0s autopkgtest [19:36:50]: starting date and time: 2024-03-14 19:36:50+0000
  0s autopkgtest [19:36:50]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [19:36:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hlomkw_y/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3,src:openmpi,src:pmix --apt-upgrade cpptraj --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 openmpi/4.1.6-5.1ubuntu3 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-12.secgroup --name adt-noble-ppc64el-cpptraj-20240314-193650-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/
107s autopkgtest [19:38:37]: testbed dpkg architecture: ppc64el
107s autopkgtest [19:38:37]: testbed apt version: 2.7.12
107s autopkgtest [19:38:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup
108s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB]
108s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [47.8 kB]
108s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B]
108s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [2966 kB]
109s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB]
109s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB]
109s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B]
109s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B]
109s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B]
109s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3308 kB]
109s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B]
109s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.5 kB]
109s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B]
114s Fetched 7560 kB in 2s (3404 kB/s)
114s Reading package lists...
116s Reading package lists...
117s Building dependency tree...
117s Reading state information...
117s Calculating upgrade...
117s The following packages will be upgraded:
117s   dosfstools
117s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
117s Need to get 101 kB of archives.
117s After this operation, 9216 B disk space will be freed.
117s Get:1 http://ftpmaster.internal/ubuntu noble/main ppc64el dosfstools ppc64el 4.2-1.1 [101 kB]
117s Fetched 101 kB in 0s (298 kB/s)
118s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70096 files and directories currently installed.)
118s Preparing to unpack .../dosfstools_4.2-1.1_ppc64el.deb ...
118s Unpacking dosfstools (4.2-1.1) over (4.2-1build3) ...
118s Setting up dosfstools (4.2-1.1) ...
118s Processing triggers for man-db (2.12.0-3) ...
118s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
119s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease
119s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease
119s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease
119s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease
120s Reading package lists...
120s Reading package lists...
121s Building dependency tree...
121s Reading state information...
121s Calculating upgrade...
121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
121s Reading package lists...
121s Building dependency tree...
121s Reading state information...
121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
124s autopkgtest [19:38:54]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024
125s autopkgtest [19:38:55]: @@@@@@@@@@@@@@@@@@@@ apt-source cpptraj
129s Get:1 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (dsc) [2160 B]
129s Get:2 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (tar) [28.4 MB]
129s Get:3 http://ftpmaster.internal/ubuntu noble/universe cpptraj 5.1.0+dfsg-3build1 (diff) [6064 B]
129s gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC
129s gpgv:                using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D
129s gpgv: Can't check signature: No public key
129s dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.dsc: no acceptable signature found
133s autopkgtest [19:39:02]: testing package cpptraj version 5.1.0+dfsg-3build1
134s autopkgtest [19:39:04]: build not needed
145s autopkgtest [19:39:15]: test command1: preparing testbed
148s Reading package lists...
148s Building dependency tree...
148s Reading state information...
149s Starting pkgProblemResolver with broken count: 0
149s Starting 2 pkgProblemResolver with broken count: 0
149s Done
149s The following additional packages will be installed:
149s   cpptraj libaec0 libarpack2 libblas3 libfftw3-double3 libgfortran5 libgomp1
149s   libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19 libopenmm8.0 libsz2
149s   netcdf-bin
149s Suggested packages:
149s   libfftw3-bin libfftw3-dev
149s The following NEW packages will be installed:
149s   autopkgtest-satdep cpptraj libaec0 libarpack2 libblas3 libfftw3-double3
149s   libgfortran5 libgomp1 libhdf5-103-1 libhdf5-hl-100 liblapack3 libnetcdf19
149s   libopenmm8.0 libsz2 netcdf-bin
149s 0 upgraded, 15 newly installed, 0 to remove and 0 not upgraded.
149s Need to get 9574 kB/9575 kB of archives.
149s After this operation, 30.6 MB of additional disk space will be used.
149s Get:1 /tmp/autopkgtest.cHW7oc/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B]
149s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB]
150s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB]
150s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB]
151s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libarpack2 ppc64el 3.9.1-1 [106 kB]
151s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB]
151s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu2 [443 kB]
152s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB]
152s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B]
152s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB]
152s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB]
152s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libnetcdf19 ppc64el 1:4.9.2-3ubuntu1 [597 kB]
152s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el libopenmm8.0 ppc64el 8.0.0+dfsg-6ubuntu1 [893 kB]
152s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el cpptraj ppc64el 5.1.0+dfsg-3build1 [2050 kB]
153s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el netcdf-bin ppc64el 1:4.9.2-3ubuntu1 [239 kB]
153s Fetched 9574 kB in 4s (2598 kB/s)
153s Selecting previously unselected package libblas3:ppc64el.
153s (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 70095 files and directories currently installed.)
153s Preparing to unpack .../00-libblas3_3.12.0-3_ppc64el.deb ...
153s Unpacking libblas3:ppc64el (3.12.0-3) ...
153s Selecting previously unselected package libgfortran5:ppc64el.
153s Preparing to unpack .../01-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ...
153s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
153s Selecting previously unselected package liblapack3:ppc64el.
153s Preparing to unpack .../02-liblapack3_3.12.0-3_ppc64el.deb ...
153s Unpacking liblapack3:ppc64el (3.12.0-3) ...
153s Selecting previously unselected package libarpack2:ppc64el.
153s Preparing to unpack .../03-libarpack2_3.9.1-1_ppc64el.deb ...
153s Unpacking libarpack2:ppc64el (3.9.1-1) ...
153s Selecting previously unselected package libgomp1:ppc64el.
153s Preparing to unpack .../04-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ...
153s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ...
153s Selecting previously unselected package libfftw3-double3:ppc64el.
153s Preparing to unpack .../05-libfftw3-double3_3.3.10-1ubuntu2_ppc64el.deb ...
153s Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ...
153s Selecting previously unselected package libaec0:ppc64el.
153s Preparing to unpack .../06-libaec0_1.1.2-1_ppc64el.deb ...
153s Unpacking libaec0:ppc64el (1.1.2-1) ...
153s Selecting previously unselected package libsz2:ppc64el.
153s Preparing to unpack .../07-libsz2_1.1.2-1_ppc64el.deb ...
153s Unpacking libsz2:ppc64el (1.1.2-1) ...
153s Selecting previously unselected package libhdf5-103-1:ppc64el.
153s Preparing to unpack .../08-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ...
153s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ...
153s Selecting previously unselected package libhdf5-hl-100:ppc64el.
153s Preparing to unpack .../09-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ...
153s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ...
153s Selecting previously unselected package libnetcdf19:ppc64el.
153s Preparing to unpack .../10-libnetcdf19_1%3a4.9.2-3ubuntu1_ppc64el.deb ...
153s Unpacking libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ...
153s Selecting previously unselected package libopenmm8.0.
153s Preparing to unpack .../11-libopenmm8.0_8.0.0+dfsg-6ubuntu1_ppc64el.deb ...
