Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/takeshi/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/takeshi/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/takeshi/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: f098c864b6652807ea943c4404d28873e3973601
TOOLS: b0af2521cbed1f2bde597ef1c5406efa376a6f85
DEMOS: 48c9239db73b9a8c828954d9215c983b9f144c92
Python: `/home/benchmark/prefix/takeshi/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 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_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 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
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict/command.mpi.sh
Running Test features_pdb_mpi
ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_pdb_mpi/command.mpi.sh
Finished simple_cycpep_predict_terminal_disulfide in 291 seconds [~ 802 test (99.62732919254658%) 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_terminal_disulfide_tails in 362 seconds [~ 803 test (99.75155279503106%) 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_lanthionine in 850 seconds [~ 804 test (99.87577639751552%) 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_cterm_isopeptide_lariat_tailless in 881 seconds [~ 805 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_sidechain_isopeptide in 886 seconds [~ 805 test (100.0%) started, 0 in queue, 23 running]
Finished simple_cycpep_predict_cterm_isopeptide_lariat in 890 seconds [~ 805 test (100.0%) started, 0 in queue, 22 running]
Finished simple_cycpep_predict_sidechain_isopeptide_reverse in 931 seconds [~ 805 test (100.0%) started, 0 in queue, 21 running]
Finished simple_cycpep_predict_nterm_isopeptide_lariat_tailless in 975 seconds [~ 805 test (100.0%) started, 0 in queue, 20 running]
dumping features_IntegrationTest.db3_1 ...
dumping features_IntegrationTest.db3_2 ...
merging dumps ...
off
exclusive
analyzing database ...
Finished features_pdb_mpi in 980 seconds [~ 805 test (100.0%) started, 0 in queue, 19 running]
Finished simple_cycpep_predict_thioether_lariat in 985 seconds [~ 805 test (100.0%) started, 0 in queue, 18 running]
Finished simple_cycpep_predict_nterm_isopeptide_lariat in 999 seconds [~ 805 test (100.0%) started, 0 in queue, 17 running]
Finished mpi_simple_cycpep_predict_4level in 1006 seconds [~ 805 test (100.0%) started, 0 in queue, 16 running]
Finished recon_design_mpi in 1015 seconds [~ 805 test (100.0%) started, 0 in queue, 15 running]
Finished mpi_simple_cycpep_predict in 1037 seconds [~ 805 test (100.0%) started, 0 in queue, 14 running]
Finished simple_cycpep_predict_beta_thioether_lariat in 1098 seconds [~ 805 test (100.0%) started, 0 in queue, 13 running]
Finished mpi_simple_cycpep_predict_computing_pnear_to_all in 1171 seconds [~ 805 test (100.0%) started, 0 in queue, 12 running]
Finished simple_cycpep_predict_bondangle_bondlength in 1189 seconds [~ 805 test (100.0%) started, 0 in queue, 11 running]
Finished threefold_symm_peptide_design in 887 seconds [~ 805 test (100.0%) started, 0 in queue, 10 running]
Finished simple_cycpep_predict_terminal_disulfide_tails_2 in 1309 seconds [~ 805 test (100.0%) started, 0 in queue, 9 running]
Finished backbonegridsampler_nstruct_mode in 495 seconds [~ 805 test (100.0%) started, 0 in queue, 8 running]
Finished simple_cycpep_predict_design in 536 seconds [~ 805 test (100.0%) started, 0 in queue, 7 running]
Finished database_md5 in 1192 seconds [~ 805 test (100.0%) started, 0 in queue, 6 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 1590 seconds [~ 805 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 1610 seconds [~ 805 test (100.0%) started, 0 in queue, 4 running]
******** (C) Copyright Rosetta Commons Member Institutions. ***************
******** (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. **********
* 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 1628 seconds [~ 805 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_with_helix_globals in 1798 seconds [~ 805 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 in 1812 seconds [~ 805 test (100.0%) started, 0 in queue, 1 running]
*** Test replica_docking exceeded the timeout=3600 and will be killed! [2025-02-04 20:20:07.282947]
Finished replica_docking in 3600 seconds [~ 805 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
──────────────── 'takeshi' comparing commits:20644 linux.gcc.mpi.serialization.integration.mpi test_id=850147 vs. main:62142 previous_test_id=847973 ────────────────
{
"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": 62142
},
"state": "failed",
"test_id": 847973
},
"summary": {
"failed": 2,
"failed_tests": [
"replica_docking",
"recon_design_mpi"
],
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62142/recon_design_mpi/log_main and /home/benchmark/working_dir/commits:20644/recon_design_mpi/log_main differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/recon_design_mpi/log_main /home/benchmark/working_dir/commits:20644/recon_design_mpi/log_main\r\n1a2\r\n> ******** (C) Copyright Rosetta Commons Member Institutions. ***************\r\n4d4\r\n< ******** (C) Copyright Rosetta Commons Member Institutions. ***************\r\n",
"state": "failed"
},
