPPTRAJ: LJ PME test.
456s 
456s   CPPTRAJ: LJ PME kappa sweep test, 0.25
457s 
457s   CPPTRAJ: LJ PME kappa sweep test, 0.35
457s 
457s   CPPTRAJ: LJ PME kappa sweep test, 0.45
457s 
457s   CPPTRAJ: LJ PME kappa sweep test, 0.5
457s 
457s   CPPTRAJ: LJ with switch function test
457s 
457s All 5 comparisons passed.
457s 
457s ********************************************************************************
457s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_TI
457s 
457s   CPPTRAJ: TI analysis test.
457s 
457s All 5 comparisons passed.
457s 
457s ********************************************************************************
457s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_FixImagedBonds
457s 
457s   CPPTRAJ: Fix imaged bonds test (Ortho.)
457s 
457s   CPPTRAJ: Fix imaged bonds test (Non-ortho.)
457s 
457s All 2 comparisons passed.
457s 
457s ********************************************************************************
457s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Distance
457s 
457s   CPPTRAJ: Distance tests
457s 
457s   CPPTRAJ: Orthogonal imaged distance
457s 
457s   CPPTRAJ: Non-orthogonal imaged distance
457s 
457s All 3 comparisons passed.
457s 
457s ********************************************************************************
457s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Volume
457s 
457s   CPPTRAJ: Volume tests
458s 
458s All 1 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_SetVelocity
458s 
458s   CPPTRAJ: Set Velocity test
458s 
458s   CPPTRAJ: Scale velocity test
458s 
458s   1 out of 3 comparisons failed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Remlog
458s 
458s   CPPTRAJ: Replica log read/analyze test.
458s 
458s All 7 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_AreaPerMol
458s 
458s   CPPTRAJ: Area per molecule test
458s 
458s All 6 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DistBasedMask
458s 
458s   CPPTRAJ: Distance-based atom mask tests (atom, residue)
458s 
458s   CPPTRAJ: Distance-based atom mask tests (molecule)
458s 
458s All 6 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Calc
458s 
458s   CPPTRAJ: Calc test
458s 
458s   CPPTRAJ: Calc test with data sets
458s 
458s   CPPTRAJ: Test math functions
458s 
458s All 4 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CalcState
458s 
458s   CPPTRAJ: Calcstate test
458s 
458s All 4 comparisons passed.
458s 
458s ********************************************************************************
458s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Change
458s 
458s   CPPTRAJ: Change atom and residue name tests
459s 
459s   CPPTRAJ: Change chain ID test
459s 
459s   CPPTRAJ: Change chain ID of COORDS set test
459s 
459s All 3 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CreateReservoir
459s 
459s   CPPTRAJ: Create RREMD NetCDF reservoir test
459s 
459s All 1 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_FixAtomOrder
459s 
459s   CPPTRAJ: Out of order molecules test
459s 
459s All 2 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_LowestCurve
459s 
459s   CPPTRAJ: LowestCurve test
459s 
459s All 1 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_MinImage
459s 
459s   CPPTRAJ: Minimum Image test.
459s 
459s All 1 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Regress
459s 
459s   CPPTRAJ: Linear regression test.
459s 
459s All 3 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Rst
459s 
459s   CPPTRAJ: Generate restraints (rst) test
459s 
459s All 1 comparisons passed.
459s 
459s ********************************************************************************
459s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Pairwise
459s 
459s   CPPTRAJ: Pairwise tests
459s 
459s   CPPTRAJ: Pairwise test, partial system
460s 
460s All 10 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_ParmBox
460s 
460s   CPPTRAJ: Parmbox test
460s 
460s All 1 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Solvent
460s 
460s   CPPTRAJ: Test solvent command with closest
460s 
460s All 1 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Translate
460s 
460s   CPPTRAJ: Translate test
460s 
460s All 1 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_ReplicateCell
460s 
460s   CPPTRAJ: Replicate cell test
460s 
460s All 1 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_ScaleDihedralK
460s 
460s   CPPTRAJ: Scale dihedral force constant test
460s 
460s   CPPTRAJ: Scale dihedral force constant with 'useall'
460s 
460s All 2 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_PhiPsi
460s 
460s   CPPTRAJ: Phipsi test
460s 
460s All 1 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Control
460s 
460s   CPPTRAJ: Loop tests
460s 
460s   CPPTRAJ: Test set command
460s 
460s   CPPTRAJ: Test reading comma-separated list of strings
460s 
460s   CPPTRAJ: Test nested loops and variables in loops
460s 
460s   CPPTRAJ: Test loop over data set blocks
460s 
460s   CPPTRAJ: Test for filename wildcards and oversets
460s 
460s All 13 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_InfraredSpec
460s 
460s   CPPTRAJ: Infrared spectrum calculation test
460s 
460s All 2 comparisons passed.
460s 
460s ********************************************************************************
460s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Cphstats
461s 
461s   CPPTRAJ: Explicit pH REMD ensemble data read / sort
461s 
461s   CPPTRAJ: Constant pH stats test
461s 
461s   CPPTRAJ: Sorted implicit constant pH stats test
461s 
461s   CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats
461s 
461s   CPPTRAJ: Unsorted pH read/write test
461s 
461s All 16 comparisons passed.
461s 
461s ********************************************************************************
461s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CmdLine
461s 
461s   CPPTRAJ: Command line trajectory args test, part 1
461s 
461s   CPPTRAJ: Command line test trajectory args test, part 2
461s 
461s   CPPTRAJ: Command line wildcard test, part 1
461s 
461s   CPPTRAJ: Command line wildcard test, part 2
461s 
461s All 2 comparisons passed.
