Test: linux.gcc.mpi.serialization.build.debug 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20658」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-4     Started at: 2025-03-12 20:19:03     Run time: 0:05:11      State: failed


Running: /home/benchmark/prefix/nobu-4/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras=mpi,serialization -j64 scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Number of option files updated: 0 Total 4682 options. Updating submodules needed for compilation. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/core/import_pose/import_pose.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/core/import_pose/import_pose.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/RealOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/RealOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/RealVectorOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/RealVectorOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/ResidueChainVectorOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/ResidueChainVectorOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/ScalarOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/ScalarOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/StringOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/StringOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/StringVectorOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/StringVectorOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/VectorOption.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/VectorOption.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/mpi_stderr.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/mpi_stderr.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/OptionKeyList.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/OptionKeyList.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/OptionKeys.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/OptionKeys.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/AnyOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/AnyOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/AnyVectorOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/AnyVectorOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/BooleanOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/BooleanOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/BooleanVectorOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/BooleanVectorOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/FileOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/FileOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/FileVectorOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/FileVectorOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/IntegerOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/IntegerOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/IntegerVectorOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/IntegerVectorOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/OptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/OptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/PathOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/PathOptionKey.cc mpiCC -o build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/utility/options/keys/PathVectorOptionKey.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/utility/options/keys/PathVectorOptionKey.cc mpiCC -o 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external/cifparse/ITTable.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/mapped_ptr_vector.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/mapped_ptr_vector.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/mapped_vector.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/mapped_vector.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/ParentChild.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/ParentChild.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/RcsbFile.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/RcsbFile.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/RcsbPlatform.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/RcsbPlatform.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/Serializer.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/Serializer.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/TableFile.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/TableFile.C mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/TTable.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/TTable.C mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/CifParser.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/CifParser.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/CifScanner.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/CifScanner.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/DICParser.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/DICParser.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/DICScanner.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/DICScanner.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/regcomp.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/regcomp.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/regerror.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/regerror.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/regexec.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/regexec.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/cifparse/regfree.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/cifparse/regfree.c src/core/import_pose/import_pose.cc: In function 'void core::import_pose::pose_from_file(core::pose::Pose&, const core::chemical::ResidueTypeSet&, const string&, const core::import_pose::ImportPoseOptions&, bool, core::import_pose::FileType)': src/core/import_pose/import_pose.cc:444:72: error: expected ';' before string constant TR.Warning << "mmCIF parser reports issues with file '" << filename "' : " << std:;endl; ^ src/core/import_pose/import_pose.cc:444:87: error: 'endl' was not declared in this scope TR.Warning << "mmCIF parser reports issues with file '" << filename "' : " << std:;endl; ^ src/core/import_pose/import_pose.cc:444:87: note: suggested alternative: In file included from /usr/include/c++/4.8.2/iostream:39:0, from external/include/cereal/access.hpp:33, from external/include/cereal/details/traits.hpp:43, from external/include/cereal/cereal.hpp:43, from external/include/cereal/archives/binary.hpp:32, from src/utility/serialization/serialization.hh:22, from src/core/chemical/ResidueTypeSet.hh:46, from src/core/import_pose/import_pose.cc:24: /usr/include/c++/4.8.2/ostream:564:5: note: 'std::endl' endl(basic_ostream<_CharT, _Traits>& __os) ^ mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/buf.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/buf.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/c14n.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/c14n.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/catalog.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/catalog.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/chvalid.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/chvalid.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/debugXML.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/debugXML.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/dict.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/dict.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/DOCBparser.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/DOCBparser.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/encoding.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/encoding.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/entities.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/entities.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/error.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/error.c mpicc -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/libxml2/globals.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -DTRIO_HAVE_CONFIG_H -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/libxml2/globals.c mpicc -o 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external/rdkit/ForceField/UFF/AngleConstraint.cpp mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/rdkit/ForceField/UFF/BondStretch.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/rdkit/ForceField/UFF/BondStretch.cpp mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/rdkit/ForceField/UFF/DistanceConstraint.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include 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build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/rdkit/GraphMol/Depictor/RDDepictor.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/rdkit/GraphMol/Depictor/RDDepictor.cpp mpiCC -o build/external/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/rdkit/GraphMol/Deprotect/Deprotect.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb -ffloat-store -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSERIALIZATION -Iexternal/include external/rdkit/GraphMol/Deprotect/Deprotect.cpp scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/mpi-serialization/core/import_pose/import_pose.os] Error 1 scons: building terminated because of errors.
{}