Test: ubuntu.clang.python310.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20604」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-1     Started at: 2024-11-08 16:46:02     Run time: 2:26:10      State: script failed


Test Log

Building PyRosetta MinSizeRel... Command line: cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/hojo-1/ubuntu/python-3.10.gcc/69716d1907a38bef273dea4dd5921890/bin/python3.10 build.py -j16 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/hojo-1/ubuntu/python-3.10.gcc/69716d1907a38bef273dea4dd5921890/include/python3.10 --python-lib=/home/benchmark/prefix/hojo-1/ubuntu/python-3.10.gcc/69716d1907a38bef273dea4dd5921890/lib Creating PyRosetta in "MinSizeRel" mode in: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.10/minsizerel Getting main repository root... cd /home/benchmark/rosetta/source && git rev-parse --show-toplevel /home/benchmark/rosetta Updating Pybind11 Git submodule... cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/external/pybind11 Updating Binder Git submodule... cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/src/python/PyRosetta/binder LLVM:6.0.1 + Binder install is detected at /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.Linux-5.4.0-84-generic-x86_64-with-glibc2.27.release, skipping LLVM installation and Binder building procedures... Updating compilation submodules, version, options and residue-type-enum files... cd /home/benchmark/rosetta/source && ./update_submodules.sh PyRosetta bcl zeromq && ./version.py && ./update_options.sh && ./update_ResidueType_enum_files.sh Updating submodules needed for compilation. Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4682 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed Generating bindings... cd /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.10/minsizerel/source/ && /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.Linux-5.4.0-84-generic-x86_64-with-glibc2.27.release/bin/binder --config ./rosetta.config --root-module rosetta --prefix /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.10/minsizerel/source/ /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.10/minsizerel/source/all_rosetta_includes.hh -- -std=c++11 -isystem external -isystem external/include -isystem external/boost_submod -isystem external/dbio -isystem external/dbio/sqlite3 -isystem external/libxml2/include -isystem external/rdkit -isystem external/bcl/include -Isrc -Isrc/platform/linux -DPYROSETTA -DNOCRASHREPORT -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DBCL_NO_OS_SIGNAL_HANDLING -DPYROSETTA_BINDER Process input file /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.10/minsizerel/source/all_rosetta_includes.hh Generate bindings, pass 1... Generate bindings, pass 2... Generate bindings, pass 3... ...truncated... protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.832 578.832 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 2/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.851 578.832 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.898 578.832 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 3/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.013 578.832 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.599 578.599 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 4/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.619 578.599 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.573 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 5/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.68 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.68 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 6/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.805 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.811 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 7/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.055 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.116 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 8/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.t┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.42.post.dev+23.HEAD.cffc584c55b5dbecd306ddc97d555a231aaea3f1 2024-11-08T16:33:37] retrieved from: git@github.com:RosettaCommons/rosetta.git Loop building -------------------------------------------------- FOLD_TREE EDGE 1 69 -1 EDGE 69 75 -1 EDGE 69 81 1 EDGE 81 76 -1 EDGE 81 116 -1 ask: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.144 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.117 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 9/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.117 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 579.14 578.573 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. protocols.loops.loop_mover.refine.LoopMover_Refine_CCD: refinement cycle (outer/inner): 5/5 10/10 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for LoopRefineInnerCycleContainer. protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for SmallMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.566 578.566 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for ShearMinCCDTrial. core.pack.task: Packer task: initialize from command line() core.pack.task: Packer task: initialize from command line() protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.566 578.566 protocols.loops.loop_mover.refine.LoopRefineInnerCycle: Setting up data for RepackTrial. core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 1038 rotamers at 42 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 578.566 578.566 protocols.moves.TrialCounter: repack trials= 6; accepts= 1.0000; energy_drop/trial= -50.02510 protocols.moves.TrialCounter: shear_ccd_min trials= 50; accepts= 0.8600; energy_drop/trial= -0.12849 protocols.moves.TrialCounter: small_ccd_min trials= 50; accepts= 0.9000; energy_drop/trial= -1.28023 Finished T660_LoopBuilding in 0:01:16.979029 *** '/home/benchmark/prefix/hojo-1/ubuntu/python_virtual_environments/python-3.10/830a5c4663d08016272af85e8346704e/bin/python self-test.py -j16' exceeded the timeout and will be killed! Killed PyRosetta self-test.py script terminated with non-zero exit code, terminating with script failure!

Sub-Tests Results

All sub-tests

JSON output

{}