461s 
461s ********************************************************************************
461s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_XYZformat
461s 
461s   CPPTRAJ: XYZ format write
461s 
461s   CPPTRAJ: Atom XYZ format read, test 1
461s 
461s   CPPTRAJ: Atom XYZ format read, test 2
461s 
461s   CPPTRAJ: Atom XYZ format read, test 3
461s 
461s   CPPTRAJ: Atom XYZ format read, test 4
461s 
461s   CPPTRAJ: Atom XYZ format read, test 5
461s 
461s   CPPTRAJ: Atom XYZ format read, test 6
461s 
461s All 6 comparisons passed.
461s 
461s ********************************************************************************
461s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Hausdorff
461s 
461s   CPPTRAJ: Simple Hausdorff distance test.
461s 
461s   CPPTRAJ: Hausdorff distance of 2D rms output test.
462s 
462s   CPPTRAJ: Hausdorff distance of 2D rms output test.
462s 
462s All 3 comparisons passed.
462s 
462s ********************************************************************************
462s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_CatCrd
462s 
462s   CPPTRAJ: Concatenate COORDS data set test
462s 
462s All 1 comparisons passed.
462s 
462s ********************************************************************************
462s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_XtalSymm
462s 
462s   CPPTRAJ: XtalSymm Reference
462s 
462s   CPPTRAJ: XtalSymm Reimaging by Atom
465s 
465s   CPPTRAJ: XtalSymm Reimaging by Molecule
468s 
468s All 3 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Time
468s 
468s   CPPTRAJ: Add time to restart test
468s 
468s   CPPTRAJ: Remove time from restart test
468s 
468s   CPPTRAJ: Add time to trajectory test
468s 
468s   CPPTRAJ: Modify time info test.
468s 
468s All 4 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_SplitCoords
468s 
468s   CPPTRAJ: SplitCoords test
468s 
468s All 1 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_DihedralRMS
468s 
468s   CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.)
468s 
468s   CPPTRAJ: Dihedral RMSD test (to previous)
468s 
468s   CPPTRAJ: Dihedral RMS fluctuation test.
468s 
468s All 5 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Slope
468s 
468s   CPPTRAJ: Finite difference test.
468s 
468s All 1 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Diagmatrix
468s 
468s   CPPTRAJ: MW covariance matrix thermo analysis test
468s 
468s All 1 comparisons passed.
468s 
468s ********************************************************************************
468s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Emin
468s 
468s   CPPTRAJ: Basic energy minimization test.
468s 
468s   CPPTRAJ: Energy minimization with angle term test.
468s 
468s   CPPTRAJ: Energy minimization with dihedral and 1-4 terms test.
468s 
468s   CPPTRAJ: Energy minimization with nonbond term test.
469s 
469s   CPPTRAJ: OpenMM basic energy minimization tests (bonds)
469s 
469s   CPPTRAJ: OpenMM basic energy minimization tests (angles)
469s 
469s   CPPTRAJ: OpenMM basic energy minimization tests (dihedrals)
469s 
469s   CPPTRAJ: OpenMM basic energy minimization tests (nonbonds)
469s 
469s   CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME)
471s 
471s All 9 comparisons passed.
471s 
471s ********************************************************************************
471s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_EvalPlateau
471s 
471s   CPPTRAJ: Evalulate plateau test
471s 
471s All 2 comparisons passed.
471s 
471s ********************************************************************************
471s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Graft
471s 
471s   CPPTRAJ: Graft test
471s 
471s All 1 comparisons passed.
471s 
471s ********************************************************************************
471s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Flatten
471s 
471s   CPPTRAJ: Flatten test.
471s 
471s All 1 comparisons passed.
471s 
471s ********************************************************************************
471s TEST: /tmp/autopkgtest.BzKBgt/build.fVS/src/test/Test_Random
471s 
471s   CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs
472s 
472s   CPPTRAJ: PCG32 RNG test.
472s 
472s   CPPTRAJ: Test Stdlib RNG
472s 
472s   CPPTRAJ: Test Mersenne Twister RNG
472s 
472s All 4 comparisons passed.
472s 
472s make[1]: Leaving directory '/tmp/autopkgtest.BzKBgt/build.fVS/src/test'
472s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 25 01:54 ../bin/cpptraj -> /usr/bin/cpptraj
472s ===================== TEST SUMMARY ======================
472s   851 out of 859 comparisons OK (2 failed, 0 warnings, 6 skipped).
472s   480 out of 480 program executions completed.
472s   168 out of 173 tests completed with no issues.
472s   2 tests skipped.
472s =========================================================
472s make: *** [Makefile:662: summary] Error 2
472s make: Leaving directory '/tmp/autopkgtest.BzKBgt/build.fVS/src/test'
472s autopkgtest [01:55:58]: test command1: -----------------------]
473s autopkgtest [01:55:59]: test command1:  - - - - - - - - - - results - - - - - - - - - -
473s command1             FAIL non-zero exit status 2
473s autopkgtest [01:55:59]: test command1:  - - - - - - - - - - stderr - - - - - - - - - -
473s make: *** [Makefile:662: summary] Error 2
473s autopkgtest [01:55:59]: @@@@@@@@@@@@@@@@@@@@ summary
473s command1             FAIL non-zero exit status 2
488s Creating nova instance adt-noble-arm64-cpptraj-20240325-014805-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 2df78aec-1bf7-4c70-8bf1-31fba04b7d21)...