Test: linux.gcc.cxx11thread.serialization.build.debug 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20511」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-3     Started at: 2024-09-24 13:47:15     Run time: 0:13:55      State: failed


Running: /home/benchmark/prefix/nobu-3/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras=cxx11thread,serialization -j48 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4707 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/libprotocols.4.so -Wl,--disable-new-dtags -shared -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/GlycanInfoMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/InterfaceAnalyzerMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/LoopAnalyzerMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/LoopAnalyzerFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/PackStatMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/simple_metrics/ConstraintsMetric.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/simple_metrics/RunSimpleMetricsMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/analysis/simple_metrics/SequenceRecoveryMetric.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/ResetBaselineMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/GenericMonteCarloMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/GenericSimulatedAnnealer.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/MonteCarloInterface.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/MonteCarloRecover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/MonteCarloTest.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/monte_carlo/MonteCarloReset.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/CreateGlycanSequonMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/GlycanSampler.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/GlycanTreeMinMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/GlycanTreeModeler.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/LinkageConformerMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/IdealizeAnomericHydrogens.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/RingPlaneFlipMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/SimpleGlycosylateMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/TautomerizeAnomerMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/carbohydrates/util.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/cutoutdomain/CutOutDomain.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/pb_potential/SetupPoissonBoltzmannPotential.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/DdgFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/ddG.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/AlaScan.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/DdGScan.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/SSElementBisectddGFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/simple_ddg/InterfaceBindingEnergyDensityFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_movers/ForceDisulfidesMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_movers/ConsensusDesignMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_movers/DesignRepackMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_movers/CreateSequenceMotifMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/SigmoidFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/MultipleSigmoidsFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/OperatorFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/ConservedPosMutationFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/RelativePoseFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/RotamerBoltzmannWeight.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/normalmode/NormalMode.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/normalmode/NormalModeMinimizer.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/normalmode/NormalModeMultiFunc.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/normalmode/NormalModeRelaxMover.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/BestTotalScoreSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/CompositeFragmentSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/ContactTypes.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/CS2ndShift.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/CSTalosIO.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/CustomScoreSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/DiversifyCrmsdByClustering.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/DiversifyCrmsdSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/DiversifyDihedralsSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/Faraggi_SA.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/FragmentCandidate.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/FragmentPicker.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/FragmentScoreFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/JCouplingIO.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/LAMBEGO_IO.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/PdbIdChunkFilter.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/PhiPsiTalosIO.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/SidechainContactDistCutoff.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/TorsionBinIO.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/VallChunk.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/VallProvider.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/VallResidue.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/ABEGO_SS_Config.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/ABEGO_SS_Map.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/ABEGO_SS_Pool.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/QuotaCollector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/QuotaConfig.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/QuotaSelector.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/quota/SecondaryStructurePool.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/ABEGO_SS_Score.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/AdaptiveScoreHistogram.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/AmbigCSScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/AtomBasedConstraintsScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/AtomPairConstraintsScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/BFactor.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/CSScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/DihedralConstraintsScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/DisulfideDistance.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/DisulfideIdentity.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FourAtomsConstraintData.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/fragment_scoring_utilities.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentAllAtomCrmsd.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentCrmsd.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentChunkCrms.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentCrmsdResDepth.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentDME.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/FragmentScoreManager.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/GunnCost.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/GunnCostScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/HydrophobicitySimilarity.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/HydrophobicityProfileSimilarity.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/InterbondAngleScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/JCoupling.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/LAMBEGO_Similarity.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/MidPhiOut.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/MidPsiOut.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/PartialSecondarySimilarity.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/PCS_FragDistance.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/Phi.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/PhiPsiRmsd.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/PhiPsiSquareWell.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/ProfileScore.os build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/protocols/frag_picker/scores/ProfileScoreBlosum62.os 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-D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/rosetta_scripts/rosetta_scripts_jd3.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/benchmark/scientific/rotamer_recovery.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/benchmark/scientific/rotamer_recovery.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/analysis/sc.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/analysis/sc.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/analysis/score.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ 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build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/rhiju/screen_phosphates.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/rhiju/screen_phosphates.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/sewing/segment_file_generator.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/sewing/segment_file_generator.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/ligand_docking/select_best_unique_ligand_poses.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic 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-DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/design/sequence_recovery.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/sequence_tolerance.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/sequence_tolerance.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/legacy_sewing/sewing_hasher.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/legacy_sewing/sewing_hasher.cc src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc: In function 'int main(int, char**)': src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:251:43: error: ambiguous overload for 'operator<<' (operand types are 'basic::TracerImpl' and 'utility::vector1<long unsigned int>') ms_tr << "Discovery residue indices: " << discovery_positions_int << std::endl; ^ src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:251:43: note: candidates are: In file included from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:57:0: src/protocols/dna/util.hh:158:16: note: std::ostream& protocols::dna::operator<<(std::ostream&, const ResTypeSequences&) std::ostream & operator << ( std::ostream & os, ResTypeSequences const & seqs ); ^ In file included from src/core/scoring/EnergyMap.hh:22:0, from src/core/scoring/ScoreFunction.hh:37, from src/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.cc:24: src/core/scoring/ScoreType.hh:775:16: note: std::ostream& core::scoring::operator<<(std::ostream&, const ScoreTypes&) std::ostream & operator <<( std::ostream & os, ScoreTypes const & score_types ); ^ g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/analysis/shobuns.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/analysis/shobuns.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/mike/silent2frag.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/mike/silent2frag.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/cyclic_peptide/simple_cycpep_predict.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store 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-Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/chen/simple_dna_regression_test.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/antibody/snugdock.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/antibody/snugdock.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/comparative_modeling/spheregrinder.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/comparative_modeling/spheregrinder.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/stepwise/stepwise.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/stepwise/stepwise.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/struc_set_fragment_picker.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb 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-Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/comparative_modeling/super_aln.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/design/supercharge.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/design/supercharge.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/surface_docking/surface_docking.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/surface_docking/surface_docking.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/stepwise/legacy/swa_protein_main.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/stepwise/legacy/swa_protein_main.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/stepwise/legacy/swa_rna_main.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 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-DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/stepwise/legacy/swa_rna_util.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/andrew/sweep_respair_energies.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/andrew/sweep_respair_energies.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/will/sym_multicomp_test.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/will/sym_multicomp_test.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/tcr/tcrmodel.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem 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-Isrc/platform/linux src/apps/pilot/jackmaguire/tensorflow_manager_multirun_test.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/jackmaguire/tensorflow_manager_test1.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/jackmaguire/tensorflow_manager_test1.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/vmullig/tensorflow_test1.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/vmullig/tensorflow_test1.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/jackmaguire/tensorflow_test2.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/pilot/jackmaguire/tensorflow_test2.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/pilot/phil/test1.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store 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-Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/tests/test_SiteConstraint.cc g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/tests/test_carbohydrate_docking.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DMULTI_THREADED -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/tests/test_carbohydrate_docking.cc scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/cxx11thread-serialization/apps/public/motif_ligand_discovery/ligand_discovery_search_protocol.o] Error 1 scons: building terminated because of errors.
{}