Branch: rosetta:commits 「revision: №20543」
Test: linux.gcc.mpi.serialization.integration.mpi
SubTest: replica_docking
SubTest files: 「file-system-view」
Daemon: takeshi    
State: replica_docking

Brief Diff: Files /home/benchmark/working_dir/main:62109/replica_docking/log and /home/benchmark/working_dir/commits:20543/replica_docking/log differ Files /home/benchmark/working_dir/main:62109/replica_docking/logs/log_0 and /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_0 differ Files /home/benchmark/working_dir/main:62109/replica_docking/logs/log_1 and /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_1 differ Files /home/benchmark/working_dir/main:62109/replica_docking/logs/log_2 and /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_2 differ Files /home/benchmark/working_dir/main:62109/replica_docking/logs/log_3 and /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_3 differ Files /home/benchmark/working_dir/main:62109/replica_docking/.test_got_timeout_kill.log and /home/benchmark/working_dir/commits:20543/replica_docking/.test_got_timeout_kill.log differ Full Diff: diff -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:20543/replica_docking/log 14c14 < mpirun noticed that process rank 5 with PID 49183 on node hojo-2 exited on signal 9 (Killed). --- > mpirun noticed that process rank 3 with PID 1174100 on node nobu-2 exited on signal 9 (Killed). diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/logs/log_0 /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_0 0a1,73 > core.init: (0) Rosetta version: 2024.19.post.dev+199.HEAD.edb0fc2 edb0fc2319eeef5a8236bffc5f224c6bdefeb198 git@github.com:RosettaCommons/rosetta.git 2024-10-03T14:35:02 > core.init: (0) Rosetta extras: [mpi, serialization] > 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 > basic.random.init_random_generator: (0) Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 > basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 > protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter > protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs > protocols.jd2.PDBJobInputter: (0) pushed P.pdb nstruct indices 1 - 4 > core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 985 residue types > core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 6.75 seconds. > core.import_pose.import_pose: (0) File 'native.pdb' automatically determined to be of type PDB > core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: CE on residue LYS 31 > core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: NZ on residue LYS 31 > core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 166 > core.conformation.Conformation: (0) [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 253 > core.pack.pack_missing_sidechains: (0) packing residue number 31 because of missing atom number 8 atom name CE > core.pack.task: (0) Packer task: initialize from command line() > core.scoring.ScoreFunctionFactory: (0) SCOREFUNCTION: ref2015 > core.scoring.etable: (0) Starting energy table calculation > core.scoring.etable: (0) smooth_etable: changing atr/rep split to bottom of energy well > core.scoring.etable: (0) smooth_etable: spline smoothing lj etables (maxdis = 6) > core.scoring.etable: (0) smooth_etable: spline smoothing solvation etables (max_dis = 6) > core.scoring.etable: (0) Finished calculating energy tables. > basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv > basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv > basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv > basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv > basic.io.database: (0) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv > basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/all.ramaProb > basic.io.database: (0) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb > basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt > basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt > basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt > basic.io.database: (0) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt > basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA > basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n > core.scoring.P_AA: (0) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. > basic.io.database: (0) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop > basic.io.database: (0) Database file opened: scoring/score_functions/elec_cp_reps.dat > core.scoring.elec.util: (0) Read 40 countpair representative atoms > core.pack.dunbrack.RotamerLibrary: (0) shapovalov_lib_fixes_enable option is true. > core.pack.dunbrack.RotamerLibrary: (0) Reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (0) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/replica_docking/logs/log_1 /home/benchmark/working_dir/commits:20543/replica_docking/logs/log_1 0a1,73 > core.init: (1) Rosetta version: 2024.19.post.dev+199.HEAD.edb0fc2 edb0fc2319eeef5a8236bffc5f224c6bdefeb198 git@github.com:RosettaCommons/rosetta.git 2024-10-03T14:35:02 > core.init: (1) Rosetta extras: [mpi, serialization] > 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 > basic.random.init_random_generator: (1) Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111112 > basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=1111112 RG_type=mt19937 > protocols.jd2.PDBJobInputter: (1) Instantiate PDBJobInputter > protocols.jd2.PDBJobInputter: (1) PDBJobInputter::fill_jobs > protocols.jd2.PDBJobInputter: (1) pushed P.pdb nstruct indices 1 - 4 > core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 985 residue types > core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 6.71 seconds. > core.import_pose.import_pose: (1) File 'native.pdb' automatically determined to be of type PDB > core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: CE on residue LYS 31 > core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: NZ on residue LYS 31 > core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 166 > core.conformation.Conformation: (1) [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 253 > core.pack.pack_missing_sidechains: (1) packing residue number 31 because of missing atom number 8 atom name CE > core.pack.task: (1) Packer task: initialize from command line() > core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 > core.scoring.etable: (1) Starting energy table calculation > core.scoring.etable: (1) smooth_etable: changing atr/rep split to bottom of energy well > core.scoring.etable: (1) smooth_etable: spline smoothing lj etables (maxdis = 6) > core.scoring.etable: (1) smooth_etable: spline smoothing solvation etables (max_dis = 6) > core.scoring.etable: (1) Finished calculating energy tables. > basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv > basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv > basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv > basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv > basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv > basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/all.ramaProb > basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb > basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt > basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt > basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt > basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt > basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA > basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n > core.scoring.P_AA: (1) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. > basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop > basic.io.database: (1) Database file opened: scoring/score_functions/elec_cp_reps.dat > core.scoring.elec.util: (1) Read 40 countpair representative atoms > core.pack.dunbrack.RotamerLibrary: (1) shapovalov_lib_fixes_enable option is true. > core.pack.dunbrack.RotamerLibrary: (1) Reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (1) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib diff -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:20543/replica_docking/logs/log_2 1c1 < core.init: (2) Rosetta version: 2024.19.post.dev+1.HEAD.ec708a4 ec708a4c40449ea419c8fcac0d507440400bf75f git@github.com:RosettaCommons/rosetta.git 2024-05-07T14:50:27 --- > core.init: (2) Rosetta version: 2024.19.post.dev+199.HEAD.edb0fc2 edb0fc2319eeef5a8236bffc5f224c6bdefeb198 git@github.com:RosettaCommons/rosetta.git 2024-10-03T14:35:02 10c10 < core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 7.43 seconds. --- > core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 6.71 seconds. 