Task 1624882807
| Name | RosettaVS_SAVE_ALL_OUT_NOJRAN_M1_real_specificity_fulldb_IGNORE_THE_REST_ZT9ExJ_5_43_3022833_1_0 |
| Workunit | 1445542825 |
| Created | 17 Dec 2025, 2:13:29 UTC |
| Sent | 17 Dec 2025, 2:36:39 UTC |
| Report deadline | 20 Dec 2025, 2:36:39 UTC |
| Received | 23 Dec 2025, 18:11:18 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 6334063 |
| Run time | 11 hours 52 min 9 sec |
| CPU time | 9 hours 39 min 6 sec |
| Validate state | Valid |
| Credit | 132.29 |
| Device peak FLOPS | 7.39 GFLOPS |
| Application version | Rosetta Beta v6.06 x86_64-apple-darwin |
| Peak working set size | 1,549.71 MB |
| Peak swap size | 35,958.43 MB |
| Peak disk usage | 25.34 MB |
Stderr output
<core_client_version>8.2.5</core_client_version> <![CDATA[ <stderr_txt> command: rosetta_beta_6.06_x86_64-apple-darwin @M1_real_specificity_fulldb_ZT9ExJ_5_43.flags -nstruct 10000 -cpu_run_time 28800 -boinc:max_nstruct 20000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 Using database: database_f5ae1de8e1/database Starting watchdog... Watchdog active. [ ERROR ]: Caught exception: File: src/core/kinematics/Stub.cc:106 Error in Stub::from_four_points(): File: src/numeric/xyzVector.hh:654 Cannot create normalized xyzVector from vector of length() zero. Error occurred when trying to normalize the vector between points A and B. A=[5986500422216674013781229043712.000000,28252514375581248848873364914176.000000,-24162068794395543595768459821056.000000], B=[5986500422216674013781229043712.000000,28252514375581248848873364914176.000000,-24162068794395543595768459821056.000000]. ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: 0 rosetta_beta_6.06_x86_64-apple-darw 0x00000001071a1ec7 backtrace_string(int) + 87 1 rosetta_beta_6.06_x86_64-apple-darw 0x00000001071b5a1d utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 205 2 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106d92037 core::kinematics::Stub::from_four_points(numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&) + 2071 3 rosetta_beta_6.06_x86_64-apple-darw 0x00000001066e18cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895 4 rosetta_beta_6.06_x86_64-apple-darw 0x00000001066e11ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270 5 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d93b53 std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo> std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo>::make_shared<core::conformation::Residue const&>(core::conformation::Residue const&) + 83 6 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d827c9 protocols::ligand_docking::ga_ligand_dock::GridScorer::score(core::pose::Pose&, protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, bool) + 777 7 rosetta_beta_6.06_x86_64-apple-darw 0x0000000105596642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130 8 rosetta_beta_6.06_x86_64-apple-darw 0x000000010559635e core::optimization::ArmijoLineMinimization::operator()(utility::vector1<double, std::__1::allocator<double>>&, utility::vector1<double, std::__1::allocator<double>>&) + 494 9 rosetta_beta_6.06_x86_64-apple-darw 0x000000010559f0b9 core::optimization::Minimizer::lbfgs(utility::vector1<double, std::__1::allocator<double>>&, double&, core::optimization::ConvergenceTest&, std::__1::shared_ptr<core::optimization::LineMinimizationAlgorithm>, int, bool) const + 3177 10 rosetta_beta_6.06_x86_64-apple-darw 0x000000010559a02f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975 11 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d9152c protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(protocols::ligand_docking::ga_ligand_dock::LigandConformer&, core::optimization::MinimizerOptions const&) + 1884 12 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d8e770 protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize(protocols::ligand_docking::ga_ligand_dock::LigandConformer&, utility::vector1<double, std::__1::allocator<double>>, utility::vector1<utility::vector1<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer>>, std::__1::allocator<utility::vector1<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer>>>>&, protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies&) + 752 13 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d9b4b4 protocols::ligand_docking::ga_ligand_dock::GAOptimizer::optimize_generation(utility::vector1<protocols::ligand_docking::ga_ligand_dock::LigandConformer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::LigandConformer>>&, utility::vector1<double, std::__1::allocator<double>> const&) + 356 14 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103d94e52 protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(utility::vector1<protocols::ligand_docking::ga_ligand_dock::LigandConformer, std::__1::allocator<protocols::ligand_docking::ga_ligand_dock::LigandConformer>>&) + 2850 15 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103db947b protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, std::__1::shared_ptr<protocols::ligand_docking::ga_ligand_dock::GridScorer>, protocols::ligand_docking::ga_ligand_dock::LigandAligner&, protocols::ligand_docking::ga_ligand_dock::OutputStructureStore&) + 715 16 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103daf32e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846 17 rosetta_beta_6.06_x86_64-apple-darw 0x00000001053a0fd8 protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&) + 1224 18 rosetta_beta_6.06_x86_64-apple-darw 0x000000010539962f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935 19 rosetta_beta_6.06_x86_64-apple-darw 0x000000010528622c protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, unsigned long&, unsigned long&, bool) + 8204 20 rosetta_beta_6.06_x86_64-apple-darw 