153s Unpacking libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
153s Selecting previously unselected package cpptraj.
153s Preparing to unpack .../12-cpptraj_5.1.0+dfsg-3build1_ppc64el.deb ...
153s Unpacking cpptraj (5.1.0+dfsg-3build1) ...
153s Selecting previously unselected package netcdf-bin.
153s Preparing to unpack .../13-netcdf-bin_1%3a4.9.2-3ubuntu1_ppc64el.deb ...
153s Unpacking netcdf-bin (1:4.9.2-3ubuntu1) ...
153s Selecting previously unselected package autopkgtest-satdep.
153s Preparing to unpack .../14-1-autopkgtest-satdep.deb ...
153s Unpacking autopkgtest-satdep (0) ...
153s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ...
153s Setting up libaec0:ppc64el (1.1.2-1) ...
153s Setting up libblas3:ppc64el (3.12.0-3) ...
153s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
153s Setting up libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ...
153s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ...
153s Setting up libopenmm8.0 (8.0.0+dfsg-6ubuntu1) ...
153s Setting up libsz2:ppc64el (1.1.2-1) ...
153s Setting up liblapack3:ppc64el (3.12.0-3) ...
153s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
153s Setting up libarpack2:ppc64el (3.9.1-1) ...
153s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ...
153s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ...
153s Setting up libnetcdf19:ppc64el (1:4.9.2-3ubuntu1) ...
153s Setting up cpptraj (5.1.0+dfsg-3build1) ...
153s Setting up netcdf-bin (1:4.9.2-3ubuntu1) ...
153s Setting up autopkgtest-satdep (0) ...
153s Processing triggers for man-db (2.12.0-3) ...
154s Processing triggers for libc-bin (2.39-0ubuntu2) ...
156s (Reading database ... 70186 files and directories currently installed.)
156s Removing autopkgtest-satdep (0) ...
157s autopkgtest [19:39:27]: test command1: mkdir bin && ln -s /usr/bin/cpptraj bin && make -C test test.complete summary
157s autopkgtest [19:39:27]: test command1: [-----------------------
157s make: Entering directory '/tmp/autopkgtest.cHW7oc/build.pfG/src/test'
157s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 14 19:39 ../bin/cpptraj -> /usr/bin/cpptraj
157s make[1]: Entering directory '/tmp/autopkgtest.cHW7oc/build.pfG/src/test'
157s ********************************************************************************
157s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_General
157s 
157s   CPPTRAJ: General tests
157s 
157s All 15 comparisons passed.
157s 
157s ********************************************************************************
157s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Parallel
157s 
157s   CPPTRAJ: Parallel tests.
157s 
157s   CPPTRAJ: Parallel test with trajectory offset
157s 
157s All 7 comparisons passed.
157s 
157s ********************************************************************************
157s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Strip
157s 
157s   CPPTRAJ: One frame strip command test
157s 
157s   CPPTRAJ: Unstrip (Lig/Rec/Complex) command test
157s 
157s   CPPTRAJ: Multi frame strip command test.
157s 
157s   CPPTRAJ: Strip topology with PDB info
157s 
157s All 11 comparisons passed.
157s 
157s ********************************************************************************
157s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_BrokenTraj
157s 
157s   CPPTRAJ: Broken Traj: Running good trajectory.
157s 
157s   CPPTRAJ: Broken Traj: Running broken trajectory.
158s 
158s   CPPTRAJ: Compressed broken trajectory test
158s 
158s All 2 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_TrajinOffset
158s 
158s   CPPTRAJ: Normal trajectory read with offsets.
158s 
158s   CPPTRAJ: Gzipped trajectory read with offsets
158s 
158s   CPPTRAJ: Bzip2ed trajectory read with offsets
158s 
158s   CPPTRAJ: Start argument offset
158s 
158s All 4 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_RemdTraj
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run with offset
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run
158s 
158s   CPPTRAJ: NetCDF Replica Trajectory Run test
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj
158s 
158s   CPPTRAJ: CRD Replica Trajectory Run with remdout
158s 
158s All 8 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_trajout_framerange
158s 
158s   CPPTRAJ: Trajout Frame Range [Amber Restart]
158s 
158s   CPPTRAJ: Trajout Frame Range [Amber Coordinates]
158s 
158s All 6 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_PerResRMSD
158s 
158s   CPPTRAJ: Per-Residue RMSD Test.
158s 
158s   CPPTRAJ: Per-Residue RMSD Test with averaging
158s 
158s   CPPTRAJ: Per-Residue RMSD Test with residue centering.
158s 
158s All 3 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DSSP
158s 
158s   CPPTRAJ: Secstruct (DSSP) command test.
158s 
158s   CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format.
158s 
158s   CPPTRAJ: Secstruct (DSSP) command with changing number of residues.
158s 
158s   CPPTRAJ: Secstruct (DSSP): SS assign output test
158s 
158s   CPPTRAJ: FtuFabI Assignment test
158s 
158s All 10 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Center
158s 
158s   CPPTRAJ: Center command test.
158s 
158s   CPPTRAJ: Center origin command test.
158s 
158s   CPPTRAJ: Center origin mass command test.
158s 
158s   CPPTRAJ: Center reference command test.
158s 
158s   CPPTRAJ: Center point test.
158s 
158s All 5 comparisons passed.
158s 
158s ********************************************************************************
158s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Hbond
158s 
158s   CPPTRAJ: Solute Hbond test
158s 
158s   CPPTRAJ: Solute Hbond test with disk caching
158s 
158s   CPPTRAJ: Solute-solvent hbond test
158s 
158s   CPPTRAJ: Hbond, no intramolecular hydrogen bonds test
158s 
158s   CPPTRAJ: Hbond, specified solute masks
158s 
158s   CPPTRAJ: Hbond, no angle cutoff test
158s 
158s   CPPTRAJ: Hbond, Bridge nointramol test
159s 
159s   CPPTRAJ: Hbond with imaging
159s 
159s   CPPTRAJ: Hbond, orthogonal imaging
159s 
159s All 23 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_NCrestart
159s 
159s   CPPTRAJ: NetCDF Restart Test - TXT->NetCDF
159s 
159s   CPPTRAJ: NetCDF Restart Test - NetCDF->TXT
159s 
159s   CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF
159s 
159s   CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt
159s 
159s All 2 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Image
159s 
159s   CPPTRAJ: Orthorhombic imaged distance test.
159s 
159s   CPPTRAJ: Non-orthorhombic imaged distance test.
159s 
159s   CPPTRAJ: Orthorhombic coordinate imaging test
159s 
159s   CPPTRAJ: Nonorthorhombic coordinate imaging test
159s 
159s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar
159s 
159s   CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM
159s 
159s All 6 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Surf
159s 
159s   CPPTRAJ: Surface calculation test
159s 
159s   CPPTRAJ: Partial Surface calculation test
159s 
159s   CPPTRAJ: LCPO test with GAFF atom types
159s 
159s All 3 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Radgyr
159s 
159s   CPPTRAJ: Radius of gyration command test
159s 
159s All 2 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Mask
159s 
159s   CPPTRAJ: Mask single frame test
159s 
159s   CPPTRAJ: Mask longer command test.
