Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/hojo-1/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin mode=release_debug cxx=gcc extras=mpi,serialization -j24
Running: unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/activate && cd /home/benchmark/rosetta/tests/integration && python ./integration.py --mode=release_debug --compiler=gcc --extras=mpi,serialization --timeout=3600 -j24 --skip-comparison --suffix mpi --additional_flags "-in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/mpiserialization.linuxgccrelease_debug"
Running integration script...
Command line: unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/activate && cd /home/benchmark/rosetta/tests/integration && python ./integration.py --mode=release_debug --compiler=gcc --extras=mpi,serialization --timeout=3600 -j24 --skip-comparison --suffix mpi --additional_flags "-in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/mpiserialization.linuxgccrelease_debug"
Using Rosetta source dir at: /home/benchmark/rosetta/source
Using Rosetta database dir at:/home/benchmark/rosetta/database
Current Versions Tested:
MAIN: 8e1ce431a48a2c8d8c3307031efc098fd9289877
TOOLS: b0af2521cbed1f2bde597ef1c5406efa376a6f85
DEMOS: 48c9239db73b9a8c828954d9215c983b9f144c92
Verifying Python /usr/bin/python2 to have version 2.*...
/usr/bin/python2 -c 'import sys; sys.exit(sys.version_info[0] != 2)'
Verifying Python /home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/python to have version 3.*...
/home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/python -c 'import sys; sys.exit(sys.version_info[0] != 3)'
Python: `/home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/python`
Python2: `/usr/bin/python2`
Python3: `/home/benchmark/prefix/hojo-1/linux/python_virtual_environments/python-3.9/f916a9c27c93a1801304b72f29630408/bin/python`
Outdir: new
Running Test simple_cycpep_predict_thioether_lariat
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_thioether_lariat/command.mpi.sh
Running Test simple_cycpep_predict_terminal_disulfide_tails_2
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails_2/command.mpi.sh
Running Test simple_cycpep_predict_terminal_disulfide_tails
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails/command.mpi.sh
Running Test simple_cycpep_predict_terminal_disulfide
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide/command.mpi.sh
Running Test simple_cycpep_predict_sidechain_isopeptide_reverse
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide_reverse/command.mpi.sh
Running Test simple_cycpep_predict_sidechain_isopeptide
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide/command.mpi.sh
Running Test simple_cycpep_predict_nterm_isopeptide_lariat_tailless
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat_tailless/command.mpi.sh
Running Test simple_cycpep_predict_nterm_isopeptide_lariat
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat/command.mpi.sh
Running Test simple_cycpep_predict_lanthionine
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_lanthionine/command.mpi.sh
Running Test simple_cycpep_predict_cterm_isopeptide_lariat_tailless
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat_tailless/command.mpi.sh
Running Test simple_cycpep_predict_cterm_isopeptide_lariat
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat/command.mpi.sh
Running Test simple_cycpep_predict_bondangle_bondlength
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_bondangle_bondlength/command.mpi.sh
Running Test simple_cycpep_predict_beta_thioether_lariat
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_beta_thioether_lariat/command.mpi.sh
Running Test replica_docking
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/replica_docking/command.mpi.sh
Running Test mpi_simple_cycpep_predict_computing_pnear_to_all
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpi_simple_cycpep_predict_computing_pnear_to_all/command.mpi.sh
Running Test recon_design_mpi
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/recon_design_mpi/command.mpi.sh
Running Test mpi_simple_cycpep_predict_4level
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpi_simple_cycpep_predict_4level/command.mpi.sh
Running Test mpi_simple_cycpep_predict
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpi_simple_cycpep_predict/command.mpi.sh
Running Test helical_bundle_predict_skipping_residues
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_skipping_residues/command.mpi.sh
Running Test helical_bundle_predict_sequence
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_sequence/command.mpi.sh
Running Test helical_bundle_predict_psipred_with_helix_globals
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_psipred_with_helix_globals/command.mpi.sh
Running Test helical_bundle_predict_psipred
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_psipred/command.mpi.sh
Running Test helical_bundle_predict
Running Test features_pdb_mpi
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict/command.mpi.sh
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_pdb_mpi/command.mpi.sh
Finished simple_cycpep_predict_lanthionine in 155 seconds [~ 799 test (99.62593516209476%) started, 3 in queue, 24 running]
Running Test database_md5
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/database_md5/command.mpi.sh
Finished simple_cycpep_predict_sidechain_isopeptide in 184 seconds [~ 800 test (99.75062344139651%) started, 2 in queue, 24 running]
Running Test threefold_symm_peptide_design
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/threefold_symm_peptide_design/command.mpi.sh
Finished simple_cycpep_predict_cterm_isopeptide_lariat in 187 seconds [~ 801 test (99.87531172069825%) started, 1 in queue, 24 running]
Running Test simple_cycpep_predict_design
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_design/command.mpi.sh
Finished simple_cycpep_predict_nterm_isopeptide_lariat_tailless in 188 seconds [~ 802 test (100.0%) started, 0 in queue, 24 running]
Running Test backbonegridsampler_nstruct_mode
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backbonegridsampler_nstruct_mode/command.mpi.sh
Finished simple_cycpep_predict_cterm_isopeptide_lariat_tailless in 195 seconds [~ 802 test (100.0%) started, 0 in queue, 23 running]
dumping features_IntegrationTest.db3_1 ...
