Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20705」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-4     Started at: 2025-04-01 16:12:08     Run time: 0:30:24      State: build failed


Test Log

Building PyRosetta MinSizeRel... Command line: cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8 build.py -j64 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 --python-lib=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib --multi-threaded --serialization 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-3.8/minsizerel.serialization.thread 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 build detected, but config/binder version has changed, perfoming a clean rebuild... Download LLVM source... cd /home/benchmark/rosetta/source/build/prefix && mkdir llvm-6.0.1.src && curl -LJ https://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz | tar --strip-components=1 -Jxom -C llvm-6.0.1.src && mv llvm-6.0.1.src /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 58 24.1M 58 14.0M 0 0 9206k 0 0:00:02 0:00:01 0:00:01 9200k 100 24.1M 100 24.1M 0 0 9429k 0 0:00:02 0:00:02 --:--:-- 9425k 100 24.1M 100 24.1M 0 0 9429k 0 0:00:02 0:00:02 --:--:-- 9425k Download Clang source... cd /home/benchmark/rosetta/source/build/prefix && mkdir clang-6.0.1.src && curl -LJ https://releases.llvm.org/6.0.1/cfe-6.0.1.src.tar.xz | tar --strip-components=1 -Jxom -C clang-6.0.1.src && mv clang-6.0.1.src /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/tools/clang % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 11.3M 100 11.3M 0 0 9869k 0 0:00:01 0:00:01 --:--:-- 9869k 100 11.3M 100 11.3M 0 0 9869k 0 0:00:01 0:00:01 --:--:-- 9869k Building tool: binder... cd /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 && cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=`which clang` -DCMAKE_CXX_COMPILER=`which clang++` -DLLVM_ENABLE_EH=1 -DLLVM_ENABLE_RTTI=ON .. && ninja binder tools/clang/lib/Headers/clang-headers -j64 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. ...truncated... ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1069:8: error: unknown type name 'ResidueTypeCOP'; did you mean 'core::chemical::ResidueTypeCOP'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~~~~ core::chemical::ResidueTypeCOP /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/core/chemical/ResidueType.fwd.hh:42:61: note: 'core::chemical::ResidueTypeCOP' declared here typedef utility::pointer::shared_ptr< ResidueType const > ResidueTypeCOP; ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1069:29: error: use of undeclared identifier 'ResidueType'; did you mean 'core::chemical::ResidueType'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~ core::chemical::ResidueType /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/core/chemical/ResidueType.hh:124:7: note: 'core::chemical::ResidueType' declared here class ResidueType : public ResidueTypeBase, public utility::pointer::enable_shared_from_this< ResidueType > ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1072:66: error: no member named 'ResidueFactory' in namespace 'core::conformation' core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ~~~~~~~~~~~~~~~~~~~~^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1072:44: warning: parentheses were disambiguated as a function declaration [-Wvexing-parse] core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1072:46: note: add a pair of parentheses to declare a variable core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^ ( /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1109:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 1); ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1117:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 2); ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1136:16: error: use of undeclared identifier 'base_10_to_base_62' atom_name = base_10_to_base_62(total_atom_counter + 1); ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1160:3: error: unknown type name 'ResidueTypeCOP'; did you mean 'core::chemical::ResidueTypeCOP'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~~~~ core::chemical::ResidueTypeCOP /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/core/chemical/ResidueType.fwd.hh:42:61: note: 'core::chemical::ResidueTypeCOP' declared here typedef utility::pointer::shared_ptr< ResidueType const > ResidueTypeCOP; ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1160:24: error: use of undeclared identifier 'ResidueType'; did you mean 'core::chemical::ResidueType'? ResidueTypeCOP my_rt(ResidueType::make(my_mrt)); ^~~~~~~~~~~ core::chemical::ResidueType /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread/source/src/core/chemical/ResidueType.hh:124:7: note: 'core::chemical::ResidueType' declared here class ResidueType : public ResidueTypeBase, public utility::pointer::enable_shared_from_this< ResidueType > ^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1163:61: error: no member named 'ResidueFactory' in namespace 'core::conformation' core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ~~~~~~~~~~~~~~~~~~~~^ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1163:39: warning: parentheses were disambiguated as a function declaration [-Wvexing-parse] core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1163:41: note: add a pair of parentheses to declare a variable core::conformation::ResidueOP my_res( core::conformation::ResidueFactory::create_residue(*my_rt)); ^ ( /home/benchmark/rosetta/source/src/protocols/protein_grid/ProteinGrid.cc:1206:27: error: out-of-line definition of 'base_10_to_base_62' does not match any declaration in 'protocols::protein_grid::ProteinGrid' std::string ProteinGrid::base_10_to_base_62(core::Size starting_num) ^~~~~~~~~~~~~~~~~~ 2 warnings and 12 errors generated. [4910/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [4911/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/LoopFragmentClaimer.cc.o [4912/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [4913/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts3.cc.o [4914/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts4.cc.o [4915/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/claims/DofClaim.cc.o [4916/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapperCreator.cc.o [4917/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [4918/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/FullatomRelaxMover.cc.o [4919/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/membrane/MPSymDockMover.cc.o [4920/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/BasicJumpClaimer.cc.o [4921/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/IdentifyLigandMotifs.cc.o [4922/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc.o [4923/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentParameters.cc.o [4924/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentClaimer.cc.o [4925/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [4926/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidBodyRandomTMHMover.cc.o [4927/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [4928/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/DisulfJumpClaimer.cc.o [4929/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNNProbabilitiesMetric.cc.o [4930/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/util.cc.o [4931/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockSlideTrialMover.cc.o [4932/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [4933/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/MotifSearch.cc.o [4934/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintClaimer.cc.o [4935/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceDockingProtocol.cc.o [4936/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingLowRes.cc.o [4937/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/motif_utils.cc.o [4938/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [4939/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockRbTrialMover.cc.o [4940/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MetalloClaimer.cc.o [4941/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentJumpClaimer.cc.o [4942/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [4943/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandMotifSearch.cc.o [4944/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/StartStructClaimer.cc.o [4945/8253] Building CXX object CMakeFiles/protocols_h.5.dir/home/benchmark/rosetta/source/src/protocols/ligand_docking/GALigandDock/GALigandDock.cc.o [4946/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimer.cc.o [4947/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/CoordConstraintClaimer.cc.o [4948/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/AsymFoldandDockClaimer.cc.o [4949/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [4950/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SymmetryClaimer.cc.o [4951/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingHiRes.cc.o [4952/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FoldandDockClaimer.cc.o [4953/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateFragmentClaimer.cc.o [4954/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/NoesyModule.cc.o [4955/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FibrilModelingClaimer.cc.o [4956/8253] Building CXX object CMakeFiles/core.5.dir/home/benchmark/rosetta/source/src/core/optimization/AtomTreeMinimizer.cc.o [4957/8253] Building CXX object CMakeFiles/core.5.dir/home/benchmark/rosetta/source/src/core/optimization/CartesianMinimizer.cc.o [4958/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimerFactory.cc.o [4959/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SequenceClaimer.cc.o [4960/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.cc.o [4961/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MembraneTopologyClaimer.cc.o [4962/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [4963/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateJumpClaimer.cc.o [4964/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o [4965/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/util.cc.o [4966/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidChunkClaimer.cc.o [4967/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockProtocol.cc.o [4968/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [4969/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/ConfChangeMover.cc.o [4970/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TMHTopologySamplerClaimer.cc.o [4971/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyBroker.cc.o [4972/8253] Building CXX object CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o ninja: build stopped: subcommand failed.

Sub-Tests Results

All sub-tests

JSON output

{}