scons: Reading SConscript files ... 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__DRPATH = $_DRPATH - __DSHLIBVERSIONFLAGS = ${__libversionflags(__env__,"DSHLIBVERSION","_DSHLIBVERSIONFLAGS")} - __LDMODULEVERSIONFLAGS = ${__libversionflags(__env__,"LDMODULEVERSION","_LDMODULEVERSIONFLAGS")} - __RPATH = $_RPATH - __SHLIBVERSIONFLAGS = ${__libversionflags(__env__,"SHLIBVERSION","_SHLIBVERSIONFLAGS")} - __libversionflags = - _concat = - _defines = - _javapathopt = - _stripixes = ------------------------------------------------------------------------ Running versioning script ... Release package detected, using rosetta/main/.release.json to acquire version information... Done. (0.0 seconds) Number of option files updated: 0 Total 4580 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/dummy_zlib.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 -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 -Iexternal/include external/dummy.cc /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/dbio/cppdb/atomic_counter.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ 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-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 -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 -Iexternal/include external/cifparse/mapped_vector.C /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/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 -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED 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external/cifparse/CifParser.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/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 -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 -Iexternal/include external/cifparse/CifScanner.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/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 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build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/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 -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 -Iexternal/include external/cifparse/regcomp.c : In function 'yy_get_next_buffer': :1470:20: warning: implicit declaration of function 'read'; did you mean 'fread'? 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-DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -Iexternal/include external/libxml2/triostr.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/uri.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 -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 -Iexternal/include external/libxml2/uri.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/valid.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 -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 -Iexternal/include external/libxml2/valid.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xinclude.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 -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 -Iexternal/include external/libxml2/xinclude.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xlink.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 -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 -Iexternal/include external/libxml2/xlink.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlIO.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 -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 -Iexternal/include external/libxml2/xmlIO.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlmemory.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 -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 -Iexternal/include external/libxml2/xmlmemory.c external/libxml2/triostr.c: In function 'trio_equal': external/libxml2/triostr.c:411:20: warning: implicit declaration of function 'strcasecmp'; did you mean 'strncmp'? [-Wimplicit-function-declaration] return (0 == strcasecmp(first, second)); ^~~~~~~~~~ strncmp external/libxml2/triostr.c: In function 'trio_equal_max': external/libxml2/triostr.c:534:20: warning: implicit declaration of function 'strncasecmp'; did you mean 'strncmp'? [-Wimplicit-function-declaration] return (0 == strncasecmp(first, second, max)); ^~~~~~~~~~~ strncmp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlmodule.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 -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 -Iexternal/include external/libxml2/xmlmodule.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlreader.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 -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 -Iexternal/include external/libxml2/xmlreader.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlregexp.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 -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 -Iexternal/include external/libxml2/xmlregexp.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlsave.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 -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 -Iexternal/include external/libxml2/xmlsave.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlschemas.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 -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 -Iexternal/include external/libxml2/xmlschemas.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlschemastypes.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 -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 -Iexternal/include external/libxml2/xmlschemastypes.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlstring.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 -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 -Iexternal/include external/libxml2/xmlstring.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xmlunicode.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 -DTRIO_HAVE_CONFIG_H -fPIC 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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 -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 -Iexternal/include external/libxml2/xpath.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xpointer.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 -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 -Iexternal/include external/libxml2/xpointer.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/libxml2/xzlib.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 -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 -Iexternal/include external/libxml2/xzlib.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/dummy_libzmq.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 -pthread -pipe -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 -Iexternal/include external/dummy.cc /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/ML/Cluster/Murtagh/hc.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 -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 -Iexternal/include external/rdkit/ML/Cluster/Murtagh/hc.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicc -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/ML/Cluster/Murtagh/hcdriver.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 -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 -Iexternal/include external/rdkit/ML/Cluster/Murtagh/hcdriver.c /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/Numerics/Optimizer/BFGSOpt.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem 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-DPTR_STD -D_GLIBCXX_DEBUG -DUSEMPI -Iexternal/include external/rdkit/GraphMol/MolCatalog/MolCatalogEntry.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/MolCatalog/MolCatalogParams.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 -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 -Iexternal/include external/rdkit/GraphMol/MolCatalog/MolCatalogParams.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.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 -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 -Iexternal/include external/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/MolInterchange/Parser.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 -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 -Iexternal/include external/rdkit/GraphMol/MolInterchange/Parser.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/MolInterchange/Writer.