Hello everyone,
I have been working with Rosetta for the past year. I have installed and used it on multiple systems but recently I wanted to generate mass structures for many sequences. I got access to a supercomputer and want to use Rosetta, but I have been facing this problem where compilation with MPI support fails and gives an error for which I couldn't find a solution anywhere with a simple web search.
If anyone else has faced this problem, I would really appreciate any help. Thanks.
Command Used:-
./scons.py -j 10 mode=release bin extras=mpi
Error Message:-
scons: Reading SConscript files ...
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 ...
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/apps/public/AbinitioRelax.o -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/apps/public/AbinitioRelax.cc
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/devel/init.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/devel/init.cc
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/init.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/init.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/register1.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register1.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register2.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register3.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/init/register4.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/AntibodyClass.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/AntibodyClass.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/AntibodyModeler.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/AntibodyModeler.cc
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/apps/public/AbinitioRelax.o] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/devel/init.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/init.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/register1.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/register2.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/register3.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/init/register4.os] Error 1
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/AntibodyClass.os] Error 1
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/CDRH3Modeler.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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/11.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/antibody_legacy/CDRH3Modeler.cc
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/AntibodyModeler.os] Error 1
nvc++-Error--tp core2 is not supported. See -help -tp for supported target processors.
scons: *** [build/src/release/linux/4.18/64/x86/gcc/11.3/mpi/protocols/antibody_legacy/CDRH3Modeler.os] Error 1
scons: building terminated because of errors.
Looks like you may need to edit the source/tools/build/site.settings file. In the "removes" section, add the following.
That's assuming your compiler is just idosyncratic. If it's for a non Intel x86 processor, then you may need to do more to adjust the compiler settings properly for that particular processor platform. (We generally test and use x86 processors, with limited support for other platforms, but we're often limited to systems which we have access to for out-of-the-box support.)