Test: ubuntu-20.04.clang.foldit.unit.release 「view this page in B3 βῆτα server」
Branch: interactive/develop 「revision: №614」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-3     Started at: 2024-05-16 16:37:28     Run time: 0:02:18      State: build failed


Compiling: cd /home/benchmark/rosetta/source/cmake_3/build_release && cmake -G Ninja . && ninja -j 48 svn: E170013: Unable to connect to a repository at URL 'svn://foldit-dev.ipd.uw.edu/local-interactive/linux_x64-ubuntu_20_04' svn: E000111: Can't connect to host 'foldit-dev.ipd.uw.edu': Connection refused Encounter error while executing: cd /home/benchmark/prefix && svn checkout svn://foldit-dev.ipd.uw.edu/local-interactive/linux_x64-ubuntu_20_04 local-interactive Updating build files ... Command line: cd /home/benchmark/rosetta && python script/make.py running: cd source && ./update_submodules.sh Updating submodules needed for compilation. running: cd source && /usr/bin/python version.py Running versioning script ... Done. (0.7 seconds) running: cd source/src/core/chemical/residue_properties && /usr/bin/python update_ResidueType_enum_files.py Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed running: cd script/novice/components && /usr/bin/python update_database.py running: cd source/src/basic/options && /usr/bin/python options.py Number of option files updated: 0 Total 4616 options. running: cd source/cmake_3 && /usr/bin/python make_test.py all project running: cd source/cmake_3 && /usr/bin/python make_test.py all files inputs running: cd source/cmake_3 && /usr/bin/python make_project.py cifparse running: cd source/cmake_3 && /usr/bin/python make_project.py libxml2 running: cd source/cmake_3 && /usr/bin/python make_project.py rdkit running: cd source/cmake_3 && /usr/bin/python make_project.py zlib running: cd source/cmake_3 && /usr/bin/python make_project.py numeric running: cd source/cmake_3 && /usr/bin/python make_project.py utility running: cd source/cmake_3 && /usr/bin/python make_project.py basic Running versioning script ... Done. (0.7 seconds) Number of option files updated: 0 Total 4616 options. Updating submodules needed for compilation. running: cd source/cmake_3 && /usr/bin/python make_project.py ObjexxFCL running: cd source/cmake_3 && /usr/bin/python make_project.py core.1 running: cd source/cmake_3 && /usr/bin/python make_project.py core.2 Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed running: cd source/cmake_3 && /usr/bin/python make_project.py core.3 running: cd source/cmake_3 && /usr/bin/python make_project.py core.4 running: cd source/cmake_3 && /usr/bin/python make_project.py core.5 running: cd source/cmake_3 && /usr/bin/python make_project.py core.6 running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.1 running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.2a running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.2b running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.3 running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.4 running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5a running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5b running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5c running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5d running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5e running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5f running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5g running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.5h running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.6a running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.6b running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.6c running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.6d running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.6e running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.7 running: cd source/cmake_3 && /usr/bin/python make_project.py protocols.8 running: cd source/cmake_3 && /usr/bin/python make_project.py interactive running: cd source/cmake_3 && /usr/bin/python make_project.py standalone running: cd source/cmake_3 && /usr/bin/python make_project.py game running: cd source/cmake_3 && /usr/bin/python make_component.py removing cmp-resources creating cmp-resources copied 2504 and skipped 0 files removing cmp-database creating cmp-database dynamic file not yet generated: database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin copied 1092 and skipped 1 files -- Detected GCC Version >= 4.8 -- Configuring done -- Generating done -- Build files have been written to: /home/benchmark/rosetta/source/cmake_3/build_release [0/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/interpolate.cc.o [0/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/prof.cc.o [0/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/pymol_chains.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxMover.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/BrokerMain.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ConstraintFragmentSampler.cc.o [0/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/adler32.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzlib.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/infback.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inffast.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inflate.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inftrees.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/trees.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/uncompr.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/compress.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/deflate.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzclose.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzread.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzwrite.c.o [0/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/zutil.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/DOCBparser.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/HTMLparser.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/HTMLtree.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/SAX.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/SAX2.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/buf.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/c14n.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/catalog.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/chvalid.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/debugXML.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/dict.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/encoding.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/entities.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/error.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/globals.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/hash.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/legacy.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/list.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/nanoftp.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/nanohttp.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/parser.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/parserInternals.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/pattern.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/relaxng.c.o [0/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/schematron.c.o [1/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/nanohttp.c.o [1/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/threads.c.o [2/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/nanoftp.c.o [2/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/tree.c.o [3/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/uncompr.c.o [3/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/trio.c.o [4/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzclose.c.o [4/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/trionan.c.o [5/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/compress.c.o [5/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/triostr.c.o [6/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/zutil.c.o [6/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/uri.c.o [7/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/SAX.c.o [7/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/valid.c.o [8/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inftrees.c.o [8/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xinclude.c.o [9/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/chvalid.c.o [9/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xlink.c.o [10/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/DOCBparser.c.o [10/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlIO.c.o [11/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inffast.c.o [11/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlmemory.c.o [12/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/adler32.c.o [12/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlmodule.c.o [13/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/threads.c.o [13/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/crc32.c.o [14/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/globals.c.o [14/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlreader.c.o [15/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzlib.c.o [15/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlregexp.c.o [16/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzwrite.c.o [16/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlsave.c.o [17/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/list.c.o [17/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlschemas.c.o [18/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/trionan.c.o [18/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlschemastypes.c.o [19/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xlink.c.o [19/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlstring.c.o [20/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/gzread.c.o [20/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlunicode.c.o [21/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlmodule.c.o [21/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlwriter.c.o [22/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/crc32.c.o [22/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xpath.c.o [23/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/entities.c.o [23/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xpointer.c.o [24/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlmemory.c.o [24/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xzlib.c.o [25/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/legacy.c.o [25/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/Catalog.cpp.o [26/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/infback.c.o [26/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/CatalogEntry.cpp.o [27/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/HTMLtree.c.o [27/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/CatalogParams.cpp.o [28/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xzlib.c.o [28/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ChemicalFeatures/FreeChemicalFeature.cpp.o [29/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/error.c.o [29/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/BitOps.cpp.o [30/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/hash.c.o [30/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/BitVect.cpp.o [31/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/dict.c.o [31/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/DiscreteDistMat.cpp.o [32/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/trees.c.o [32/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/DiscreteValueVect.cpp.o [33/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/buf.c.o [33/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/ExplicitBitVect.cpp.o [34/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/triostr.c.o [34/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/FPBReader.cpp.o [35/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/pymol_chains.cc.o [35/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/MultiFPBReader.cpp.o [36/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/schematron.c.o [36/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/SparseBitVect.cpp.o [37/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/c14n.c.o [37/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/Utils.cpp.o [38/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/parserInternals.c.o [38/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/base64.cpp.o [39/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlstring.c.o [39/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/ChiralViolationContrib.cpp.o [40/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/deflate.c.o [40/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/DistGeomUtils.cpp.o [41/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlunicode.c.o [41/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/DistViolationContrib.cpp.o [42/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/CatalogParams.cpp.o [42/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/TriangleSmooth.cpp.o [43/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/interpolate.cc.o [43/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/ForceField.cpp.o [44/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlIO.c.o [44/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/AngleBend.cpp.o [45/6111] Building C object CMakeFiles/zlib.dir/home/benchmark/rosetta/source/external/zlib-1.2.8/inflate.c.o [45/6111] Linking C static library bin/libzlib.a [46/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/encoding.c.o [46/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/AngleConstraint.cpp.o [47/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/SAX2.c.o [47/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/BondStretch.cpp.o [48/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/CatalogEntry.cpp.o [48/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/DistanceConstraint.cpp.o [49/6111] Linking C static library bin/libzlib.a [49/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/Nonbonded.cpp.o [50/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/pattern.c.o [50/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/OopBend.cpp.o [51/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xinclude.c.o [51/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/Params.cpp.o [52/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/uri.c.o [52/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/PositionConstraint.cpp.o [53/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlsave.c.o [53/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/StretchBend.cpp.o [54/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/debugXML.c.o [54/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/TorsionAngle.cpp.o [55/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/catalog.c.o [55/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/TorsionConstraint.cpp.o [56/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/base64.cpp.o [56/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/AngleBend.cpp.o [57/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xpointer.c.o [57/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/AngleConstraint.cpp.o [58/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/DiscreteDistMat.cpp.o [58/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/BondStretch.cpp.o [59/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlwriter.c.o [59/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/DistanceConstraint.cpp.o [60/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlreader.c.o [60/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Inversion.cpp.o [61/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/valid.c.o [61/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Nonbonded.cpp.o [62/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/trio.c.o [62/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Params.cpp.o [63/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlschemastypes.c.o [63/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/PositionConstraint.cpp.o [64/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/HTMLparser.c.o [64/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/TorsionAngle.cpp.o [65/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlregexp.c.o [65/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/TorsionConstraint.cpp.o [66/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/tree.c.o [66/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/GridUtils.cpp.o [67/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/relaxng.c.o [67/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/Transform2D.cpp.o [68/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/Utils.cpp.o [68/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/Transform3D.cpp.o [69/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/BitVect.cpp.o [69/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/UniformGrid3D.cpp.o [70/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ChemicalFeatures/FreeChemicalFeature.cpp.o [70/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/point.cpp.o [71/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/DiscreteValueVect.cpp.o [71/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AddHs.cpp.o [72/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/MultiFPBReader.cpp.o [72/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AdjustQuery.cpp.o [73/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/SparseBitVect.cpp.o [73/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Aromaticity.cpp.o [74/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Catalogs/Catalog.cpp.o [74/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Atom.cpp.o [75/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/DistViolationContrib.cpp.o [75/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AtomIterators.cpp.o [76/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/ExplicitBitVect.cpp.o [76/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Bond.cpp.o [77/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/ChiralViolationContrib.cpp.o [77/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/BondIterators.cpp.o [78/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/TriangleSmooth.cpp.o [78/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Canon.cpp.o [79/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/PositionConstraint.cpp.o [79/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Chirality.cpp.o [80/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/DistanceConstraint.cpp.o [80/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Conformer.cpp.o [81/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/BondStretch.cpp.o [81/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ConjugHybrid.cpp.o [82/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/AngleBend.cpp.o [82/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FindRings.cpp.o [83/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/BondStretch.cpp.o [83/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FindStereo.cpp.o [84/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/StretchBend.cpp.o [84/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Kekulize.cpp.o [85/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xpath.c.o [85/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Matrices.cpp.o [86/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/DistanceConstraint.cpp.o [86/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDiscriminators.cpp.o [87/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/OopBend.cpp.o [87/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolOps.cpp.o [88/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/AngleBend.cpp.o [88/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolPickler.cpp.o [89/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/TorsionConstraint.cpp.o [89/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PeriodicTable.cpp.o [90/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/AngleConstraint.cpp.o [90/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryAtom.cpp.o [91/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/TorsionAngle.cpp.o [91/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryBond.cpp.o [92/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/AngleConstraint.cpp.o [92/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryOps.cpp.o [93/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/BitOps.cpp.o [93/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ROMol.cpp.o [94/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/BrokerMain.cc.o [94/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RWMol.cpp.o [95/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Nonbonded.cpp.o [95/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Renumber.cpp.o [96/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/parser.c.o /home/benchmark/rosetta/source/external/libxml2/parser.c: In function ‘xmlParseReference’: /home/benchmark/rosetta/source/external/libxml2/parser.c:7230:44: warning: ‘%d’ directive output may be truncated writing between 3 and 10 bytes into a region of size 9 [-Wformat-truncation=] 7230 | snprintf((char *)out, sizeof(out), "#%d", value); | ^~ /home/benchmark/rosetta/source/external/libxml2/parser.c:7230:42: note: directive argument in the range [256, 2147483647] 7230 | snprintf((char *)out, sizeof(out), "#%d", value); | ^~~~~ In file included from /usr/include/stdio.h:867, from /home/benchmark/rosetta/source/external/libxml2/trio.h:37, from /home/benchmark/rosetta/source/external/libxml2/libxml.h:58, from /home/benchmark/rosetta/source/external/libxml2/parser.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 5 and 12 bytes into a destination of size 10 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/benchmark/rosetta/source/external/libxml2/parser.c:7228:47: warning: ‘__builtin___snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 7228 | snprintf((char *)out, sizeof(out), "#x%X", value); | ^ In file included from /usr/include/stdio.h:867, from /home/benchmark/rosetta/source/external/libxml2/trio.h:37, from /home/benchmark/rosetta/source/external/libxml2/libxml.h:58, from /home/benchmark/rosetta/source/external/libxml2/parser.c:34: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:10: note: ‘__builtin___snprintf_chk’ output between 6 and 11 bytes into a destination of size 10 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [96/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Resonance.cpp.o [97/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/PositionConstraint.cpp.o [97/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RingInfo.cpp.o [98/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Inversion.cpp.o [98/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StereoGroup.cpp.o [99/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DataStructs/FPBReader.cpp.o [99/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstanceGroup.cpp.o [100/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/ForceField.cpp.o [100/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/atomic_data.cpp.o [101/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/Params.cpp.o [101/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/new_canon.cpp.o [102/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/TorsionAngle.cpp.o [102/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Abbreviations/Abbreviations.cpp.o [103/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/UFF/TorsionConstraint.cpp.o [103/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Abbreviations/AbbreviationsUtils.cpp.o [104/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/prof.cc.o [104/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/CIPLabeler.cpp.o [105/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StereoGroup.cpp.o [105/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/CIPMol.cpp.o [106/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/GridUtils.cpp.o [106/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Digraph.cpp.o [107/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/Nonbonded.cpp.o [107/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Edge.cpp.o [108/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/Transform2D.cpp.o [108/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Mancude.cpp.o [109/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/Transform3D.cpp.o [109/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Node.cpp.o [110/6111] Building C object CMakeFiles/libxml2.dir/home/benchmark/rosetta/source/external/libxml2/xmlschemas.c.o [110/6111] Linking C static library bin/liblibxml2.a [111/6111] Linking C static library bin/liblibxml2.a [111/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Sort.cpp.o [112/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/point.cpp.o [112/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/DaylightParser.cpp.o [113/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Geometry/UniformGrid3D.cpp.o [113/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/MDLParser.cpp.o [114/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RingInfo.cpp.o [114/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/MoleculeParser.cpp.o [115/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ForceField/MMFF/Params.cpp.o [115/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/PNGParser.cpp.o [116/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ConstraintFragmentSampler.cc.o [116/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/PreprocessRxn.cpp.o [117/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Sort.cpp.o [117/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Reaction.cpp.o [118/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Edge.cpp.o [118/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionDepict.cpp.o [119/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/DistGeom/DistGeomUtils.cpp.o [119/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionFingerprints.cpp.o [120/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/atomic_data.cpp.o [120/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionPickler.cpp.o [121/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PeriodicTable.cpp.o [121/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionRunner.cpp.o [122/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/BondIterators.cpp.o [122/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionUtils.cpp.o [123/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ConjugHybrid.cpp.o [123/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionWriter.cpp.o [124/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Conformer.cpp.o [124/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/SanitizeRxn.cpp.o [125/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Bond.cpp.o [125/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.cpp.o [126/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/DomainAssembly.cc.o [126/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp.o [127/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxMover.cc.o [127/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp.o [128/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDiscriminators.cpp.o [128/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemTransforms/ChemTransforms.cpp.o [129/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AtomIterators.cpp.o [129/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemTransforms/MolFragmenter.cpp.o [130/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Matrices.cpp.o [130/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/DepictUtils.cpp.o [131/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryAtom.cpp.o [131/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/EmbeddedFrag.cpp.o [132/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Renumber.cpp.o [132/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/RDDepictor.cpp.o [133/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Aromaticity.cpp.o [133/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Deprotect/Deprotect.cpp.o [134/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryBond.cpp.o [134/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/AUTOCORR2D.cpp.o [135/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Digraph.cpp.o [135/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/AtomFeat.cpp.o [136/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/CIPMol.cpp.o [136/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/BCUT.cpp.o [137/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/BCUT.cpp.o [137/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.cpp.o [138/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Mancude.cpp.o [138/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Crippen.cpp.o [139/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Atom.cpp.o [139/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Data3Ddescriptors.cpp.o [140/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/CIPLabeler.cpp.o [140/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Lipinski.cpp.o [141/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/CIPLabeler/Node.cpp.o [141/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MQN.cpp.o [142/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Abbreviations/AbbreviationsUtils.cpp.o [142/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.cpp.o [143/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Kekulize.cpp.o [143/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolDescriptors.cpp.o [144/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Data3Ddescriptors.cpp.o [144/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolSurf.cpp.o [145/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/QueryOps.cpp.o [145/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Property.cpp.o [146/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionDepict.cpp.o [146/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/USRDescriptor.cpp.o [147/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Canon.cpp.o [147/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp.o [148/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RWMol.cpp.o [148/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/DistGeomHelpers/Embedder.cpp.o [149/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/MoleculeParser.cpp.o [149/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/FMCS.cpp.o [150/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/DaylightParser.cpp.o [150/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.cpp.o [151/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/PreprocessRxn.cpp.o [151/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/Seed.cpp.o [152/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FindStereo.cpp.o [152/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/SubstructMatchCustom.cpp.o [153/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AdjustQuery.cpp.o [153/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructureFlags.cpp.o [154/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ClassicAbinitio.cc.o [154/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/ForwardSDMolSupplier.cpp.o [155/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/PNGParser.cpp.o [155/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/Mol2FileParser.cpp.o [156/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstanceGroup.cpp.o [156/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileParser.cpp.o [157/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ROMol.cpp.o [157/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileStereochem.cpp.o [158/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Abbreviations/Abbreviations.cpp.o [158/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileWriter.cpp.o [159/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Resonance.cpp.o [159/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolSGroupParsing.cpp.o [160/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FindRings.cpp.o [160/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolSGroupWriting.cpp.o [161/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionFingerprints.cpp.o [161/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.cpp.o [162/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/AddHs.cpp.o [162/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp.o [163/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.cpp.o [163/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp.o [164/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp.o [164/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBParser.cpp.o [165/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp.o [165/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBSupplier.cpp.o [166/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp.o [166/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBWriter.cpp.o [167/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolOps.cpp.o [167/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PNGParser.cpp.o [168/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionUtils.cpp.o [168/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/ProximityBonds.cpp.o [169/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/new_canon.cpp.o [169/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SDMolSupplier.cpp.o [170/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionWriter.cpp.o [170/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SDWriter.cpp.o [171/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionPickler.cpp.o [171/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SVGParser.cpp.o [172/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/MDLParser.cpp.o [172/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SequenceParsers.cpp.o [173/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Reaction.cpp.o [173/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SequenceWriters.cpp.o [174/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/AUTOCORR2D.cpp.o [174/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SmilesMolSupplier.cpp.o [175/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Chirality.cpp.o [175/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SmilesWriter.cpp.o [176/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/AtomFeat.cpp.o [176/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TDTMolSupplier.cpp.o [177/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MQN.cpp.o [177/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TDTWriter.cpp.o [178/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.cpp.o [178/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TplFileParser.cpp.o [179/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolDescriptors.cpp.o [179/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TplFileWriter.cpp.o [180/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/RDDepictor.cpp.o [180/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/XYZFileWriter.cpp.o [181/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.cpp.o [181/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalog.cpp.o [182/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Deprotect/Deprotect.cpp.o [182/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.cpp.o [183/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/SanitizeRxn.cpp.o [183/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalogRunner.cpp.o [184/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp.o [184/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterMatchers.cpp.o [185/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.cpp.o [185/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/Filters.cpp.o [186/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/DepictUtils.cpp.o [186/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp.o [187/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructureFlags.cpp.o [187/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/AtomPairGenerator.cpp.o [188/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/MolSurf.cpp.o [188/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/AtomPairs.cpp.o [189/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Lipinski.cpp.o [189/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/FingerprintGenerator.cpp.o [190/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBSupplier.cpp.o [190/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/FingerprintUtil.cpp.o [191/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Crippen.cpp.o [191/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/Fingerprints.cpp.o [192/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/SubstructMatchCustom.cpp.o [192/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MACCS.cpp.o [193/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/Property.cpp.o [193/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MHFP.cpp.o [194/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolPickler.cpp.o [194/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MorganFingerprints.cpp.o [195/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemReactions/ReactionRunner.cpp.o [195/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MorganGenerator.cpp.o [196/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Descriptors/USRDescriptor.cpp.o [196/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/PatternFingerprints.cpp.o [197/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileStereochem.cpp.o [197/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.cpp.o [198/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/ProximityBonds.cpp.o [198/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp.o [199/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/Seed.cpp.o [199/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp.o [200/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Depictor/EmbeddedFrag.cpp.o [200/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp.o [201/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SDMolSupplier.cpp.o [201/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp.o [202/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PNGParser.cpp.o [202/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp.o [203/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemTransforms/ChemTransforms.cpp.o [203/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp.o [204/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SDWriter.cpp.o [204/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.cpp.o [205/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp.o [205/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatGenerator.cpp.o [206/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/DistGeomHelpers/Embedder.cpp.o [206/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatParams.cpp.o [207/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/ForwardSDMolSupplier.cpp.o [207/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatalogEntry.cpp.o [208/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SequenceWriters.cpp.o [208/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatalogUtils.cpp.o [209/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBParser.cpp.o [209/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragFPGenerator.cpp.o [210/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SmilesWriter.cpp.o [210/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MMPA/MMPA.cpp.o [211/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SmilesMolSupplier.cpp.o [211/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolAlign/AlignMolecules.cpp.o [212/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SequenceParsers.cpp.o [212/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolAlign/O3AAlignMolecules.cpp.o [213/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/FMCS.cpp.o [213/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolCatalog/MolCatalogEntry.cpp.o [214/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/Mol2FileParser.cpp.o [214/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolCatalog/MolCatalogParams.cpp.o [215/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/Filters.cpp.o [215/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.cpp.o [216/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/PDBWriter.cpp.o [216/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp.o [217/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TplFileWriter.cpp.o [217/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp.o [218/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TDTMolSupplier.cpp.o [218/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp.o [219/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalogRunner.cpp.o [219/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawText.cpp.o [220/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolSGroupWriting.cpp.o [220/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawTextJS.cpp.o [221/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawTextJS.cpp.o [221/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawTextSVG.cpp.o [222/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolSGroupParsing.cpp.o [222/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2D.cpp.o [223/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp.o [223/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DDetails.cpp.o [224/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ChemTransforms/MolFragmenter.cpp.o [224/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.cpp.o [225/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.cpp.o [225/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.cpp.o [226/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/AtomPairGenerator.cpp.o [226/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.cpp.o [227/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterMatchers.cpp.o [227/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/LinkNode.cpp.o [228/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalog.cpp.o [228/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/MolEnumerator.cpp.o [229/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.cpp.o [229/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/PositionVariation.cpp.o [230/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolCatalog/MolCatalogParams.cpp.o [230/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolHash/hashfunctions.cpp.o [231/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/SVGParser.cpp.o [231/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolHash/normalize.cpp.o [232/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TDTWriter.cpp.o [232/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolInterchange/Parser.cpp.o [233/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/XYZFileWriter.cpp.o [233/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolInterchange/Writer.cpp.o [234/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/AtomPairs.cpp.o [234/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Charge.cpp.o [235/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp.o [235/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Fragment.cpp.o [236/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp.o [236/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Metal.cpp.o [237/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MHFP.cpp.o [237/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/MolStandardize.cpp.o [238/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileWriter.cpp.o [238/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Normalize.cpp.o [239/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/FingerprintGenerator.cpp.o [239/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Tautomer.cpp.o [240/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/TplFileParser.cpp.o [240/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Validate.cpp.o [241/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.cpp.o [241/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o [242/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/PatternFingerprints.cpp.o [242/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o [243/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.cpp.o [243/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o [244/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp.o [244/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp.o [245/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/Fingerprints.cpp.o [245/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp.o [246/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/FingerprintUtil.cpp.o [246/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp.o [247/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/AbrelaxApplication.cc.o [247/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp.o [248/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MACCS.cpp.o [248/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp.o [249/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MorganFingerprints.cpp.o [249/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp.o [250/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp.o [250/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp.o [251/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp.o [251/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp.o [252/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Fingerprints/MorganGenerator.cpp.o [252/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp.o [253/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragFPGenerator.cpp.o [253/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolTransforms/MolTransforms.cpp.o [254/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.cpp.o [254/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PartialCharges/GasteigerCharges.cpp.o [255/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatParams.cpp.o [255/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PartialCharges/GasteigerParams.cpp.o [256/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp.o [256/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.cpp.o [257/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolCatalog/MolCatalogEntry.cpp.o [257/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp.o [258/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp.o [258/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp.o [259/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatGenerator.cpp.o [259/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupGa.cpp.o [260/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolAlign/AlignMolecules.cpp.o [260/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupScore.cpp.o [261/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp.o [261/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupUtils.cpp.o [262/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatalogEntry.cpp.o [262/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.cpp.o [263/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MMPA/MMPA.cpp.o [263/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp.o [264/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawText.cpp.o [264/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.cpp.o [265/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FragCatalog/FragCatalogUtils.cpp.o [265/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ShapeHelpers/ShapeUtils.cpp.o [266/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/DrawTextSVG.cpp.o [266/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/CXSmilesOps.cpp.o [267/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolHash/normalize.cpp.o [267/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmartsWrite.cpp.o [268/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp.o [268/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesParse.cpp.o [269/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o [269/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesParseOps.cpp.o [270/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolAlign/O3AAlignMolecules.cpp.o [270/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesWrite.cpp.o [271/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/PositionVariation.cpp.o [271/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/lex.yysmarts.cpp.o [272/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o [272/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/lex.yysmiles.cpp.o [273/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolHash/hashfunctions.cpp.o [273/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/smarts.tab.cpp.o [274/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Metal.cpp.o [274/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/smiles.tab.cpp.o [275/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp.o [275/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/AtomSymbolMatch.cpp.o [276/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.cpp.o [276/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Pattern.cpp.o [277/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp.o [277/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/ReCharge.cpp.o [278/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp.o [278/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Stereo.cpp.o [279/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/MolEnumerator.cpp.o [279/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StripSmallFragments.cpp.o [280/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp.o [280/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructChecker.cpp.o [281/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/MolStandardize.cpp.o [281/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructCheckerOptions.cpp.o [282/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PartialCharges/GasteigerParams.cpp.o [282/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Tautomer.cpp.o [283/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DDetails.cpp.o [283/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Utilites.cpp.o [284/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp.o [284/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Subgraphs/SubgraphUtils.cpp.o [285/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o [285/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Subgraphs/Subgraphs.cpp.o [286/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Fragment.cpp.o [286/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Substruct/SubstructMatch.cpp.o [287/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp.o [287/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Substruct/SubstructUtils.cpp.o [288/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.cpp.o [288/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstructLibrary/PatternFactory.cpp.o [289/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/PartialCharges/GasteigerCharges.cpp.o [289/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.cpp.o [290/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp.o [290/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/TautomerQuery/TautomerQuery.cpp.o [291/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolEnumerator/LinkNode.cpp.o [291/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Trajectory/Trajectory.cpp.o [292/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.cpp.o [292/6111] Building C object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/Cluster/Murtagh/hc.c.o [293/6111] Building C object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/Cluster/Murtagh/hc.c.o [293/6111] Building C object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/Cluster/Murtagh/hcdriver.c.o [294/6111] Building C object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/Cluster/Murtagh/hcdriver.c.o [294/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/InfoTheory/InfoBitRanker.cpp.o [295/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Normalize.cpp.o [295/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Alignment/AlignPoints.cpp.o [296/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.cpp.o [296/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/EigenSolvers/PowerEigenSolver.cpp.o [297/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolInterchange/Writer.cpp.o [297/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Optimizer/BFGSOpt.cpp.o [298/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Charge.cpp.o [298/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Optimizer/LinearSearch.cpp.o [299/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Validate.cpp.o [299/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/Invariant.cpp.o [300/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ShapeHelpers/ShapeUtils.cpp.o [300/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/LocaleSwitcher.cpp.o [301/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp.o [301/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/RDGeneralExceptions.cpp.o [302/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolInterchange/Parser.cpp.o [302/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/RDLog.cpp.o [303/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/LocaleSwitcher.cpp.o [303/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/types.cpp.o [304/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/RDGeneralExceptions.cpp.o [304/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/utils.cpp.o [305/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp.o [305/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/versions.cpp.o [306/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp.o [306/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDStreams/streams.cpp.o [307/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolTransforms/MolTransforms.cpp.o [307/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/DistPicker.cpp.o [308/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/versions.cpp.o [308/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/HierarchicalClusterPicker.cpp.o [309/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDStreams/streams.cpp.o [309/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/MaxMinPicker.cpp.o [310/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp.o [310/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/TracerToFile.cc.o [311/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupScore.cpp.o [311/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/Tracer.cc.o [312/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolStandardize/Tautomer.cpp.o [312/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/MemTracer.cc.o [313/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/AtomSymbolMatch.cpp.o [313/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/MetricValueIO.cc.o [314/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.cpp.o [314/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/TracerImpl.cc.o [315/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/TracerToFile.cc.o [315/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/report.cc.o [316/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp.o [316/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/Citation.cc.o [317/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/Invariant.cpp.o [317/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationCollection.cc.o [318/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupUtils.cpp.o [318/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/Emitter.cc.o [319/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/Tracer.cc.o [319/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/ComparingTracer.cc.o [320/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructChecker.cpp.o [320/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/execute.cc.o [321/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Tautomer.cpp.o [321/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/init.cc.o [322/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/init.cc.o [322/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/basic.cc.o [323/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Optimizer/BFGSOpt.cpp.o [323/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/open.cc.o [324/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/RDLog.cpp.o [324/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/sql_utils.cc.o [325/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/ReCharge.cpp.o [325/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Column.cc.o [326/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Optimizer/LinearSearch.cpp.o [326/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Constraint.cc.o [327/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/MemTracer.cc.o [327/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationCollectionBase.cc.o [328/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/lex.yysmarts.cpp.o [328/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationManager.cc.o [329/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/basic.cc.o [329/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/UnpublishedModuleAuthor.cc.o [330/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/EigenSolvers/PowerEigenSolver.cpp.o [330/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/UnpublishedModuleInfo.cc.o [331/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/Numerics/Alignment/AlignPoints.cpp.o [331/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/motif_hash_stuff.cc.o [332/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/DistPicker.cpp.o [332/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/util.cc.o [333/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/types.cpp.o [333/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/xfrags.cc.o [334/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/lex.yysmiles.cpp.o [334/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/netcharge_energy/NetChargeConstraint.cc.o [335/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/smiles.tab.cpp.o [335/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/netcharge_energy/NetChargeEnergySetup.cc.o [336/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/MaxMinPicker.cpp.o [336/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/DbDataType.cc.o [337/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/ML/InfoTheory/InfoBitRanker.cpp.o [337/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/ForeignKey.cc.o [338/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Pattern.cpp.o [338/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Index.cc.o [339/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/SimDivPickers/HierarchicalClusterPicker.cpp.o [339/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/PrimaryKey.cc.o [340/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationCollectionBase.cc.o [340/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Schema.cc.o [341/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Column.cc.o [341/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/insert_statement_generator/InsertGenerator.cc.o [342/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/Emitter.cc.o [342/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/insert_statement_generator/RowData.cc.o [343/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Constraint.cc.o [343/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/BasicDataCache.cc.o [344/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationCollection.cc.o [344/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableData.cc.o [345/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmartsWrite.cpp.o [345/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableResRotPairFloatMap.cc.o [346/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/UnpublishedModuleAuthor.cc.o [346/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableString.cc.o [347/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StripSmallFragments.cpp.o [347/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringFloatMap.cc.o [348/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/insert_statement_generator/RowData.cc.o [348/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringIntegerMap.cc.o [349/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupGa.cpp.o [349/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringMap.cc.o [350/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableData.cc.o [350/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableUint64MathMatrixFloatMap.cc.o [351/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesParse.cpp.o [351/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/ConstDataMap.cc.o [352/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Utilites.cpp.o [352/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DataMap.cc.o [353/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Subgraphs/Subgraphs.cpp.o [353/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DataMapObj.cc.o [354/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/execute.cc.o [354/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DiagnosticData.cc.o [355/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/UnpublishedModuleInfo.cc.o [355/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/HierarchicalDataMap.cc.o [356/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableString.cc.o [356/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableData.cc.o [357/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Subgraphs/SubgraphUtils.cpp.o [357/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableDataCreator.cc.o [358/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/MetricValueIO.cc.o [358/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableDataFactory.cc.o [359/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/FileParsers/MolFileParser.cpp.o [359/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableMap.cc.o [360/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/PrimaryKey.cc.o [360/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/gpu/GPU.cc.o [361/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DataMapObj.cc.o [361/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/gpu/Timer.cc.o [362/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/gpu/GPU.cc.o [362/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/DbMoverMessageListener.cc.o [363/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringFloatMap.cc.o [363/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/MessageListenerFactory.cc.o [364/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstructLibrary/PatternFactory.cpp.o [364/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/util.cc.o [365/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/smarts.tab.cpp.o [365/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/PyRosettaFunctions.cc.o [366/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringIntegerMap.cc.o [366/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/after_opts.cc.o [367/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableStringMap.cc.o [367/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/option.cc.o [368/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/RDGeneral/utils.cpp.o [368/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/util.cc.o [369/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/Citation.cc.o [369/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys0.cc.o [370/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableDataCreator.cc.o [370/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys1.cc.o [371/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DiagnosticData.cc.o [371/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys10.cc.o [372/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableData.cc.o [372/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys11.cc.o [373/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/BasicDataCache.cc.o [373/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys12.cc.o [374/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesWrite.cpp.o [374/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys13.cc.o [375/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Index.cc.o [375/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys14.cc.o [376/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/ForeignKey.cc.o [376/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys15.cc.o [377/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/TracerImpl.cc.o [377/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys2.cc.o [378/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/insert_statement_generator/InsertGenerator.cc.o [378/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys3.cc.o [379/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/DbDataType.cc.o [379/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys4.cc.o [380/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/SmilesParseOps.cpp.o [380/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys5.cc.o [381/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Substruct/SubstructUtils.cpp.o [381/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys6.cc.o [382/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableUint64MathMatrixFloatMap.cc.o [382/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys7.cc.o [383/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/Stereo.cpp.o [383/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys8.cc.o [384/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/CacheableResRotPairFloatMap.cc.o [384/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys9.cc.o [385/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Trajectory/Trajectory.cpp.o [385/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/random/RandomGeneratorSettings.cc.o [386/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/ComparingTracer.cc.o [386/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/random/init_random_generator.cc.o [387/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.cpp.o [387/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoader.cc.o [388/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableMap.cc.o [388/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoaderCreator.cc.o [389/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/HierarchicalDataMap.cc.o [389/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoaderFactory.cc.o [390/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/gpu/Timer.cc.o [390/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocator.cc.o [391/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/report.cc.o [391/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocatorCreator.cc.o [392/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/util.cc.o [392/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocatorFactory.cc.o [393/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/citation_manager/CitationManager.cc.o [393/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc.o [394/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoaderCreator.cc.o [394/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManagerCreator.cc.o [395/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/DataMap.cc.o [395/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManagerFactory.cc.o [396/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/ConstDataMap.cc.o [396/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/loader_schemas.cc.o [397/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/datacache/WriteableCacheableDataFactory.cc.o [397/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/DatabaseResourceLocator.cc.o [398/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocator.cc.o [398/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/FileListResourceLocator.cc.o [399/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/MessageListenerFactory.cc.o [399/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/FileSystemResourceLocator.cc.o [400/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocatorCreator.cc.o [400/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/NullResourceLocator.cc.o [401/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManagerCreator.cc.o [401/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/StringResourceStream.cc.o [402/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/StructChecker/StructCheckerOptions.cpp.o [402/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/locator_schemas.cc.o [403/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/schema_generator/Schema.cc.o [403/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/sampling/orientations/QuaternionGrid.cc.o [404/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/TautomerQuery/TautomerQuery.cpp.o [404/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/svd/SVD_Solver.cc.o [405/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/Substruct/SubstructMatch.cpp.o [405/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowManager.cc.o [406/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/open.cc.o [406/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowProtocolBase.cc.o [407/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/StringResourceStream.cc.o [407/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowSessionContainer.cc.o [408/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/locator_schemas.cc.o [408/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowTensorContainer.cc.o [409/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowProtocolBase.cc.o [409/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/util.cc.o [410/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowTensorContainer.cc.o [410/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThread.cc.o [411/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLocatorFactory.cc.o [411/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadAllocation.cc.o [412/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/SmilesParse/CXSmilesOps.cpp.o [412/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadAssignmentInfo.cc.o [413/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/netcharge_energy/NetChargeConstraint.cc.o [413/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadManager.cc.o [414/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManagerFactory.cc.o [414/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadManagerInitializationTracker.cc.o [415/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoader.cc.o [415/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadPool.cc.o [416/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/mpi/DbMoverMessageListener.cc.o [416/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/coupled_moves/CoupledMovesProtocol.cc.o [417/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowManager.cc.o [417/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/loops/loop_closure/jacobi/JacobiLoopClosureMover.cc.o [418/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceLoaderFactory.cc.o [418/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorJobDistributor.cc.o [419/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/RosettaTensorflowSessionContainer.cc.o [419/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/cartesian/md.cc.o [420/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/NullResourceLocator.cc.o [420/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc.o [421/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/FileListResourceLocator.cc.o [421/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc.o [422/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/loader_schemas.cc.o [422/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorUtil.cc.o [423/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadAllocation.cc.o [423/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/mainchain_potential/GenerateMainchainPotential.cc.o [424/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/after_opts.cc.o [424/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/mainchain_potential/GenerateMainchainPotentialOptions.cc.o [425/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThread.cc.o [425/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/atomic_counter.cpp.o [426/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/svd/SVD_Solver.cc.o [426/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/backend.cpp.o [427/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/atomic_counter.cpp.o [427/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/conn_manager.cpp.o [428/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/random/init_random_generator.cc.o [428/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/driver_manager.cpp.o [429/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/netcharge_energy/NetChargeEnergySetup.cc.o [429/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/frontend.cpp.o [430/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadAssignmentInfo.cc.o [430/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/mutex.cpp.o [431/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/mutex.cpp.o [431/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/pool.cpp.o [432/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/tensorflow_manager/util.cc.o [432/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/shared_object.cpp.o [433/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/DatabaseResourceLocator.cc.o [433/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/sqlite3_backend.cpp.o [434/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/random/RandomGeneratorSettings.cc.o [434/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/utils.cpp.o [435/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/shared_object.cpp.o [435/6111] Building C object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/sqlite3/sqlite3.c.o [436/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadPool.cc.o [436/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/carbohydrates/GlycanTreeSetObserver.cc.o [437/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/PyRosettaFunctions.cc.o [437/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/carbohydrates/util.cc.o [438/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/pool.cpp.o [438/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/AqueousPoreParameters.cc.o [439/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/conn_manager.cpp.o [439/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/ImplicitLipidInfo.cc.o [440/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/backend.cpp.o [440/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/MembraneInfo.cc.o [441/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorUtil.cc.o [441/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/Span.cc.o [442/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorJobDistributor.cc.o [442/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/SpanningTopology.cc.o [443/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc.o [443/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/util.cc.o [444/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/driver_manager.cpp.o [444/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/orbitals/OrbitalXYZCoords.cc.o [445/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/utils.cpp.o [445/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/BooleanValuedParameter.cc.o [446/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadManagerInitializationTracker.cc.o [446/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/Parameter.cc.o [447/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/database/sql_utils.cc.o [447/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/Parameters.cc.o [448/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/orbitals/OrbitalXYZCoords.cc.o [448/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/ParametersSet.cc.o [449/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/sampling/orientations/QuaternionGrid.cc.o [449/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/ParametrizationCalculator.cc.o [450/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/frontend.cpp.o [450/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/DoubleLayerKinematicAbinitio.cc.o [451/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys1.cc.o [451/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/FoldConstraints.cc.o [452/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/Span.cc.o [452/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/FragmentSampler.cc.o [453/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys0.cc.o [453/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/HedgeArchive.cc.o [454/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys10.cc.o [454/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeAbrelax.cc.o [455/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc.o [455/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [456/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys6.cc.o [456/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeCentroid.cc.o [457/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys14.cc.o [457/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeFullatom.cc.o [458/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys2.cc.o [458/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicAbinitio.cc.o [459/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys15.cc.o [459/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicControl.cc.o [460/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys5.cc.o [460/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicTaskControl.cc.o [461/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys7.cc.o [461/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/LoopJumpFoldCst.cc.o [462/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/MolDraw2D/MolDraw2D.cpp.o [462/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/MembraneAbinitio.cc.o [463/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys13.cc.o [463/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/PairingStatistics.cc.o [464/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys3.cc.o [464/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Protocol.cc.o [465/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys12.cc.o [465/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ResolutionSwitcher.cc.o [466/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys4.cc.o [466/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/StrandConstraints.cc.o [467/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys11.cc.o [467/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Template.cc.o [468/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/locator/FileSystemResourceLocator.cc.o [468/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/TemplateJumpSetup.cc.o [469/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys9.cc.o [469/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Templates.cc.o [470/6111] Building CXX object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/cppdb/sqlite3_backend.cpp.o [470/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/util.cc.o [471/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/Parameter.cc.o [471/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/vs_test.cc.o [472/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/keys/OptionKeys8.cc.o [472/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc.o [473/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/AqueousPoreParameters.cc.o [473/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptMover.cc.o [474/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/thread_manager/RosettaThreadManager.cc.o [474/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptStageMover.cc.o [475/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/ParametrizationCalculator.cc.o [475/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/ConstraintPreparer.cc.o [476/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/mainchain_potential/GenerateMainchainPotentialOptions.cc.o [476/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/FragmentCM.cc.o [477/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/BooleanValuedParameter.cc.o [477/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/FragmentJumpCM.cc.o [478/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/carbohydrates/GlycanTreeSetObserver.cc.o [478/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/JumpSampleData.cc.o [479/6111] Building CXX object CMakeFiles/rdkit.dir/home/benchmark/rosetta/source/external/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.cpp.o [479/6111] Linking CXX static library bin/librdkit.a [480/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/MembraneInfo.cc.o [480/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/RigidChunkCM.cc.o [481/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/xfrags.cc.o [481/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/StagePreparer.cc.o [482/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/Parameters.cc.o [482/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/StructPerturberCM.cc.o [483/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/util.cc.o [483/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/CartesianddG.cc.o [484/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc.o [484/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddGData.cc.o [485/6111] Linking CXX static library bin/librdkit.a [485/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddGMover.cc.o [486/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/util.cc.o [486/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddG_main.cc.o [487/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeCentroid.cc.o [487/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/BackboneTorsionPerturbation.cc.o [488/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/parametric/ParametersSet.cc.o [488/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/BackboneTorsionSampler.cc.o [489/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/ImplicitLipidInfo.cc.o [489/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/CartesianHybridize.cc.o [490/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/HedgeArchive.cc.o [490/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/CartesianSampler.cc.o [491/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/membrane/SpanningTopology.cc.o [491/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/ChunkTrialMover.cc.o [492/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicControl.cc.o [492/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/DDomainParse.cc.o [493/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/mainchain_potential/GenerateMainchainPotential.cc.o [493/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/DomainAssembly.cc.o [494/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicTaskControl.cc.o [494/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [495/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/StrandConstraints.cc.o [495/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FragmentBiasAssigner.cc.o [496/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/util.cc.o [496/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeFoldtreeDynamic.cc.o [497/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/StagePreparer.cc.o [497/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [498/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/ResolutionSwitcher.cc.o [498/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/InsertChunkMover.cc.o [499/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddGData.cc.o [499/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/MRMover.cc.o [500/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/JumpSampleData.cc.o [500/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/TMalign.cc.o [501/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Protocol.cc.o [501/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/TemplateHistory.cc.o [502/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/loops/loop_closure/jacobi/JacobiLoopClosureMover.cc.o [502/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/WeightedFragmentSmoothTrialMover.cc.o [503/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/TemplateJumpSetup.cc.o [503/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/WeightedFragmentTrialMover.cc.o [504/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeAbrelax.cc.o [504/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/util.cc.o [505/6111] Building CXX object CMakeFiles/core.2.dir/home/benchmark/rosetta/source/src/core/conformation/carbohydrates/util.cc.o [505/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/DisulfPairingLibrary.cc.o [506/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/FoldConstraints.cc.o [506/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/DisulfPairingsList.cc.o [507/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/PairingStatistics.cc.o [507/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSample.cc.o [508/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeFullatom.cc.o [508/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSetup.cc.o [509/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/StructPerturberCM.cc.o [509/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/MembraneJump.cc.o [510/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/cartesian/md.cc.o [510/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/PairingLibrary.cc.o [511/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/DoubleLayerKinematicAbinitio.cc.o [511/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/RandomSheetBuilder.cc.o [512/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/WeightedFragmentTrialMover.cc.o [512/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJump.cc.o [513/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/TemplateHistory.cc.o [513/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJumpSetup.cc.o [514/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptStageMover.cc.o [514/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/SameStrand.cc.o [515/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/ConstraintPreparer.cc.o [515/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/SheetBuilder.cc.o [516/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/DisulfPairingsList.cc.o [516/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/util.cc.o [517/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Template.cc.o [517/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopBuild.cc.o [518/6111] Building CXX object CMakeFiles/protocols.5d.dir/home/benchmark/rosetta/source/src/protocols/coupled_moves/CoupledMovesProtocol.cc.o [518/6111] Linking CXX static library bin/libprotocols.5d.a [519/6111] Linking CXX static library bin/libprotocols.5d.a [519/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopBuildMover.cc.o [520/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/DDomainParse.cc.o [520/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindow.cc.o [521/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/WeightedFragmentSmoothTrialMover.cc.o [521/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindowCreator.cc.o [522/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/LoopJumpFoldCst.cc.o [522/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopmodelWrapper.cc.o [523/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/SameStrand.cc.o [523/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/DensSkeleton.cc.o [524/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/FragmentSampler.cc.o [524/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [525/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/RandomSheetBuilder.cc.o [525/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o [526/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/Templates.cc.o [526/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [527/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/ChunkTrialMover.cc.o [527/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/util.cc.o [528/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindowCreator.cc.o [528/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CovalentCompliance.cc.o [529/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddG_main.cc.o [529/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [530/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/FragmentCM.cc.o [530/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakInfo.cc.o [531/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/FragmentJumpCM.cc.o [531/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [532/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc.o [532/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/DistanceScoreMover.cc.o [533/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FragmentBiasAssigner.cc.o [533/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/FloatingResonance.cc.o [534/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/TMalign.cc.o [534/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/FragsToAtomDist.cc.o [535/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/InsertChunkMover.cc.o [535/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/LabelResonance.cc.o [536/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/BackboneTorsionPerturbation.cc.o [536/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/MethylNames.cc.o [537/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/BackboneTorsionSampler.cc.o [537/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/NoesyModule.cc.o [538/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CovalentCompliance.cc.o [538/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [539/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/SheetBuilder.cc.o [539/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentParameters.cc.o [540/6111] Building CXX object CMakeFiles/core.3.dir/home/benchmark/rosetta/source/src/core/scoring/motif/motif_hash_stuff.cc.o [540/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentResidueMap.cc.o [541/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakInfo.cc.o [541/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakCalibrator.cc.o [542/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/AbscriptMover.cc.o [542/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat.cc.o [543/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSetup.cc.o [543/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat_Sparky.cc.o [544/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/FloatingResonance.cc.o [544/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat_xpk.cc.o [545/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/vs_test.cc.o [545/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/ProtonResonance.cc.o [546/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/DisulfPairingLibrary.cc.o [546/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/Resonance.cc.o [547/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/abscript/RigidChunkCM.cc.o [547/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/ResonanceList.cc.o [548/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/LabelResonance.cc.o [548/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureDependentPeakCalibrator.cc.o [549/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/MembraneJump.cc.o [549/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureIndependentPeakCalibrator.cc.o [550/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJump.cc.o [550/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/util.cc.o [551/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopBuild.cc.o [551/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [552/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/ddGMover.cc.o [552/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [553/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/DomainAssembly.cc.o [553/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [554/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/ProtonResonance.cc.o [554/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/MakeStarTopology.cc.o [555/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat_Sparky.cc.o [555/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [556/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/ResiduePairJumpSetup.cc.o [556/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegment.cc.o [557/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakCalibrator.cc.o [557/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [558/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat_xpk.cc.o [558/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [559/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopmodelWrapper.cc.o [559/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax_main.cc.o [560/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/util.cc.o [560/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/util.cc.o [561/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/util.cc.o [561/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/CentroidRelaxMover.cc.o [562/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/JumpSample.cc.o [562/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/FullatomRelaxMover.cc.o [563/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/Resonance.cc.o [563/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceDockingProtocol.cc.o [564/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureIndependentPeakCalibrator.cc.o [564/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceOrientMover.cc.o [565/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/PairingLibrary.cc.o [565/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceParameters.cc.o [566/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopBuildMover.cc.o [566/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceVectorLoader.cc.o [567/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/jumping/util.cc.o [567/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockBaseProtocol.cc.o [568/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/DistanceScoreMover.cc.o [568/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockProtocol.cc.o [569/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/CartesianHybridize.cc.o [569/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingHiRes.cc.o [570/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/DensSkeleton.cc.o [570/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingLowRes.cc.o [571/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/util.cc.o [571/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockMoveRbJumpMover.cc.o [572/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/util.cc.o [572/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockRbTrialMover.cc.o [573/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/KinematicAbinitio.cc.o [573/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockSlideTrialMover.cc.o [574/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/MethylNames.cc.o [574/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymRestrictTaskForDocking.cc.o [575/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_build/LoopMover_SlidingWindow.cc.o [575/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymSidechainMinMover.cc.o [576/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeFoldtreeDynamic.cc.o [576/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/membrane/MPSymDockMover.cc.o [577/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/StructureDependentPeakCalibrator.cc.o [577/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/AsymFoldandDockClaimer.cc.o [578/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/MRMover.cc.o [578/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/BasicJumpClaimer.cc.o [579/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeak.cc.o [579/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ClaimerMessage.cc.o [580/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockBaseProtocol.cc.o [580/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintClaimer.cc.o [581/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/CrossPeakList.cc.o [581/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapper.cc.o [582/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignment.cc.o [582/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapperCreator.cc.o [583/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceParameters.cc.o [583/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/CoordConstraintClaimer.cc.o [584/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymRestrictTaskForDocking.cc.o [584/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/CutBiasClaimer.cc.o [585/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceVectorLoader.cc.o [585/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/DensityScoringClaimer.cc.o [586/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockMoveRbJumpMover.cc.o [586/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/DisulfJumpClaimer.cc.o [587/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceOrientMover.cc.o [587/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FibrilModelingClaimer.cc.o [588/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegment.cc.o [588/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FoldandDockClaimer.cc.o [589/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/ResonanceList.cc.o [589/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentClaimer.cc.o [590/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/FragsToAtomDist.cc.o [590/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentJumpClaimer.cc.o [591/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentResidueMap.cc.o [591/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/LoopFragmentClaimer.cc.o [592/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ClaimerMessage.cc.o [592/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MembraneTopologyClaimer.cc.o [593/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymSidechainMinMover.cc.o [593/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MetalloClaimer.cc.o [594/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/ddg/CartesianddG.cc.o [594/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PcsEnergyController.cc.o [595/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/MembraneAbinitio.cc.o [595/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController.cc.o [596/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax_main.cc.o [596/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts1.cc.o [597/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/SheetSampler.cc.o [597/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts2.cc.o [598/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/CartesianSampler.cc.o [598/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts3.cc.o [599/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/CentroidRelaxMover.cc.o [599/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts4.cc.o [600/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapper.cc.o [600/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidBodyRandomTMHMover.cc.o [601/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakFileFormat.cc.o [601/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidChunkClaimer.cc.o [602/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/BasicJumpClaimer.cc.o [602/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SequenceClaimer.cc.o [603/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/CutBiasClaimer.cc.o [603/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SequenceNumberResolver.cc.o [604/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/membrane/MPSymDockMover.cc.o [604/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/StartStructClaimer.cc.o [605/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentMover.cc.o [605/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SymmetryClaimer.cc.o [606/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/MakeStarTopology.cc.o [606/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TMHTopologySamplerClaimer.cc.o [607/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/FullatomRelaxMover.cc.o [607/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateFragmentClaimer.cc.o [608/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/DensityScoringClaimer.cc.o [608/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateJumpClaimer.cc.o [609/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockSlideTrialMover.cc.o [609/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyBroker.cc.o [610/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/PeakAssignmentParameters.cc.o [610/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimer.cc.o [611/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/LoopFragmentClaimer.cc.o [611/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimerFactory.cc.o [612/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SequenceNumberResolver.cc.o [612/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/util.cc.o [613/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc.o [613/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/claims/DofClaim.cc.o [614/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintEvaluatorWrapperCreator.cc.o [614/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc.o [615/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingLowRes.cc.o [615/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.cc.o [616/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymFoldandDockRbTrialMover.cc.o [616/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o [617/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/AutoRBRelaxMover.cc.o [617/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o [618/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PcsEnergyController.cc.o [618/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/filters/ConstraintFulfilmentFilter.cc.o [619/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o FAILED: CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o /usr/bin/c++ -DBOOST_ALL_NO_LIB -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\"a\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=0 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0\" -DCPPDB_WITH_SQLITE3 -DCXX14 -DCXX14_OR_LATER -DENABLE_MPNN -DLINUX -DMULTI_THREADED -DNDEBUG -DNOCRASHREPORT -DNO_PROF -DPTR_MODERN -DPTR_STD -DTRIO_HAVE_CONFIG_H -DUSE_GL_GLUT_H -DUSE_GL_GL_H -DUSE_RDKIT -I../.. -I../../src -I../../src/platform/linux -I../../external -I../../external/boost_submod -I../../external/boost_1_62_0-interactive -I../../external/cxxtest -I../../external/dbio -I../../external/dbio/sqlite3 -I../../external/include -I../../external/libxml2/include -I../../external/rdkit -I/home/benchmark/prefix/local-interactive/curl-7.76.1/include -I/home/benchmark/prefix/local-interactive/lua-5.1.4-c/include -I/home/benchmark/prefix/local-interactive/oscpack-1.1.0/include -I/home/benchmark/prefix/local-interactive/pytorch-1.12.0/include -std=c++14 -pipe -fPIC -Wno-deprecated -O2 -MD -MT CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o -MF CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o.d -o CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc.o -c /home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc In file included from /home/benchmark/rosetta/source/src/protocols/protein_mpnn/ProteinMPNN.cc:16: ../../src/protocols/protein_mpnn/ProteinMPNN.hh:34:10: fatal error: torch/script.h: No such file or directory 34 | #include <torch/script.h> | ^~~~~~~~~~~~~~~~ compilation terminated. [620/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o FAILED: CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o /usr/bin/c++ -DBOOST_ALL_NO_LIB -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\"a\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=0 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0\" -DCPPDB_WITH_SQLITE3 -DCXX14 -DCXX14_OR_LATER -DENABLE_MPNN -DLINUX -DMULTI_THREADED -DNDEBUG -DNOCRASHREPORT -DNO_PROF -DPTR_MODERN -DPTR_STD -DTRIO_HAVE_CONFIG_H -DUSE_GL_GLUT_H -DUSE_GL_GL_H -DUSE_RDKIT -I../.. -I../../src -I../../src/platform/linux -I../../external -I../../external/boost_submod -I../../external/boost_1_62_0-interactive -I../../external/cxxtest -I../../external/dbio -I../../external/dbio/sqlite3 -I../../external/include -I../../external/libxml2/include -I../../external/rdkit -I/home/benchmark/prefix/local-interactive/curl-7.76.1/include -I/home/benchmark/prefix/local-interactive/lua-5.1.4-c/include -I/home/benchmark/prefix/local-interactive/oscpack-1.1.0/include -I/home/benchmark/prefix/local-interactive/pytorch-1.12.0/include -std=c++14 -pipe -fPIC -Wno-deprecated -O2 -MD -MT CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o -MF CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o.d -o CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc.o -c /home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc In file included from /home/benchmark/rosetta/source/src/protocols/protein_mpnn/util.cc:15: ../../src/protocols/protein_mpnn/util.hh:29:10: fatal error: torch/script.h: No such file or directory 29 | #include <torch/script.h> | ^~~~~~~~~~~~~~~~ compilation terminated. [621/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/ConstraintClaimer.cc.o [622/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController.cc.o [623/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/util.cc.o [624/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/RBSegmentRelax.cc.o [625/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentClaimer.cc.o [626/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/DisulfJumpClaimer.cc.o [627/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/FoldTreeHybridize.cc.o [628/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/surface_docking/SurfaceDockingProtocol.cc.o [629/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/CoordConstraintClaimer.cc.o [630/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FragmentJumpClaimer.cc.o [631/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/IdealizeHelices.cc.o [632/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/rbsegment_relax/OptimizeThreading.cc.o [633/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/AsymFoldandDockClaimer.cc.o [634/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockingHiRes.cc.o [635/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts4.cc.o [636/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FoldandDockClaimer.cc.o [637/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/claims/DofClaim.cc.o [638/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts2.cc.o [639/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts1.cc.o [640/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/PseudocontactShiftEnergyController_Ts3.cc.o [641/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MetalloClaimer.cc.o [642/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/noesy_assign/NoesyModule.cc.o [643/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidBodyRandomTMHMover.cc.o [644/6111] Building C object CMakeFiles/external.dir/home/benchmark/rosetta/source/external/dbio/sqlite3/sqlite3.c.o [645/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/StartStructClaimer.cc.o [646/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SymmetryClaimer.cc.o [647/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/FibrilModelingClaimer.cc.o [648/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/filters/ConstraintFulfilmentFilter.cc.o [649/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimer.cc.o [650/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.cc.o [651/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/MembraneTopologyClaimer.cc.o [652/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyClaimerFactory.cc.o [653/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/FragmentExtension.cc.o [654/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/SequenceClaimer.cc.o [655/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/abinitio/IterativeBase.cc.o [656/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateFragmentClaimer.cc.o [657/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TemplateJumpClaimer.cc.o [658/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/symmetric_docking/SymDockProtocol.cc.o [659/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/util.cc.o [660/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/RigidChunkClaimer.cc.o [661/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/trRosetta_protocols/movers/trRosettaProtocolMover.cc.o [662/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/hybridization/HybridizeProtocol.cc.o [663/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TMHTopologySamplerClaimer.cc.o [664/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/topology_broker/TopologyBroker.cc.o [665/6111] Building CXX object CMakeFiles/protocols.6b.dir/home/benchmark/rosetta/source/src/protocols/loop_grower/LoopGrower.cc.o [666/6111] Building CXX object CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/options/option.cc.o ninja: build stopped: subcommand failed.
null