"replica_docking": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62142/replica_docking/log and /home/benchmark/working_dir/commits:20644/replica_docking/log differ\r\nFiles /home/benchmark/working_dir/main:62142/replica_docking/logs/log_0 and /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_0 differ\r\nFiles /home/benchmark/working_dir/main:62142/replica_docking/logs/log_1 and /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_1 differ\r\nFiles /home/benchmark/working_dir/main:62142/replica_docking/logs/log_2 and /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_2 differ\r\nFiles /home/benchmark/working_dir/main:62142/replica_docking/logs/log_3 and /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_3 differ\r\nFiles /home/benchmark/working_dir/main:62142/replica_docking/.test_got_timeout_kill.log and /home/benchmark/working_dir/commits:20644/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:62142/replica_docking/log /home/benchmark/working_dir/commits:20644/replica_docking/log\r\n1a2\r\n> ******** (C) Copyright Rosetta Commons Member Institutions. ***************\r\n4d4\r\n< ******** (C) Copyright Rosetta Commons Member Institutions. ***************\r\n14c14\r\n< mpirun noticed that process rank 3 with PID 63971 on node nobu-4 exited on signal 9 (Killed).\r\n---\r\n> mpirun noticed that process rank 3 with PID 2236065 on node takeshi exited on signal 9 (Killed).\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/replica_docking/logs/log_0 /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_0\r\n0a1,73\r\n> core.init: (0) Rosetta version: 2025.03.post.dev+7.HEAD.f098c86 f098c864b6652807ea943c4404d28873e3973601 git@github.com:RosettaCommons/rosetta.git 2025-02-04T18:26:12\r\n> core.init: (0) Rosetta extras: [mpi, serialization]\r\n> core.init: (0) command: ROSETTA/source/bin/rosetta_scripts.mpiserialization.linuxgccrelease_debug -in:path:database_cache_dir ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug @flags_replica_dock -database ROSETTA/database -testing:INTEGRATION_TEST\r\n> basic.random.init_random_generator: (0) Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\r\n> basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\r\n> protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter\r\n> protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs\r\n> protocols.jd2.PDBJobInputter: (0) pushed P.pdb nstruct indices 1 - 4\r\n> core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 985 residue types\r\n> core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 8.01 seconds.\r\n> core.import_pose.import_pose: (0) File 'native.pdb' automatically determined to be of type PDB\r\n> core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 31\r\n> core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 31\r\n> core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 166\r\n> core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 253\r\n> core.pack.pack_missing_sidechains: (0) packing residue number 31 because of missing atom number 8 atom name CE \r\n> core.pack.task: (0) Packer task: initialize from command line() \r\n> core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015\r\n> core.scoring.etable: (0) Starting energy table calculation\r\n> core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well\r\n> core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6)\r\n> core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6)\r\n> core.scoring.etable: (0) Finished calculating energy tables.\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\r\n> core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\r\n> basic.io.database: (0) Database file opened: scoring/score_functions/elec_cp_reps.dat\r\n> core.scoring.elec.util: (0) Read 40 countpair representative atoms\r\n> core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib_fixes_enable option is true.\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/replica_docking/logs/log_1 /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_1\r\n0a1,73\r\n> core.init: (1) Rosetta version: 2025.03.post.dev+7.HEAD.f098c86 f098c864b6652807ea943c4404d28873e3973601 git@github.com:RosettaCommons/rosetta.git 2025-02-04T18:26:12\r\n> core.init: (1) Rosetta extras: [mpi, serialization]\r\n> core.init: (1) command: ROSETTA/source/bin/rosetta_scripts.mpiserialization.linuxgccrelease_debug -in:path:database_cache_dir ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug @flags_replica_dock -database ROSETTA/database -testing:INTEGRATION_TEST\r\n> basic.random.init_random_generator: (1) Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111112\r\n> basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=1111112 RG_type=mt19937\r\n> protocols.jd2.PDBJobInputter: (1) Instantiate PDBJobInputter\r\n> protocols.jd2.PDBJobInputter: (1) PDBJobInputter::fill_jobs\r\n> protocols.jd2.PDBJobInputter: (1) pushed P.pdb nstruct indices 1 - 4\r\n> core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 985 residue types\r\n> core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 7.96 seconds.\r\n> core.import_pose.import_pose: (1) File 'native.pdb' automatically determined to be of type PDB\r\n> core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: CE on residue LYS 31\r\n> core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: NZ on residue LYS 31\r\n> core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 166\r\n> core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 253\r\n> core.pack.pack_missing_sidechains: (1) packing residue number 31 because of missing atom number 8 atom name CE \r\n> core.pack.task: (1) Packer task: initialize from command line() \r\n> core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015\r\n> core.scoring.etable: (1) Starting energy table calculation\r\n> core.scoring.etable: (1) smooth_etable: changing atr/rep split to bottom of energy well\r\n> core.scoring.etable: (1) smooth_etable: spline smoothing lj etables (maxdis = 6)\r\n> core.scoring.etable: (1) smooth_etable: spline smoothing solvation etables (max_dis = 6)\r\n> core.scoring.etable: (1) Finished calculating energy tables.\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/all.ramaProb\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\r\n> core.scoring.P_AA: (1) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\r\n> basic.io.database: (1) Database file opened: scoring/score_functions/elec_cp_reps.dat\r\n> core.scoring.elec.util: (1) Read 40 countpair representative atoms\r\n> core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib_fixes_enable option is true.\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/replica_docking/logs/log_2 /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_2\r\n1c1\r\n< core.init: (2) Rosetta version: 2025.03.post.dev+2.HEAD.a1e0e99 a1e0e9908af05092868be83ae85c6c7c4b04fcf6 git@github.com:RosettaCommons/rosetta.git 2025-01-16T10:26:25\r\n---\r\n> core.init: (2) Rosetta version: 2025.03.post.dev+7.HEAD.f098c86 f098c864b6652807ea943c4404d28873e3973601 git@github.com:RosettaCommons/rosetta.git 2025-02-04T18:26:12\r\n10c10\r\n< core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 3.92 seconds.