159s 
159s All 5 comparisons passed.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Jcoupling
159s 
159s   CPPTRAJ: J-Coupling single frame test
159s   J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set.
159s   Skipped test: J-Coupling extended test
159s 
159s All 1 comparisons passed.
159s 1 comparisons skipped.
159s 
159s ********************************************************************************
159s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Diffusion
159s 
159s   CPPTRAJ: Diffusion test, no imaging.
159s 
159s   CPPTRAJ: Diffusion test, old syntax.
159s 
159s   CPPTRAJ: Diffusion test, new syntax.
160s 
160s   CPPTRAJ: Diffusion test, nonorthogonal box
160s 
160s   CPPTRAJ: STFC Diffusion Test
160s 
160s   CPPTRAJ: STFC Diffusion Test with individual distances
160s 
160s   CPPTRAJ: STFC Diffusion Test with COM
160s 
160s   CPPTRAJ: STFC Diffusion Test with second mask
160s 
160s All 16 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Outtraj
160s 
160s   CPPTRAJ: RMSD Test with outtraj.
160s 
160s   CPPTRAJ: Outtraj Test with maxmin.
160s 
160s All 4 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Charmm
160s 
160s   CPPTRAJ: CHARMM PSF/DCD test
160s 
160s   CPPTRAJ: CHARMM DCD Write, step 1.
160s 
160s   CPPTRAJ: CHARMM DCD Write, step 2.
160s 
160s   CPPTRAJ: CHAMBER topology read/strip test.
160s 
160s   CPPTRAJ: Read CHARMM restart
160s 
160s   CPPTRAJ: CHARMM PSF write
160s 
160s   CPPTRAJ: CHARMM COORdinates test
160s 
160s All 6 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CharmmParams
160s 
160s   CPPTRAJ: Test updating topology with Charmm parameters (single residue)
160s 
160s All 2 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Rotdif
160s 
160s   CPPTRAJ: Rotational diffusion calculation test
160s 
160s All 4 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_NetcdfTraj
160s 
160s   CPPTRAJ: Convert mdcrd -> NetCDF
160s 
160s   CPPTRAJ: Convert NetCDF -> mdcrd
160s 
160s All 1 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Runavg
160s 
160s   CPPTRAJ: Coordinate Running Average test.
160s 
160s   CPPTRAJ: Coordinate Running Average Traj Write
160s 
160s All 2 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_RMSD
160s 
160s   CPPTRAJ: Basic RMSD tests
160s 
160s   CPPTRAJ: RMS coordinate rotation/rotation matrices test
160s 
160s   CPPTRAJ: RMS fit with no coordinates modification test.
160s 
160s   CPPTRAJ: RMS fit to previous test
160s 
160s   CPPTRAJ: RMS: imaging after unit cell rotation
160s 
160s All 12 comparisons passed.
160s 
160s ********************************************************************************
160s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_2DRMS
160s 
160s   CPPTRAJ: 2D RMSD Test.
160s 
160s   CPPTRAJ: 2D RMSD Test, mass-weighted.
160s 
160s   CPPTRAJ: 2D RMSD Test with reference trajectory
160s 
160s   CPPTRAJ: 2D DME Test.
160s 
160s   CPPTRAJ: 2D RMSD with reference mask test.
160s 
160s   CPPTRAJ: 2D RMSD test, no fitting.
161s 
161s All 6 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Mol2
161s 
161s   CPPTRAJ: Mol2 Parm/Traj Read/Write Test.
161s 
161s   CPPTRAJ: PDB => Mol2
161s 
161s   CPPTRAJ: Amber Top/Rst => Mol2
161s   Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set.
161s   Skipped test: Amber Top/Rst => Mol2, SYBYL atom types
161s 
161s All 4 comparisons passed.
161s 1 comparisons skipped.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_NAstruct
161s 
161s   CPPTRAJ: NAstruct command test.
161s 
161s   CPPTRAJ: NAstruct command test, single strand
161s 
161s All 11 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_NAstruct_8OG
161s 
161s   CPPTRAJ: NA test (8OG)
161s 
161s All 3 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Average
161s 
161s   CPPTRAJ: Average Test.
161s 
161s All 2 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Pucker
161s 
161s   CPPTRAJ: Pucker command test
161s 
161s   CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test
161s 
161s   CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test.
161s 
161s All 3 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AtomMap
161s 
161s   CPPTRAJ: AtomMap Test
161s 
161s   CPPTRAJ: AtomMap with 'rmsfit'
161s 
161s   CPPTRAJ: Atom map charmm->amber atom order
161s 
161s   CPPTRAJ: Atom map charmm->amber atom order, by residue
161s 
161s All 9 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Datafile
161s 
161s   CPPTRAJ: Data file output precision test
161s 
161s   CPPTRAJ: Standard -> Grace Data
161s 
161s   CPPTRAJ: Grace -> Standard Data
161s 
161s   CPPTRAJ: X column format/precision test.
161s 
161s   CPPTRAJ: Data file group by name test
161s 
161s   CPPTRAJ: Data file group by aspect test
161s 
161s All 6 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Radial
161s 
161s   CPPTRAJ: Radial test, non-orthogonal imaging
161s 
161s   CPPTRAJ: Radial test, orthogonal and no imaging
161s 
161s All 9 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Hist
161s 
161s   CPPTRAJ: 1D/2D Histogram Analysis test
161s 
161s   CPPTRAJ: 3D histogram test.
161s 
161s All 7 comparisons passed.
161s 
161s ********************************************************************************
161s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Closest
161s 
161s   CPPTRAJ: Closest command test using first solvent atom.
161s 
161s   CPPTRAJ: Closest command test using all solvent atoms.
161s 
161s   CPPTRAJ: Closest command test, using mask center
161s 
161s   CPPTRAJ: Closest command test, using mask center and solvent mask
161s 
161s   CPPTRAJ: Closest command test, solvent mask, water oxygen only
162s 
162s All 8 comparisons passed.
162s 
162s ********************************************************************************
162s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DRMSD
162s 
162s   CPPTRAJ: Distance RMSD test
162s 
162s All 1 comparisons passed.
162s 
162s ********************************************************************************
162s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster
162s 
162s   CPPTRAJ: Cluster command test, in-memory pairwise distances.
162s 
162s   CPPTRAJ: Cluster command test, read pairwise distances.
162s 
162s   CPPTRAJ: Cluster command test, read NetCDF pairwise distances.
162s 
162s   CPPTRAJ: Cluster command test, write ASCII pairwise distances.
162s 
162s   CPPTRAJ: Cluster command test, read ASCII pairwise distances.
162s 
162s All 9 comparisons passed.