dumping features_IntegrationTest.db3_2 ...
merging dumps ...
off
exclusive
analyzing database ...
Finished features_pdb_mpi in 201 seconds [~ 802 test (100.0%) started, 0 in queue, 22 running]
Finished simple_cycpep_predict_nterm_isopeptide_lariat in 207 seconds [~ 802 test (100.0%) started, 0 in queue, 21 running]
Finished recon_design_mpi in 225 seconds [~ 802 test (100.0%) started, 0 in queue, 20 running]
Finished simple_cycpep_predict_sidechain_isopeptide_reverse in 230 seconds [~ 802 test (100.0%) started, 0 in queue, 19 running]
Finished simple_cycpep_predict_terminal_disulfide in 258 seconds [~ 802 test (100.0%) started, 0 in queue, 18 running]
Finished mpi_simple_cycpep_predict in 263 seconds [~ 802 test (100.0%) started, 0 in queue, 17 running]
Finished simple_cycpep_predict_thioether_lariat in 289 seconds [~ 802 test (100.0%) started, 0 in queue, 16 running]
Finished mpi_simple_cycpep_predict_4level in 298 seconds [~ 802 test (100.0%) started, 0 in queue, 15 running]
Finished simple_cycpep_predict_terminal_disulfide_tails in 309 seconds [~ 802 test (100.0%) started, 0 in queue, 14 running]
Finished backbonegridsampler_nstruct_mode in 130 seconds [~ 802 test (100.0%) started, 0 in queue, 13 running]
Finished mpi_simple_cycpep_predict_computing_pnear_to_all in 381 seconds [~ 802 test (100.0%) started, 0 in queue, 12 running]
Finished threefold_symm_peptide_design in 213 seconds [~ 802 test (100.0%) started, 0 in queue, 11 running]
Finished simple_cycpep_predict_beta_thioether_lariat in 399 seconds [~ 802 test (100.0%) started, 0 in queue, 10 running]
Finished simple_cycpep_predict_bondangle_bondlength in 460 seconds [~ 802 test (100.0%) started, 0 in queue, 9 running]
Finished simple_cycpep_predict_terminal_disulfide_tails_2 in 500 seconds [~ 802 test (100.0%) started, 0 in queue, 8 running]
Finished simple_cycpep_predict_design in 429 seconds [~ 802 test (100.0%) started, 0 in queue, 7 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
Finished helical_bundle_predict_skipping_residues in 785 seconds [~ 802 test (100.0%) started, 0 in queue, 6 running]
Finished database_md5 in 655 seconds [~ 802 test (100.0%) started, 0 in queue, 5 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
Finished helical_bundle_predict_sequence in 819 seconds [~ 802 test (100.0%) started, 0 in queue, 4 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
Finished helical_bundle_predict in 831 seconds [~ 802 test (100.0%) started, 0 in queue, 3 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
Finished helical_bundle_predict_psipred in 923 seconds [~ 802 test (100.0%) started, 0 in queue, 2 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
Finished helical_bundle_predict_psipred_with_helix_globals in 951 seconds [~ 802 test (100.0%) started, 0 in queue, 1 running]
*** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-05-14 17:53:48.684488]
Finished replica_docking in 3600 seconds [~ 802 test (100.0%) started, 0 in queue, 0 running]
Skipping comparison/analysis phase because command line option "--skip-comparison" was specified...