\r\n---\r\n> core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 8.02 seconds.\r\n42,45c42,98\r\n< core.pack.dunbrack.RotamerLibrary: (2) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\r\n< core.pack.dunbrack.RotamerLibrary: (2) Binary rotamer library selected: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\r\n< core.pack.dunbrack.RotamerLibrary: (2) Using Dunbrack library binary file 'ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\r\n< core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.31 seconds to load from binary\r\n---\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (2) Finished reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 195.13 seconds to load from ASCII\r\n> core.pack.dunbrack.RotamerLibrary: (2) Memory usage: \r\n> core.pack.dunbrack.RotamerLibrary: (2) CYS with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) ILE with 842400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) LYS with 8335520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) LEU with 842400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) MET with 2803920 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) PRO with 209320 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) ARG with 8563824 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) SER with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) THR with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) VAL with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) ASP with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) GLU with 31361400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) PHE with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) HIS with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) ASN with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) GLN with 34161624 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) TRP with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) TYR with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (2) Total memory on Dunbrack Libraries: 153284952 bytes.\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/replica_docking/logs/log_3 /home/benchmark/working_dir/commits:20644/replica_docking/logs/log_3\r\n1c1\r\n< core.init: (3) Rosetta version: 2025.03.post.dev+2.HEAD.a1e0e99 a1e0e9908af05092868be83ae85c6c7c4b04fcf6 git@github.com:RosettaCommons/rosetta.git 2025-01-16T10:26:25\r\n---\r\n> core.init: (3) Rosetta version: 2025.03.post.dev+7.HEAD.f098c86 f098c864b6652807ea943c4404d28873e3973601 git@github.com:RosettaCommons/rosetta.git 2025-02-04T18:26:12\r\n10c10\r\n< core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 3.91 seconds.\r\n---\r\n> core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 7.99 seconds.\r\n42,45c42,101\r\n< core.pack.dunbrack.RotamerLibrary: (3) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\r\n< core.pack.dunbrack.RotamerLibrary: (3) Binary rotamer library selected: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\r\n< core.pack.dunbrack.RotamerLibrary: (3) Using Dunbrack library binary file 'ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.\r\n< core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 0.31 seconds to load from binary\r\n---\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.rotamers.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.densities.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbind.chi2.Definitions.lib\r\n> core.pack.dunbrack.RotamerLibrary: (3) Finished reading Dunbrack Libraries\r\n> core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 200.02 seconds to load from ASCII\r\n> core.pack.dunbrack.RotamerLibrary: (3) Memory usage: \r\n> core.pack.dunbrack.RotamerLibrary: (3) CYS with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) ILE with 842400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) LYS with 8335520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) LEU with 842400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) MET with 2803920 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) PRO with 209320 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) ARG with 8563824 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) SER with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) THR with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) VAL with 250800 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) ASP with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) GLU with 31361400 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) PHE with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) HIS with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) ASN with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) GLN with 34161624 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) TRP with 11326928 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) TYR with 10393520 bytes\r\n> core.pack.dunbrack.RotamerLibrary: (3) Total memory on Dunbrack Libraries: 153284952 bytes.\r\n> core.pack.dunbrack.RotamerLibrary: (3) Random tempname will be: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/dun10_binaryBGU1IWP5\r\n> core.pack.dunbrack.RotamerLibrary: (3) Opening file ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/dun10_binaryBGU1IWP5 for output.\r\n> core.pack.dunbrack.RotamerLibrary: (3) Moving temporary file to ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62142/replica_docking/.test_got_timeout_kill.log /home/benchmark/working_dir/commits:20644/replica_docking/.test_got_timeout_kill.log\r\n1c1\r\n< *** Test replica_docking exceeded the timeout=3600 and will be killed! [2025-01-16 13:22:51.066030]\r\n---\r\n> *** Test replica_docking exceeded the timeout=3600 and will be killed! [2025-02-04 20:20:07.282947]\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"
}
}
}