162s 
162s ********************************************************************************
162s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_Sieve
162s 
162s   CPPTRAJ: Cluster, nosieve 
163s 
163s   CPPTRAJ: Cluster, sieve5 
163s 
163s   CPPTRAJ: Cluster, nosieve savepairdist
163s 
163s   CPPTRAJ: Cluster, nosieve loadpairdist
163s 
163s   CPPTRAJ: Cluster, sieve5 savepairdist
163s 
163s   CPPTRAJ: Cluster, sieve5 loadpairdist
163s 
163s   CPPTRAJ: Cluster, nosieve pairwisecache none
163s 
163s   CPPTRAJ: Cluster, sieve5 pairwisecache none
163s 
163s   CPPTRAJ: Cluster, random 
163s 
163s All 28 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_RandomSieve
163s 
163s   CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances).
163s 
163s   CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances).
163s 
163s All 4 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_DataSet
163s 
163s   CPPTRAJ: Clustering, One DataSet
163s 
163s   CPPTRAJ: Clustering, Two DataSets
163s 
163s   CPPTRAJ: Clustering, dihedral DataSet
163s 
163s   CPPTRAJ: Clustering, two dihedral DataSets
163s 
163s   CPPTRAJ: Clustering, dihedral DataSet, K-means
163s 
163s   CPPTRAJ: Clustering, two dihedral DataSets, K-means
163s 
163s All 8 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_DBSCAN
163s 
163s   CPPTRAJ: DBSCAN test
163s 
163s   CPPTRAJ: DBSCAN automatic parameter determination test.
163s 
163s   CPPTRAJ: DBSCAN kdist map test
163s 
163s   CPPTRAJ: DBSCAN with sieve
163s 
163s All 4 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_Kmeans
163s 
163s   CPPTRAJ: Cpptraj Kmeans
163s 
163s   CPPTRAJ: Cpptraj Kmeans random
163s 
163s All 6 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_SymmRMSD
163s 
163s   CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD)
163s 
163s All 5 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_TrajWrites
163s 
163s   CPPTRAJ: Cluster command test, coordinate writes.
163s 
163s   CPPTRAJ: Cluster command test, coordinate writes using info file.
163s 
163s All 8 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_Dpeaks
163s 
163s   CPPTRAJ: Density peaks clustering test
163s 
163s All 3 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cluster_Nreps
163s 
163s   CPPTRAJ: Clustering with specified # reps
163s 
163s All 2 comparisons passed.
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_IRED
163s 
163s   CPPTRAJ: IRED vector/matrix test
163s 
163s 
163s ********************************************************************************
163s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_RandomizeIons
163s 
163s   CPPTRAJ: randomizeions test (original algorithm)
164s 
164s   CPPTRAJ: Randomize (around, overlap)
164s 
164s   CPPTRAJ: Randomize (around)
164s 
164s   CPPTRAJ: Randomize (overlap)
164s 
164s   CPPTRAJ: Randomize (no restrictions)
164s 
164s All 5 comparisons passed.
164s 
164s ********************************************************************************
164s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Molsurf
164s 
164s   CPPTRAJ: Molsurf test
164s 
164s All 1 comparisons passed.
164s 
164s ********************************************************************************
164s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Corr
164s 
164s   CPPTRAJ: Correlation test
164s 
164s All 2 comparisons passed.
164s 
164s ********************************************************************************
164s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CheckStructure
164s 
164s   CPPTRAJ: Structure Check
164s 
164s   CPPTRAJ: Structure Check with Around and Skip
165s 
165s   CPPTRAJ: Structure Check with PBC
165s 
165s   CPPTRAJ: Structure Check with Around
165s 
165s All 8 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_RmsAvgCorr
165s 
165s   CPPTRAJ: RmsAvgCorr Reference
165s 
165s   CPPTRAJ: RmsAvgCorr First
165s 
165s All 3 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Contacts
165s 
165s   CPPTRAJ: Contacts test.
165s 
165s All 3 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Principal
165s 
165s   CPPTRAJ: Principal Test
165s 
165s All 3 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_ClusterDihedral
165s 
165s   CPPTRAJ: clusterdihedral test
165s 
165s All 4 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Vector
165s 
165s   CPPTRAJ: Basic vector tests
165s 
165s   CPPTRAJ: Test vector center with magnitude
165s 
165s   CPPTRAJ: Momentum/velocity vector test.
165s 
165s   CPPTRAJ: Force vector test.
165s 
165s All 14 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Matrix
165s 
165s   CPPTRAJ: Matrix Tests
165s 
165s   CPPTRAJ: Generate matrix with trajectory start/stop/offset
165s 
165s   CPPTRAJ: Generate matrix with action stop/start/offset
165s 
165s All 15 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AtomicFluct
165s 
165s   CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor].
165s 
165s   CPPTRAJ: Atomic fluctuations test [:2-12 byatom].
165s 
165s   CPPTRAJ: Atomic fluctuations test [bymask :3,4,5].
165s 
165s   CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor].
165s 
165s   CPPTRAJ: Atomicfluct test with ADP output
165s 
165s   CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output.
165s 
165s All 13 comparisons passed.
165s 
165s ********************************************************************************
165s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Grid
165s 
165s   CPPTRAJ: Dipole test
166s 
166s   CPPTRAJ: Grid test
166s 
166s   CPPTRAJ: OpenDX Grid read test
166s 
166s   CPPTRAJ: Grid with specified center test.
166s 
166s   CPPTRAJ: Grid with box center offset test.
166s 
166s   CPPTRAJ: Grid with mask center offset test.
166s 
166s   CPPTRAJ: Non-orthogonal grid test.
166s 
166s   CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test
166s 
166s   CPPTRAJ: Grid generation from 'bounds' test.
166s 
166s All 13 comparisons passed.
166s 
166s ********************************************************************************
166s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Unwrap
166s 
166s   CPPTRAJ: Unwrap non-orthogonal test
166s 
166s   CPPTRAJ: Unwrap orthogonal test
166s 
166s All 2 comparisons passed.
166s 
166s ********************************************************************************
166s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Project
166s 
166s   CPPTRAJ: Projection
166s 
166s All 1 comparisons passed.
166s 
166s ********************************************************************************
166s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Analyze_Modes
166s 
166s   CPPTRAJ: Modes analysis, RMS fluctuations
166s 
166s   CPPTRAJ: Modes analysis, displacements
166s 
166s   CPPTRAJ: Modes analysis, dipole correlation
166s 
166s   CPPTRAJ: Modes analysis, pseudo trajectory creation test
166s 
166s   CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test
166s 
166s All 6 comparisons passed.
166s 
166s ********************************************************************************
166s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Watershell
166s 
166s   CPPTRAJ: Watershell Test, non-orthorhombic imaging.
167s 
167s   CPPTRAJ: Watershell Test, orthorhombic imaging.
167s 
167s   CPPTRAJ: Watershell Test, no imaging.
167s 
167s All 3 comparisons passed.
