Branch: rosetta:main 「revision: №62124」
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:62123/replica_docking/log and /home/benchmark/working_dir/main:62124/replica_docking/log differ Files /home/benchmark/working_dir/main:62123/replica_docking/logs/log_0 and /home/benchmark/working_dir/main:62124/replica_docking/logs/log_0 differ Files /home/benchmark/working_dir/main:62123/replica_docking/logs/log_1 and /home/benchmark/working_dir/main:62124/replica_docking/logs/log_1 differ Files /home/benchmark/working_dir/main:62123/replica_docking/logs/log_2 and /home/benchmark/working_dir/main:62124/replica_docking/logs/log_2 differ Files /home/benchmark/working_dir/main:62123/replica_docking/logs/log_3 and /home/benchmark/working_dir/main:62124/replica_docking/logs/log_3 differ Files /home/benchmark/working_dir/main:62123/replica_docking/.test_got_timeout_kill.log and /home/benchmark/working_dir/main:62124/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:62123/replica_docking/log /home/benchmark/working_dir/main:62124/replica_docking/log 6d5 < ******** See LICENSE.md or email license@uw.edu for more details. ********** 9a9 > ******** See LICENSE.md or email license@uw.edu for more details. ********** 14c14 < mpirun noticed that process rank 2 with PID 2733510 on node nobu-4 exited on signal 9 (Killed). --- > mpirun noticed that process rank 3 with PID 576384 on node nobu-1 exited on signal 9 (Killed). diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62123/replica_docking/logs/log_0 /home/benchmark/working_dir/main:62124/replica_docking/logs/log_0 1,73d0 < core.init: (0) Rosetta version: 2024.24.post.dev+6.HEAD.45abd6a 45abd6ab3e15d27b06950672a1bb868f76c03266 git@github.com:RosettaCommons/rosetta.git 2024-08-28T11:40:28 < 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 6.36 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:62123/replica_docking/logs/log_1 /home/benchmark/working_dir/main:62124/replica_docking/logs/log_1 1,73d0 < core.init: (1) Rosetta version: 2024.24.post.dev+6.HEAD.45abd6a 45abd6ab3e15d27b06950672a1bb868f76c03266 git@github.com:RosettaCommons/rosetta.git 2024-08-28T11:40:28 < 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 6.36 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:62123/replica_docking/logs/log_2 /home/benchmark/working_dir/main:62124/replica_docking/logs/log_2 1c1 < core.init: (2) Rosetta version: 2024.24.post.dev+6.HEAD.45abd6a 45abd6ab3e15d27b06950672a1bb868f76c03266 git@github.com:RosettaCommons/rosetta.git 2024-08-28T11:40:28 --- > core.init: (2) Rosetta version: 2024.24.post.dev+7.HEAD.c75854a c75854a9a1a572c8c9b6466511a1c25c9c276a44 git@github.com:RosettaCommons/rosetta.git 2024-08-28T14:22:45 10c10 < core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 6.36 seconds. --- > core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 6.73 seconds. 42,98c42,45 < 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 115.09 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. --- > 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 0.48 seconds to load from binary diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62123/replica_docking/logs/log_3 /home/benchmark/working_dir/main:62124/replica_docking/logs/log_3 1c1 < core.init: (3) Rosetta version: 2024.24.post.dev+6.HEAD.45abd6a 45abd6ab3e15d27b06950672a1bb868f76c03266 git@github.com:RosettaCommons/rosetta.git 2024-08-28T11:40:28 --- > core.init: (3) Rosetta version: 2024.24.post.dev+7.HEAD.c75854a c75854a9a1a572c8c9b6466511a1c25c9c276a44 git@github.com:RosettaCommons/rosetta.git 2024-08-28T14:22:45 10c10 < core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 4.86 seconds. --- > core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 6.72 seconds. 42,98c42,45 < 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 116.73 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) 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 0.47 seconds to load from binary diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62123/replica_docking/.test_got_timeout_kill.log /home/benchmark/working_dir/main:62124/replica_docking/.test_got_timeout_kill.log 1c1 < *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-08-28 15:10:33.483464] --- > *** Test replica_docking exceeded the timeout=3600 and will be killed! [2024-08-28 18:19:36.858881] Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!