0x0000000105283572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194 21 rosetta_beta_6.06_x86_64-apple-darw 0x000000010527e612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 22 rosetta_beta_6.06_x86_64-apple-darw 0x00000001052740e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246 23 rosetta_beta_6.06_x86_64-apple-darw 0x00000001027c2254 main + 22020 24 dyld 0x000000020af0d781 start + 3457 ------------------------- End developer's backtrace -------------------------- Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. Starting watchdog... Watchdog active. [ ERROR ]: Caught exception: File: src/core/kinematics/Stub.cc:106 Error in Stub::from_four_points(): File: src/numeric/xyzVector.hh:654 Cannot create normalized xyzVector from vector of length() zero. Error occurred when trying to normalize the vector between points A and B. A=[687674035290633797632.000000,634358175811381231616.000000,-284619632190344462336.000000], B=[687674035290633797632.000000,634358175811381231616.000000,-284619632190344462336.000000]. ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: 0 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106b33ec7 backtrace_string(int) + 87 1 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106b47a1d utility::excn::Exception::Exception(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) + 205 2 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106724037 core::kinematics::Stub::from_four_points(numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&, numeric::xyzVector<double> const&) + 2071 3 rosetta_beta_6.06_x86_64-apple-darw 0x00000001060738cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895 4 rosetta_beta_6.06_x86_64-apple-darw 0x00000001060731ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270 5 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103725b53 std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo> std::__1::shared_ptr<core::scoring::lkball::LKB_ResidueInfo>::make_shared<core::conformation::Residue const&>(core::conformation::Residue const&) + 83 6 rosetta_beta_6.06_x86_64-apple-darw 0x00000001037147c9 protocols::ligand_docking::ga_ligand_dock::GridScorer::score(core::pose::Pose&, protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, bool) + 777 7 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104f28642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130 8 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104f2835e core::optimization::ArmijoLineMinimization::operator()(utility::vector1<double, std::__1::allocator<double>>&, utility::vector1<double, std::__1::allocator<double>>&) + 494 9 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104f310b9 core::optimization::Minimizer::lbfgs(utility::vector1<double, std::__1::allocator<double>>&, double&, core::optimization::ConvergenceTest&, std::__1::shared_ptr<core::optimization::LineMinimizationAlgorithm>, int, bool) const + 3177 10 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104f2c02f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975 11 rosetta_beta_6.06_x86_64-apple-darw 0x00000001036f344c protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(protocols::ligand_docking::ga_ligand_dock::LigandConformer&) + 5308 12 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103752c1f protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, std::__1::shared_ptr<protocols::ligand_docking::ga_ligand_dock::GridScorer>, unsigned long, protocols::ligand_docking::ga_ligand_dock::LigandAligner) const + 4799 13 rosetta_beta_6.06_x86_64-apple-darw 0x000000010374b315 protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(protocols::ligand_docking::ga_ligand_dock::LigandConformer const&, std::__1::shared_ptr<protocols::ligand_docking::ga_ligand_dock::GridScorer>, protocols::ligand_docking::ga_ligand_dock::LigandAligner&, protocols::ligand_docking::ga_ligand_dock::OutputStructureStore&) + 357 14 rosetta_beta_6.06_x86_64-apple-darw 0x000000010374132e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846 15 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104d32fd8 protocols::rosetta_scripts::ParsedProtocol::apply_mover(core::pose::Pose&, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep const&) + 1224 16 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104d2b62f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935 17 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c1822c protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>&, unsigned long&, unsigned long&, bool) + 8204 18 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c15572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194 19 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c10612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 20 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c060e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246 21 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102154254 main + 22020 22 dyld 0x000000020ab4f781 start + 3457 ------------------------- End developer's backtrace -------------------------- ====================================================== DONE :: 8 starting structures 30129 cpu seconds This process generated 8 decoys from 8 attempts ====================================================== BOINC :: WS_max 1.08522e+09 BOINC :: Watchdog shutting down... 07:44:58 (16282): called boinc_finish(0) Starting watchdog... Watchdog active. ====================================================== DONE :: 1 starting structures 34746.3 cpu seconds This process generated 1 decoys from 1 attempts ====================================================== BOINC :: WS_max 5.92159e+08 BOINC :: Watchdog shutting down... 19:11:07 (63491): called boinc_finish(0) </stderr_txt> ]]>
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