167s 
167s ********************************************************************************
167s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AnalysisRunAvg
167s 
167s   CPPTRAJ: Analysis Running Average
167s 
167s All 2 comparisons passed.
167s 
167s ********************************************************************************
167s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Volmap
167s 
167s   CPPTRAJ: VMD VolMap Algorithm test
167s   VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run.
167s   Skipped test: VMD VolMap Algorithm longer tests
167s 
167s All 2 comparisons passed.
167s 1 comparisons skipped.
167s 
167s ********************************************************************************
167s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_SPAM
167s 
167s   CPPTRAJ: SPAM Test
167s 
167s   CPPTRAJ: SPAM Pure Solvent Test
169s 
169s   1 out of 5 comparisons failed.
169s 
169s ********************************************************************************
169s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LIE
169s 
169s   CPPTRAJ: LIE test
169s 
169s All 1 comparisons passed.
169s 
169s ********************************************************************************
169s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Density
169s 
169s   CPPTRAJ: Density along axis tests
169s 
169s   CPPTRAJ: Multi-frame density along axis test
169s 
169s   CPPTRAJ: Total system density test
169s 
169s All 7 comparisons passed.
169s 
169s ********************************************************************************
169s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LipidOrder
169s 
169s   CPPTRAJ: Lipid Order Parameter Test.
169s 
169s All 6 comparisons passed.
169s 
169s ********************************************************************************
169s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LipidSCD
169s 
169s   CPPTRAJ: Basic lipid order parameter test
169s 
169s   CPPTRAJ: New Lipid Order Parameter Test, DOPC.
169s 
169s All 4 comparisons passed.
169s 
169s ********************************************************************************
169s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_PairDist
169s 
169s   CPPTRAJ: PairDist Test.
170s 
170s   CPPTRAJ: Pairdist test, orthogonal imaging.
170s 
170s   CPPTRAJ: Pairdist test, nonorthogonal imaging.
170s 
170s   CPPTRAJ: Pairdist test, 2 masks.
170s 
170s All 4 comparisons passed.
170s 
170s ********************************************************************************
170s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_ReadData
170s 
170s   CPPTRAJ: Read vector data test (no origins, origins)
170s 
170s   CPPTRAJ: Read vector data set (origins, no origins)
170s 
170s   CPPTRAJ: Read Amber output test
170s 
170s   CPPTRAJ: Read CHARMM output test
170s 
170s   CPPTRAJ: 3D data read/write test
170s 
170s   CPPTRAJ: Standard 3D data write test
170s 
170s   CPPTRAJ: Standard 3D data read test
170s 
170s   CPPTRAJ: Standard 3D data read/append test
170s 
170s   CPPTRAJ: Standard 3D data, sparse
170s 
170s   CPPTRAJ: Nonorthogonal grid standard write/read tests.
171s 
171s   CPPTRAJ: Read specific columns test.
171s 
171s   CPPTRAJ: Write non-square matrix
171s 
171s   CPPTRAJ: Read non-square matrix
171s 
171s   CPPTRAJ: Read square matrix
171s 
171s All 15 comparisons passed.
171s 
171s ********************************************************************************
171s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_GIST
171s 
171s   CPPTRAJ: GIST water-water interaction test
172s 
172s   CPPTRAJ: GIST test, orthogonal cell
174s 
174s   CPPTRAJ: GIST test, nonorthogonal cell
178s 
178s All 11 comparisons passed.
178s 
178s ********************************************************************************
178s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_GIST_Order
178s 
178s   CPPTRAJ: TIP3P water cluster test
178s 
178s   CPPTRAJ: TIP4P water cluster test
178s 
178s   CPPTRAJ: TIP5P water cluster test
178s 
178s All 4 comparisons passed.
178s 
178s ********************************************************************************
178s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_systemVF
178s 
178s   CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test
178s 
178s All 1 comparisons passed.
178s 
178s ********************************************************************************
178s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AtomicCorr
178s 
178s   CPPTRAJ: Atomic Correlation test
178s 
178s All 1 comparisons passed.
178s 
178s ********************************************************************************
178s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AutoCorr
178s 
178s   CPPTRAJ: AutoCorr test.
179s 
179s All 1 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Box
179s 
179s   CPPTRAJ: Box Test (Add box info)
179s 
179s   CPPTRAJ: Box test (remove box info)
179s 
179s   CPPTRAJ: Box test (Modify box length)
179s 
179s   CPPTRAJ: Box test (auto orthogonal box, no radii)
179s 
179s   CPPTRAJ: Box test (auto orthogonal box, VDW radii)
179s 
179s All 7 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AtomTypeSelect
179s 
179s   CPPTRAJ: Selection by atom type test.
179s 
179s All 1 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AvgRef
179s 
179s   CPPTRAJ: RMSD Test with averaged reference coordinates.
179s 
179s All 1 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Crank_Stat
179s 
179s   CPPTRAJ: Crankshaft test
179s 
179s All 3 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CreateCrd
179s 
179s   CPPTRAJ: COORDS data set creation and CRDFLUCT test.
179s 
179s   CPPTRAJ: COORDS data set creation with velocities test
179s 
179s   CPPTRAJ: TRAJ data set creation and CRDFLUCT test.
179s 
179s   CPPTRAJ: TRAJ data set creation with velocities test.
179s 
179s   CPPTRAJ: COORDS data set append test
179s 
179s   CPPTRAJ: COORDS test storing frame metadata
179s 
179s   CPPTRAJ: TRAJ test storing frame metadata
179s 
179s All 8 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AutoImage
179s 
179s   CPPTRAJ: AutoImage test (split DNA duplex)
179s 
179s   CPPTRAJ: AutoImage test, use anchor mask
179s 
179s All 2 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LoadCrd
179s 
179s   CPPTRAJ: LoadCrd test.
179s 
179s   CPPTRAJ: LoadTraj test.
179s 
179s   CPPTRAJ: LoadTraj from trajin test.
179s 
179s   CPPTRAJ: LoadCrd append from multiple files test
179s 
179s All 4 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_MultiVector
179s 
179s   CPPTRAJ: Multivector test
179s 
179s All 1 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Lifetime
179s 
179s   CPPTRAJ: Lifetime test.
179s 
179s   CPPTRAJ: Lifetime test with data set caching.
179s 
179s   CPPTRAJ: Lifetime average and cumulative average test.
179s 
179s All 12 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_FFT
179s 
179s   CPPTRAJ: FFT test.
179s 
179s All 5 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Timecorr
179s 
179s   CPPTRAJ: Timecorr test.
179s 
179s All 7 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CrossCorr
179s 
179s   CPPTRAJ: CrossCorr test
179s 
179s All 1 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_SymmRmsd
179s 
179s   CPPTRAJ: SymmRmsd
179s 
179s   CPPTRAJ: ASP symmetry-corrected RMSD test
179s 
179s   CPPTRAJ: GLU symmetry-corrected RMSD test
179s 
179s   CPPTRAJ: TYR symmetry-corrected RMSD test
179s 
179s   CPPTRAJ: Longer symmetry-corrected RMSD test.