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 -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 -Iexternal/include external/rdkit/GraphMol/MolInterchange/Writer.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/AUTOCORR2D.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 -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 -Iexternal/include external/rdkit/GraphMol/Descriptors/AUTOCORR2D.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/AtomFeat.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 -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 -Iexternal/include external/rdkit/GraphMol/Descriptors/AtomFeat.cpp external/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.cpp: In member function 'void RDKit::FMCS::MaximumCommonSubgraph::makeInitialSeeds()': external/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.cpp:337:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr initialSeedMolecule( ^~~~~~~~ In file included from /apps/compiler/gcc/8.3.0/include/c++/8.3.0/bits/locale_conv.h:41, from /apps/compiler/gcc/8.3.0/include/c++/8.3.0/locale:43, from external/boost_submod/boost/iostreams/detail/config/codecvt.hpp:63, from external/boost_submod/boost/iostreams/positioning.hpp:21, from external/boost_submod/boost/iostreams/seek.hpp:23, from external/boost_submod/boost/iostreams/detail/adapter/non_blocking_adapter.hpp:13, from external/boost_submod/boost/iostreams/close.hpp:19, from external/boost_submod/boost/iostreams/operations.hpp:16, from external/boost_submod/boost/iostreams/detail/adapter/device_adapter.hpp:24, from external/boost_submod/boost/iostreams/tee.hpp:18, from external/rdkit/RDGeneral/RDLog.h:17, from external/rdkit/RDGeneral/Invariant.h:22, from external/rdkit/GraphMol/FMCS/../Atom.h:24, from external/rdkit/GraphMol/FMCS/../QueryAtom.h:14, from external/rdkit/GraphMol/FMCS/MaximumCommonSubgraph.cpp:13: /apps/compiler/gcc/8.3.0/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/BCUT.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 -fPIC 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/apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/MQN.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 -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 -Iexternal/include external/rdkit/GraphMol/Descriptors/MQN.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.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 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external/rdkit/GraphMol/Descriptors/MolDescriptors.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/MolSurf.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 -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 -Iexternal/include external/rdkit/GraphMol/Descriptors/MolSurf.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Descriptors/Property.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem 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-Iexternal/include external/rdkit/GraphMol/Descriptors/USRDescriptor.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/ForceField/MMFF/AngleBend.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 -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 -Iexternal/include external/rdkit/ForceField/MMFF/AngleBend.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/ForceField/MMFF/AngleConstraint.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem 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build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/FileParsers/TDTMolSupplier.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 -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 -Iexternal/include external/rdkit/GraphMol/FileParsers/TDTMolSupplier.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/FileParsers/TDTWriter.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 -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 -Iexternal/include external/rdkit/GraphMol/FileParsers/TDTWriter.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/FileParsers/TplFileParser.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 -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 -Iexternal/include external/rdkit/GraphMol/FileParsers/TplFileParser.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/FileParsers/TplFileWriter.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 -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 -Iexternal/include external/rdkit/GraphMol/FileParsers/TplFileWriter.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/FileParsers/XYZFileWriter.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 -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 -Iexternal/include external/rdkit/GraphMol/FileParsers/XYZFileWriter.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/SubstructLibrary/PatternFactory.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 -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 -Iexternal/include external/rdkit/GraphMol/SubstructLibrary/PatternFactory.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.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 -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 -Iexternal/include external/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.cpp external/rdkit/GraphMol/MMPA/MMPA.cpp: In function 'bool RDKit::MMPA::fragmentMol(const RDKit::ROMol&, std::__debug::vector, boost::shared_ptr > >&, unsigned int, unsigned int, unsigned int, const string&)': external/rdkit/GraphMol/MMPA/MMPA.cpp:468:8: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr smarts((const ROMol*)SmartsToMol(pattern)); ^~~~~~~~ In file included from /apps/compiler/gcc/8.3.0/include/c++/8.3.0/memory:80, from external/boost_submod/boost/smart_ptr/scoped_ptr.hpp:22, from external/boost_submod/boost/scoped_ptr.hpp:13, from external/boost_submod/boost/smart_ptr.hpp:17, from external/rdkit/GraphMol/MMPA/../MolOps.h:19, from external/rdkit/GraphMol/MMPA/MMPA.cpp:15: /apps/compiler/gcc/8.3.0/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/AddHs.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 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build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Aromaticity.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 -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 -Iexternal/include external/rdkit/GraphMol/Aromaticity.cpp /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/external/debug/linux/3.10/64/x86/gcc/8.3/mpi/rdkit/GraphMol/Atom.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 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src/protocols/init/register1.cc /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/init/register2.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 -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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/8.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register2.cc /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/init/register3.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 -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 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/8.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register3.cc /apps/compiler/gcc/8.3.0/mvapich2/2.3.1/bin/mpicxx -o build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/init/register4.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 -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O0 -g -ggdb 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build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzdesJobInputter.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzdesJobOutputter.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzdesMovers.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzdesTaskOperations.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzFilters.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/EnzRepackMinimize.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/ModifyStoredLigandRBConfsMovers.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/PackRotamersMoverPartGreedy.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/SecondaryMatchProtocol.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/enzdes/RemoveLigandFilter.os build/src/debug/linux/3.10/64/x86/gcc/8.3/mpi/protocols/antibody/design/AntibodyDesignEnumManager.os 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-lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit scons: done building targets.