Missing new/runtimes.yaml
──────────────── 'hojo-1' comparing commits:20420 linux.gcc.mpi.serialization.integration.mpi test_id=828529 vs. main:62109 previous_test_id=827817 ────────────────
{
"compared_with_test": {
"full_name": "linux.gcc.mpi.serialization.integration.mpi",
"name": "integration.mpi",
"platform": {
"compiler": "gcc",
"extras": [
"mpi",
"serialization"
],
"os": "linux"
},
"platform_as_string": "linux.gcc.mpi.serialization",
"revision": {
"branch": "main",
"revision_id": 62109
},
"state": "failed",
"test_id": 827817
},
"summary": {
"failed": 1,
"failed_tests": [
"replica_docking"
],
"total": 28
},
"tests": {
"backbonegridsampler_nstruct_mode": {
"log": "",
"state": "passed"
},
"database_md5": {
"log": "",
"state": "passed"
},
"features_pdb_mpi": {
"log": "",
"state": "passed"
},
"helical_bundle_predict": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred_with_helix_globals": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_sequence": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_skipping_residues": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict_4level": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict_computing_pnear_to_all": {
"log": "",
"state": "passed"
},
"recon_design_mpi": {
"log": "",
"state": "passed"
},
"replica_docking": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62109/replica_docking/log and /home/benchmark/working_dir/commits:20420/replica_docking/log differ\r\nFiles /home/benchmark/working_dir/main:62109/replica_docking/logs/log_2 and /home/benchmark/working_dir/commits:20420/replica_docking/logs/log_2 differ\r\nFiles /home/benchmark/working_dir/main:62109/replica_docking/logs/log_3 and /home/benchmark/working_dir/commits:20420/replica_docking/logs/log_3 differ\r\nFiles /home/benchmark/working_dir/main:62109/replica_docking/.test_got_timeout_kill.log and /home/benchmark/working_dir/commits:20420/replica_docking/.test_got_timeout_kill.log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/log /home/benchmark/working_dir/commits:20420/replica_docking/log\r\n14c14\r\n< mpirun noticed that process rank 5 with PID 49183 on node hojo-2 exited on signal 9 (Killed).\r\n---\r\n> mpirun noticed that process rank 5 with PID 605745 on node hojo-1 exited on signal 9 (Killed).\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/logs/log_2 /home/benchmark/working_dir/commits:20420/replica_docking/logs/log_2\r\n1c1\r\n< core.init: (2) Rosetta version: 2024.19.post.dev+1.HEAD.ec708a4 ec708a4c40449ea419c8fcac0d507440400bf75f git@github.com:RosettaCommons/rosetta.git 2024-05-07T14:50:27\r\n---\r\n> core.init: (2) Rosetta version: 2024.19.post.dev+43.HEAD.8e1ce43 8e1ce431a48a2c8d8c3307031efc098fd9289877 git@github.com:RosettaCommons/rosetta.git 2024-05-14T16:33:02\r\n10c10\r\n< core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 7.43 seconds.\r\n---\r\n> core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 7.53 seconds.\r\n45c45\r\n< core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.57 seconds to load from binary\r\n---\r\n> core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.51 seconds to load from binary\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/logs/log_3 /home/benchmark/working_dir/commits:20420/replica_docking/logs/log_3\r\n1c1\r\n< core.init: (3) Rosetta version: 2024.19.post.dev+1.HEAD.ec708a4 ec708a4c40449ea419c8fcac0d507440400bf75f git@github.com:RosettaCommons/rosetta.git 2024-05-07T14:50:27\r\n---\r\n> core.init: (3) Rosetta version: 2024.19.post.dev+43.HEAD.8e1ce43 8e1ce431a48a2c8d8c3307031efc098fd9289877 git@github.com:RosettaCommons/rosetta.git 2024-05-14T16:33:02\r\n10c10\r\n< core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 7.78 seconds.\r\n---\r\n> core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 7.54 seconds.\r\n45c45\r\n< core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 0.51 seconds to load from binary\r\n---\r\n> core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 0.55 seconds to load from binary\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/.test_got_timeout_kill.log /home/benchmark/working_dir/commits:20420/replica_docking/.test_got_timeout_kill.log\r\n1c1\r\n< *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-05-08 12:58:12.147951]\r\n---\r\n> *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-05-14 17:53:48.684488]\r\n\nCompare(...): Marking as \"Script failed\" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!\n",
"state": "script failed"
},
"simple_cycpep_predict_beta_thioether_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_bondangle_bondlength": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_design": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_lanthionine": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide_reverse": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_tails": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_tails_2": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_thioether_lariat": {
"log": "",
"state": "passed"
},
"threefold_symm_peptide_design": {
"log": "",
"state": "passed"
}
}
}