179s 
179s All 8 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Multidihedral
179s 
179s   CPPTRAJ: Multidihedral test
179s 
179s   CPPTRAJ: Multidihedral Nucleotide CHI test
179s 
179s   CPPTRAJ: Multidihedral protein dihedrals test
179s 
179s   CPPTRAJ: Multidihedral cyclic molecule test
179s 
179s All 6 comparisons passed.
179s 
179s ********************************************************************************
179s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Ensemble_MREMD
179s 
179s   CPPTRAJ: M-REMD sort test.
180s 
180s   CPPTRAJ: M-REMD actions test.
180s 
180s   CPPTRAJ: M-REMD ensemble outtraj test.
180s 
180s   CPPTRAJ: M-REMD no sort, running average test
180s 
180s   CPPTRAJ: M-REMD, generate RMS data
180s 
180s   CPPTRAJ: M-REMD, meltcurve analysis
180s 
180s All 17 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_MakeStructure
180s 
180s   CPPTRAJ: Basic makestructure test
180s 
180s   CPPTRAJ: Makestructure test with reference.
180s 
180s All 5 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Rotate
180s 
180s   CPPTRAJ: Rotation (and inverse) of coords from matrices
180s 
180s   CPPTRAJ: Rotate with defined axis
180s 
180s All 3 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Integrate
180s 
180s   CPPTRAJ: Integration test.
180s 
180s All 2 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_NativeContacts
180s 
180s   CPPTRAJ: NativeContacts test.
180s 
180s   CPPTRAJ: NativeContacts test, save non-native contacts, residue time series
180s 
180s   CPPTRAJ: NativeContacts test, orthorhombic imaging.
180s 
180s All 17 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CheckChiral
180s 
180s   CPPTRAJ: Check chirality test
180s 
180s All 1 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Energy
180s 
180s   CPPTRAJ: Simple energy tests
180s 
180s   CPPTRAJ: Test kinetic energy calculation
180s 
180s   CPPTRAJ: Test total energy calculation
180s 
180s   CPPTRAJ: Test partial energy calculation
180s 
180s All 6 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LESsplit
180s 
180s   CPPTRAJ: LES split/average test
180s 
180s All 2 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_PermuteDihedrals
180s 
180s   CPPTRAJ: PermuteDihedrals interval -120, phi psi
180s 
180s   CPPTRAJ: PermuteDihedrals, random rotations
180s 
180s All 4 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CCP4
180s 
180s   CPPTRAJ: CCP4 read/write and DX conversion test.
180s 
180s All 2 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DihCovar
180s 
180s   CPPTRAJ: Dihedral Covariance Matrix Test
180s 
180s All 3 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CurveFit
180s 
180s   CPPTRAJ: Curve fitting test.
180s 
180s   CPPTRAJ: Curve fitting multi-exponential tests.
180s 
180s   CPPTRAJ: Curve fitting, custom output range.
180s 
180s All 6 comparisons passed.
180s 
180s ********************************************************************************
180s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Multicurve
180s 
180s   CPPTRAJ: Multicurve test
181s 
181s All 1 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DataSetAverage
181s 
181s   CPPTRAJ: Data set averaging and averaging over all sets test.
181s 
181s All 2 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_VectorMath
181s 
181s   CPPTRAJ: Vector dot/cross product test
181s 
181s All 2 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Esander
181s   SANDER energy tests (long) requires SANDER API from AmberTools.
181s   Cpptraj was compiled without SANDER API from AmberTools support.
181s   SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run.
181s   SKIP: SANDER energy tests (long)
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Esander_Short
181s   Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools.
181s   Cpptraj was compiled without SANDER API from AmberTools support.
181s   SKIP: Energy via sander API short tests (GB/PME)
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Temperature
181s 
181s   CPPTRAJ: Temperature test.
181s 
181s   CPPTRAJ: Temperature with SHAKE on hydrogens.
181s 
181s   CPPTRAJ: Temperature with SHAKE on all atoms.
181s 
181s   CPPTRAJ: Temperature calc with extra points.
181s 
181s All 5 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Spline
181s 
181s   CPPTRAJ: Spline test
181s 
181s All 1 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_KDE
181s 
181s   CPPTRAJ: KDE test.
181s 
181s   CPPTRAJ: KDE with Kullback-Leibler divergence test
181s 
181s All 4 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Wavelet
181s 
181s   CPPTRAJ: Wavelet analysis test
181s 
181s   CPPTRAJ: Wavelet WAFEX test
181s 
181s All 3 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CIF
181s 
181s   CPPTRAJ: CIF read test
181s 
181s   CPPTRAJ: Generate offset traj from PDB
181s 
181s   CPPTRAJ: Generate offset traj from CIF
181s 
181s All 2 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_PDB
181s 
181s   CPPTRAJ: PDB format read/write test
181s 
181s   CPPTRAJ: PQR file write with various radii
181s 
181s   CPPTRAJ: PDB filter alternate atom location IDs test
181s 
181s   CPPTRAJ: Adding PDB info to topology
181s 
181s All 10 comparisons passed.
181s 
181s ********************************************************************************
181s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Align
181s 
181s   CPPTRAJ: Align Tests.
181s 
181s   CPPTRAJ: Align, unit cell rotation/imaging test.
182s 
182s All 4 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_VelocityAutoCorr
182s 
182s   CPPTRAJ: Velocity autocorrelation test
182s 
182s All 3 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_VelFrc
182s 
182s   CPPTRAJ: Test combining coordinates, velocities, and forces.
182s 
182s   CPPTRAJ: Test using velocities as coordinates.
182s 
182s   CPPTRAJ: Test writing velocities (MDVEL)
182s 
182s   CPPTRAJ: Test using forces as coordinates.
182s 
182s   CPPTRAJ: Test writing forces (MDFRC)
182s 
182s   CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart.
182s 
182s   CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart.
182s 
182s All 5 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_RotateDihedral
182s 
182s   CPPTRAJ: Rotate dihedral to target value.
182s 
182s   CPPTRAJ: Rotate dihedral by increment
182s 
182s   CPPTRAJ: Rotate dihedral in TRAJ data set
182s 
182s All 3 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DataSetCmd
182s 
182s   CPPTRAJ: Data Set commands test
182s 
182s All 10 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Remap
182s 
182s   CPPTRAJ: Remap Test
182s 
182s All 1 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CompareTop
182s 
182s   CPPTRAJ: Compare topology test
182s 
182s All 1 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Filter
182s 
182s   CPPTRAJ: Basic filter test
182s 
182s   CPPTRAJ: Data filter test.
182s 
182s   CPPTRAJ: Filter matrix test.
182s 
182s All 5 comparisons passed.
182s 
182s ********************************************************************************
182s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CombineCrd
182s 
182s   CPPTRAJ: Combine COORDS test.
182s 
182s   CPPTRAJ: Combine COORDS test with box info.
