Task 1604619923
| Name | RosettaVS_SAVE_ALL_OUT_NOJRAN_M2_substructure_real_fulldb_IGNORE_THE_REST_zb230H_3_1803_3011194_2_0 |
| Workunit | 1427173205 |
| Created | 9 Mar 2025, 9:06:08 UTC |
| Sent | 9 Mar 2025, 9:38:43 UTC |
| Report deadline | 12 Mar 2025, 9:38:43 UTC |
| Received | 10 Mar 2025, 5:59:53 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 194 (0x000000C2) EXIT_ABORTED_BY_CLIENT |
| Computer ID | 6063783 |
| Run time | 11 hours 24 min 38 sec |
| CPU time | 5 hours 34 min 2 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 3.71 GFLOPS |
| Application version | Rosetta Beta v6.06 x86_64-apple-darwin |
| Peak working set size | 254.61 MB |
| Peak swap size | 35,282.53 MB |
| Peak disk usage | 1,206.64 MB |
Stderr output
<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
Process still present 5 min after writing finish file; aborting</message>
<stderr_txt>
command: rosetta_beta_6.06_x86_64-apple-darwin @M2_substructure_real_fulldb_zb230H_3_1803.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
Extracting in slot directory: minirosetta_database.zip
Using database: database/
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=[1299239993727957504.000000,-974009957670458624.000000,-1602511837984504064.000000], B=[1299239993727957504.000000,-974009957670458624.000000,-1602511837984504064.000000].
------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
0 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106b37ec7 backtrace_string(int) + 87
1 rosetta_beta_6.06_x86_64-apple-darw 0x0000000106b4ba1d 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 0x0000000106728037 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 0x00000001060778cf core::scoring::lkball::LKB_ResidueInfo::build_waters(core::conformation::Residue const&, bool) + 895
4 rosetta_beta_6.06_x86_64-apple-darw 0x00000001060771ae core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo(core::conformation::Residue const&, bool) + 270
5 rosetta_beta_6.06_x86_64-apple-darw 0x0000000103729b53 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 0x00000001037187c9 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 0x0000000104f2c642 core::optimization::ArmijoLineMinimization::Armijo(double, core::optimization::func_1d&) + 130
8 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104f2c35e 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 0x0000000104f350b9 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 0x0000000104f3002f core::optimization::Minimizer::run(utility::vector1<double, std::__1::allocator<double>>&) + 6975
11 rosetta_beta_6.06_x86_64-apple-darw 0x000000010372752c 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 0x0000000103724770 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 0x00000001037314b4 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 0x000000010372ae52 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 0x000000010374f47b 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 0x000000010374532e protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(core::pose::Pose&) + 14846
17 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104d36fd8 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 0x0000000104d2f62f protocols::rosetta_scripts::ParsedProtocol::apply(core::pose::Pose&) + 1935
19 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c1c22c 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 0x0000000104c19572 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 194
21 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c14612 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66
22 rosetta_beta_6.06_x86_64-apple-darw 0x0000000104c0a0e6 protocols::jd2::BOINCJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 246
23 rosetta_beta_6.06_x86_64-apple-darw 0x0000000102158254 main + 22020
24 dyld 0x000000020a94e2cd start + 1805
------------------------- End developer's backtrace --------------------------
======================================================
DONE :: 2 starting structures 19987 cpu seconds
This process generated 2 decoys from 2 attempts
======================================================
BOINC :: WS_max 1.53641e+08
BOINC :: Watchdog shutting down...
05:04:03 (1551): called boinc_finish(0)
Starting watchdog...
Watchdog active.
Starting watchdog...
Watchdog active.
Crashed executable name: rosetta_beta_6.06_x86_64-apple-darwin
built using BOINC library version 7.9.0
Machine type Intel 80486 (64-bit executable)
System version: Macintosh OS 15.3.1 build 24D70
Mon Mar 10 06:04:20 2025
atos cannot load symbols for the file rosetta_beta_6.06_x86_64-apple-darwin for architecture x86_64.
0 rosetta_beta_6.06_x86_64-apple-darw 0x000000010561aa66
1 rosetta_beta_6.06_x86_64-apple-darw 0x00000001056064d6
SIGPIPE: write on a pipe with no reader
SIGPIPE: write on a pipe with no reader
2 libsystem_pthread.dylib 0x00007ff811d44253
SIGPIPE: write on a pipe with no reader
3 libsystem_pthread.dylib 0x00007ff811d3fbef
Thread 2 crashed with X86 Thread State (64-bit):
rax: 0x0100002f rbx: 0x30d532500 rcx: 0x299700001b07 rdx: 0x2800001513
rdi: 0x30d532500 rsi: 0x200000003 rbp: 0x30d5324e0 rsp: 0x30d532478
r8: 0xe1300000000 r9: 0x299700000000 r10: 0x299700001b07 r11: 0xf4e2c017
r12: 0x00000000 r13: 0x200000003 r14: 0x00001470 r15: 0x299700000000
rip: 0x7ff811d02f0e rfl: 0x00000246
Binary Images Description:
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</stderr_txt>
]]>
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