Task 1625010244
| Name | RosettaVS_SAVE_ALL_OUT_NOJRAN_M1_real_specificity_fulldb_IGNORE_THE_REST_ZT9ExJ_3_5070_3022831_2_1 |
| Workunit | 1445552435 |
| Created | 20 Dec 2025, 4:00:20 UTC |
| Sent | 20 Dec 2025, 4:00:27 UTC |
| Report deadline | 23 Dec 2025, 4:00:27 UTC |
| Received | 22 Dec 2025, 4:00:23 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 1058712 |
| Run time | 8 hours 34 min 24 sec |
| CPU time | 7 hours 51 min 22 sec |
| Validate state | Valid |
| Credit | 912.64 |
| Device peak FLOPS | 8.38 GFLOPS |
| Application version | Rosetta Beta v6.06 x86_64-apple-darwin |
| Peak working set size | 1,602.09 MB |
| Peak swap size | 36,242.38 MB |
| Peak disk usage | 25.72 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_3_5070.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=[11302748195339926170475316641792.000000,22352226949434885913091476815872.000000,-22624319664705218353474308145152.000000], B=[11302748195339926170475316641792.000000,22352226949434885913091476815872.000000,-22624319664705218353474308145152.000000]. ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: 0 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104cd9ec7 backtrace_string(int) + 87 1 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104ceda1d 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 0x00000001048ca037 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 0x00000001042198cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895 4 rosetta_beta_6.06_x86_64-apple-darw 0x00000001042191ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270 5 rosetta_beta_6.06_x86_64-apple-darw 0x00000001018cbb53 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 0x00000001018ba7c9 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 0x00000001030ce642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130 8 rosetta_beta_6.06_x86_64-apple-darw 0x00000001030ce35e 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 0x00000001030d70b9 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 0x00000001030d202f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975 11 rosetta_beta_6.06_x86_64-apple-darw 0x00000001018c952c 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 0x00000001018c6770 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 0x00000001018d34b4 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 0x00000001018cce52 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 0x00000001018f147b 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 0x00000001018e732e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846 17 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102ed8fd8 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 0x0000000102ed162f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935 19 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102dbe22c 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 0x0000000102dbb572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194 21 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102db6612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 22 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102dac0e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246 23 rosetta_beta_6.06_x86_64-apple-darw 0x00000001002fa254 main + 22020 24 dyld 0x0000000208a1a530 start + 3056 ------------------------- End developer's backtrace -------------------------- [ 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=[37404203216040111342671890481152.000000,-12164605191800192753591140745216.000000,-5651545812374237810699968446464.000000], B=[37404203216040111342671890481152.000000,-12164605191800192753591140745216.000000,-5651545812374237810699968446464.000000]. ------------------------ Begin developer's backtrace ------------------------- BACKTRACE: 0 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104cd9ec7 backtrace_string(int) + 87 1 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104ceda1d 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 0x00000001048ca037 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 0x00000001042198cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895 4 rosetta_beta_6.06_x86_64-apple-darw 0x00000001042191ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270 5 rosetta_beta_6.06_x86_64-apple-darw 0x00000001018cbb53 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 0x00000001018ba7c9 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 0x00000001030ce642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130 8 rosetta_beta_6.06_x86_64-apple-darw 0x00000001030ce35e 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 0x00000001030d70b9 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 0x00000001030d202f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975 11 rosetta_beta_6.06_x86_64-apple-darw 0x000000010189944c 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 0x00000001018f8c1f 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 0x00000001018f1315 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 0x00000001018e732e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846 15 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102ed8fd8 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 0x0000000102ed162f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935 17 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102dbe22c 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 0x0000000102dbb572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194 19 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102db6612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66 20 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102dac0e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246 21 rosetta_beta_6.06_x86_64-apple-darw 0x00000001002fa254 main + 22020 22 dyld 0x0000000208a1a530 start + 3056 ------------------------- End developer's backtrace -------------------------- ====================================================== DONE :: 14 starting structures 28282.1 cpu seconds This process generated 14 decoys from 14 attempts ====================================================== BOINC :: WS_max 1.67431e+09 BOINC :: Watchdog shutting down... 14:29:51 (26005): called boinc_finish(0) </stderr_txt> ]]>
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