182s 
182s   CPPTRAJ: Split coords and recombine test.
183s 
183s All 5 comparisons passed.
183s 
183s ********************************************************************************
183s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_TopInfo
183s 
183s   CPPTRAJ: Topology info print test.
183s 
183s   CPPTRAJ: Topology info with reference coords test
183s 
183s All 12 comparisons passed.
183s 
183s ********************************************************************************
183s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_GromacsTrr
183s 
183s   CPPTRAJ: TRR force/velocity read -> NetCDF write test
183s 
183s   CPPTRAJ: TRR force/velocity read -> TRR write test
183s 
183s   CPPTRAJ: CRD => TRR
183s 
183s   CPPTRAJ: TRR => CRD
183s 
183s   CPPTRAJ: CRD(1-5) => TRR
183s 
183s   CPPTRAJ: CRD(6-10) => TRR
183s 
183s   CPPTRAJ: TRR (appended) => CRD
183s 
183s   CPPTRAJ: GMX: CRD with offset
183s 
183s   CPPTRAJ: GMX: TRR with offset
183s 
183s All 5 comparisons passed.
183s 
183s ********************************************************************************
183s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_GromacsXtc
183s 
183s   CPPTRAJ: XTC read test
183s 
183s   CPPTRAJ: CRD => XTC
183s 
183s   CPPTRAJ: XTC => CRD
183s 
183s   CPPTRAJ: CRD(1-5) => XTC
183s 
183s   CPPTRAJ: CRD(6-10) => XTC
183s 
183s   CPPTRAJ: XTC (appended) => CRD
183s 
183s   CPPTRAJ: GMX: CRD with offset
184s 
184s   CPPTRAJ: GMX: XTC with offset
184s 
184s All 4 comparisons passed.
184s 
184s ********************************************************************************
184s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_GromacsTNG
184s 
184s   CPPTRAJ: TNG read test
184s 
184s   CPPTRAJ: TNG read test (with offset)
184s 
184s All 6 comparisons passed.
184s 
184s ********************************************************************************
184s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Ewald
184s 
184s   CPPTRAJ: Direct sum test
184s 
184s   CPPTRAJ: Ewald test (NaCl crystal)
184s 
184s   CPPTRAJ: Ewald test (trunc. oct)
185s 
185s   CPPTRAJ: Ewald test (partial system, trunc. oct)
185s   Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
185s   Skipped test: Ewald test (trunc. oct), 10 frames
185s   Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run.
185s   Skipped test: Ewald test (ortho), 10 frames
185s 
185s All 4 comparisons passed.
185s 2 comparisons skipped.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LibPME
185s 
185s   CPPTRAJ: Particle mesh Ewald test (NaCl crystal)
185s 
185s   CPPTRAJ: Particle mesh Ewald test (trunc. oct)
185s 
185s   CPPTRAJ: Particle mesh Ewald test (ortho)
185s 
185s   CPPTRAJ: Particle mesh Ewald test (ortho, with mask)
185s 
185s   CPPTRAJ: PME test (partial system, trunc. oct)
185s   PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run.
185s   Skipped test: PME test (trunc. oct), 10 frames
185s 
185s All 5 comparisons passed.
185s 1 comparisons skipped.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LJ_PME
185s 
185s   CPPTRAJ: LJ PME test.
185s 
185s   CPPTRAJ: LJ PME kappa sweep test, 0.25
185s 
185s   CPPTRAJ: LJ PME kappa sweep test, 0.35
185s 
185s   CPPTRAJ: LJ PME kappa sweep test, 0.45
185s 
185s   CPPTRAJ: LJ PME kappa sweep test, 0.5
185s 
185s   CPPTRAJ: LJ with switch function test
185s 
185s All 5 comparisons passed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_TI
185s 
185s   CPPTRAJ: TI analysis test.
185s 
185s All 5 comparisons passed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_FixImagedBonds
185s 
185s   CPPTRAJ: Fix imaged bonds test (Ortho.)
185s 
185s   CPPTRAJ: Fix imaged bonds test (Non-ortho.)
185s 
185s All 2 comparisons passed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Distance
185s 
185s   CPPTRAJ: Distance tests
185s 
185s   CPPTRAJ: Orthogonal imaged distance
185s 
185s   CPPTRAJ: Non-orthogonal imaged distance
185s 
185s All 3 comparisons passed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Volume
185s 
185s   CPPTRAJ: Volume tests
185s 
185s All 1 comparisons passed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_SetVelocity
185s 
185s   CPPTRAJ: Set Velocity test
185s 
185s   CPPTRAJ: Scale velocity test
185s 
185s   1 out of 3 comparisons failed.
185s 
185s ********************************************************************************
185s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Remlog
185s 
185s   CPPTRAJ: Replica log read/analyze test.
185s 
185s All 7 comparisons passed.
185s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_AreaPerMol
186s 
186s   CPPTRAJ: Area per molecule test
186s 
186s All 6 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DistBasedMask
186s 
186s   CPPTRAJ: Distance-based atom mask tests (atom, residue)
186s 
186s   CPPTRAJ: Distance-based atom mask tests (molecule)
186s 
186s All 6 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Calc
186s 
186s   CPPTRAJ: Calc test
186s 
186s   CPPTRAJ: Calc test with data sets
186s 
186s   CPPTRAJ: Test math functions
186s 
186s All 4 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CalcState
186s 
186s   CPPTRAJ: Calcstate test
186s 
186s All 4 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Change
186s 
186s   CPPTRAJ: Change atom and residue name tests
186s 
186s   CPPTRAJ: Change chain ID test
186s 
186s   CPPTRAJ: Change chain ID of COORDS set test
186s 
186s All 3 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CreateReservoir
186s 
186s   CPPTRAJ: Create RREMD NetCDF reservoir test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_FixAtomOrder
186s 
186s   CPPTRAJ: Out of order molecules test
186s 
186s All 2 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_LowestCurve
186s 
186s   CPPTRAJ: LowestCurve test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_MinImage
186s 
186s   CPPTRAJ: Minimum Image test.
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Regress
186s 
186s   CPPTRAJ: Linear regression test.
186s 
186s All 3 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Rst
186s 
186s   CPPTRAJ: Generate restraints (rst) test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Pairwise
186s 
186s   CPPTRAJ: Pairwise tests
186s 
186s   CPPTRAJ: Pairwise test, partial system
186s 
186s All 10 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_ParmBox
186s 
186s   CPPTRAJ: Parmbox test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Solvent
186s 
186s   CPPTRAJ: Test solvent command with closest
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Translate
186s 
186s   CPPTRAJ: Translate test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_ReplicateCell
186s 
186s   CPPTRAJ: Replicate cell test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_ScaleDihedralK
186s 
186s   CPPTRAJ: Scale dihedral force constant test
186s 
186s   CPPTRAJ: Scale dihedral force constant with 'useall'
186s 
186s All 2 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_PhiPsi
186s 
186s   CPPTRAJ: Phipsi test
186s 
186s All 1 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Control
186s 
186s   CPPTRAJ: Loop tests
186s 
186s   CPPTRAJ: Test set command
186s 
186s   CPPTRAJ: Test reading comma-separated list of strings
186s 
186s   CPPTRAJ: Test nested loops and variables in loops
186s 
186s   CPPTRAJ: Test loop over data set blocks
186s 
186s   CPPTRAJ: Test for filename wildcards and oversets
186s 
186s All 13 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_InfraredSpec
186s 
186s   CPPTRAJ: Infrared spectrum calculation test
186s 
186s All 2 comparisons passed.