42,45c42,98 < core.pack.dunbrack.RotamerLibrary: (2) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. < core.pack.dunbrack.RotamerLibrary: (2) Binary rotamer library selected: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin < 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'. < core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 0.57 seconds to load from binary --- > core.pack.dunbrack.RotamerLibrary: (2) Reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (2) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (2) Finished reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (2) Dunbrack 2010 library took 148.16 seconds to load from ASCII > core.pack.dunbrack.RotamerLibrary: (2) Memory usage: > core.pack.dunbrack.RotamerLibrary: (2) CYS with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (2) ILE with 842400 bytes > core.pack.dunbrack.RotamerLibrary: (2) LYS with 8335520 bytes > core.pack.dunbrack.RotamerLibrary: (2) LEU with 842400 bytes > core.pack.dunbrack.RotamerLibrary: (2) MET with 2803920 bytes > core.pack.dunbrack.RotamerLibrary: (2) PRO with 209320 bytes > core.pack.dunbrack.RotamerLibrary: (2) ARG with 8563824 bytes > core.pack.dunbrack.RotamerLibrary: (2) SER with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (2) THR with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (2) VAL with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (2) ASP with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (2) GLU with 31361400 bytes > core.pack.dunbrack.RotamerLibrary: (2) PHE with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (2) HIS with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (2) ASN with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (2) GLN with 34161624 bytes > core.pack.dunbrack.RotamerLibrary: (2) TRP with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (2) TYR with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (2) Total memory on Dunbrack Libraries: 153284952 bytes. diff -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:20543/replica_docking/logs/log_3 1c1 < core.init: (3) Rosetta version: 2024.19.post.dev+1.HEAD.ec708a4 ec708a4c40449ea419c8fcac0d507440400bf75f git@github.com:RosettaCommons/rosetta.git 2024-05-07T14:50:27 --- > core.init: (3) Rosetta version: 2024.19.post.dev+199.HEAD.edb0fc2 edb0fc2319eeef5a8236bffc5f224c6bdefeb198 git@github.com:RosettaCommons/rosetta.git 2024-10-03T14:35:02 10c10 < core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 7.78 seconds. --- > core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 6.73 seconds. 42,45c42,101 < core.pack.dunbrack.RotamerLibrary: (3) shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. < core.pack.dunbrack.RotamerLibrary: (3) Binary rotamer library selected: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin < 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'. < core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 0.51 seconds to load from binary --- > core.pack.dunbrack.RotamerLibrary: (3) Reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/cys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ile.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/lys.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/leu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/met.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/pro.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/arg.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/ser.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/thr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/val.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/glu.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/phe.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/his.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/asn.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/gln.bbind.chi3.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/trp.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.rotamers.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbdep.densities.lib > core.pack.dunbrack.RotamerLibrary: (3) Reading ROSETTA/database/rotamer/shapovalov/StpDwn_0-0-0/tyr.bbind.chi2.Definitions.lib > core.pack.dunbrack.RotamerLibrary: (3) Finished reading Dunbrack Libraries > core.pack.dunbrack.RotamerLibrary: (3) Dunbrack 2010 library took 151.53 seconds to load from ASCII > core.pack.dunbrack.RotamerLibrary: (3) Memory usage: > core.pack.dunbrack.RotamerLibrary: (3) CYS with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (3) ILE with 842400 bytes > core.pack.dunbrack.RotamerLibrary: (3) LYS with 8335520 bytes > core.pack.dunbrack.RotamerLibrary: (3) LEU with 842400 bytes > core.pack.dunbrack.RotamerLibrary: (3) MET with 2803920 bytes > core.pack.dunbrack.RotamerLibrary: (3) PRO with 209320 bytes > core.pack.dunbrack.RotamerLibrary: (3) ARG with 8563824 bytes > core.pack.dunbrack.RotamerLibrary: (3) SER with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (3) THR with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (3) VAL with 250800 bytes > core.pack.dunbrack.RotamerLibrary: (3) ASP with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (3) GLU with 31361400 bytes > core.pack.dunbrack.RotamerLibrary: (3) PHE with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (3) HIS with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (3) ASN with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (3) GLN with 34161624 bytes > core.pack.dunbrack.RotamerLibrary: (3) TRP with 11326928 bytes > core.pack.dunbrack.RotamerLibrary: (3) TYR with 10393520 bytes > core.pack.dunbrack.RotamerLibrary: (3) Total memory on Dunbrack Libraries: 153284952 bytes. > core.pack.dunbrack.RotamerLibrary: (3) Random tempname will be: ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/dun10_binary6F7H5P80 > core.pack.dunbrack.RotamerLibrary: (3) Opening file ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/dun10_binary6F7H5P80 for output. > core.pack.dunbrack.RotamerLibrary: (3) Moving temporary file to ROSETTA/.database-binaries/mpiserialization.linuxgccrelease_debug/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin diff -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:20543/replica_docking/.test_got_timeout_kill.log 1c1 < *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-05-08 12:58:12.147951] --- > *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-10-03 16:02:38.057848] Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!