186s 
186s ********************************************************************************
186s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Cphstats
186s 
186s   CPPTRAJ: Explicit pH REMD ensemble data read / sort
186s 
186s   CPPTRAJ: Constant pH stats test
186s 
186s   CPPTRAJ: Sorted implicit constant pH stats test
186s 
186s   CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats
186s 
186s   CPPTRAJ: Unsorted pH read/write test
187s 
187s All 16 comparisons passed.
187s 
187s ********************************************************************************
187s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CmdLine
187s 
187s   CPPTRAJ: Command line trajectory args test, part 1
187s 
187s   CPPTRAJ: Command line test trajectory args test, part 2
187s 
187s   CPPTRAJ: Command line wildcard test, part 1
187s 
187s   CPPTRAJ: Command line wildcard test, part 2
187s 
187s All 2 comparisons passed.
187s 
187s ********************************************************************************
187s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_XYZformat
187s 
187s   CPPTRAJ: XYZ format write
187s 
187s   CPPTRAJ: Atom XYZ format read, test 1
187s 
187s   CPPTRAJ: Atom XYZ format read, test 2
187s 
187s   CPPTRAJ: Atom XYZ format read, test 3
187s 
187s   CPPTRAJ: Atom XYZ format read, test 4
187s 
187s   CPPTRAJ: Atom XYZ format read, test 5
187s 
187s   CPPTRAJ: Atom XYZ format read, test 6
187s 
187s All 6 comparisons passed.
187s 
187s ********************************************************************************
187s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Hausdorff
187s 
187s   CPPTRAJ: Simple Hausdorff distance test.
187s 
187s   CPPTRAJ: Hausdorff distance of 2D rms output test.
187s 
187s   CPPTRAJ: Hausdorff distance of 2D rms output test.
187s 
187s All 3 comparisons passed.
187s 
187s ********************************************************************************
187s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_CatCrd
187s 
187s   CPPTRAJ: Concatenate COORDS data set test
187s 
187s All 1 comparisons passed.
187s 
187s ********************************************************************************
187s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_XtalSymm
187s 
187s   CPPTRAJ: XtalSymm Reference
187s 
187s   CPPTRAJ: XtalSymm Reimaging by Atom
188s 
188s   CPPTRAJ: XtalSymm Reimaging by Molecule
189s 
189s All 3 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Time
189s 
189s   CPPTRAJ: Add time to restart test
189s 
189s   CPPTRAJ: Remove time from restart test
189s 
189s   CPPTRAJ: Add time to trajectory test
189s 
189s   CPPTRAJ: Modify time info test.
189s 
189s All 4 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_SplitCoords
189s 
189s   CPPTRAJ: SplitCoords test
189s 
189s All 1 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_DihedralRMS
189s 
189s   CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.)
189s 
189s   CPPTRAJ: Dihedral RMSD test (to previous)
189s 
189s   CPPTRAJ: Dihedral RMS fluctuation test.
189s 
189s All 5 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Slope
189s 
189s   CPPTRAJ: Finite difference test.
189s 
189s All 1 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Diagmatrix
189s 
189s   CPPTRAJ: MW covariance matrix thermo analysis test
189s 
189s All 1 comparisons passed.
189s 
189s ********************************************************************************
189s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Emin
189s 
189s   CPPTRAJ: Basic energy minimization test.
189s 
189s   CPPTRAJ: Energy minimization with angle term test.
189s 
189s   CPPTRAJ: Energy minimization with dihedral and 1-4 terms test.
189s 
189s   CPPTRAJ: Energy minimization with nonbond term test.
189s 
189s   CPPTRAJ: OpenMM basic energy minimization tests (bonds)
189s 
189s   CPPTRAJ: OpenMM basic energy minimization tests (angles)
189s 
189s   CPPTRAJ: OpenMM basic energy minimization tests (dihedrals)
189s 
189s   CPPTRAJ: OpenMM basic energy minimization tests (nonbonds)
190s 
190s   CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME)
190s 
190s All 9 comparisons passed.
190s 
190s ********************************************************************************
190s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_EvalPlateau
190s 
190s   CPPTRAJ: Evalulate plateau test
191s 
191s All 2 comparisons passed.
191s 
191s ********************************************************************************
191s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Graft
191s 
191s   CPPTRAJ: Graft test
191s 
191s All 1 comparisons passed.
191s 
191s ********************************************************************************
191s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Flatten
191s 
191s   CPPTRAJ: Flatten test.
191s 
191s All 1 comparisons passed.
191s 
191s ********************************************************************************
191s TEST: /tmp/autopkgtest.cHW7oc/build.pfG/src/test/Test_Random
191s 
191s   CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs
191s 
191s   CPPTRAJ: PCG32 RNG test.
191s 
191s   CPPTRAJ: Test Stdlib RNG
191s 
191s   CPPTRAJ: Test Mersenne Twister RNG
191s 
191s All 4 comparisons passed.
191s 
191s make[1]: Leaving directory '/tmp/autopkgtest.cHW7oc/build.pfG/src/test'
191s lrwxrwxrwx 1 ubuntu ubuntu 16 Mar 14 19:39 ../bin/cpptraj -> /usr/bin/cpptraj
191s ===================== TEST SUMMARY ======================
191s   851 out of 859 comparisons OK (2 failed, 0 warnings, 6 skipped).
191s   480 out of 480 program executions completed.
191s   168 out of 173 tests completed with no issues.
191s   2 tests skipped.
191s =========================================================
191s make: Leaving directory '/tmp/autopkgtest.cHW7oc/build.pfG/src/test'
191s make: *** [Makefile:662: summary] Error 2
191s autopkgtest [19:40:01]: test command1: -----------------------]
192s command1             FAIL non-zero exit status 2
192s autopkgtest [19:40:02]: test command1:  - - - - - - - - - - results - - - - - - - - - -
192s autopkgtest [19:40:02]: test command1:  - - - - - - - - - - stderr - - - - - - - - - -
192s make: *** [Makefile:662: summary] Error 2
192s autopkgtest [19:40:02]: @@@@@@@@@@@@@@@@@@@@ summary
192s command1             FAIL non-zero exit status 2
207s Creating nova instance adt-noble-ppc64el-cpptraj-20240314-193650-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID 438daa89-732e-4eab-98ca-4d7eade8166d)...