mpi build problem

[Mikukub]

I am trying to install GCC, but I still have a problem building Rosetta with MPI. I have Rosetta installed, and I can install it from Conda, but I am still encountering issues with MPI.

(base) [tlarnd2@edam source]$ export PATH=$HOME/Program/gcc-9.4.0-build/bin:$PATH
(base) [tlarnd2@edam source]$ ./scons.py -j40 mode=release extras=mpi
scons: Reading SConscript files ...
Running versioning script ... Done. (0.0 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/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dummy_zlib.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/dummy.cc
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/atomic_counter.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/atomic_counter.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/conn_manager.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/conn_manager.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/driver_manager.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/driver_manager.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/frontend.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/frontend.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/backend.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/backend.cpp
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/mutex.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/mutex.cpp
sh: mpiCC: command not found
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/pool.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/pool.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/shared_object.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/shared_object.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/sqlite3_backend.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/sqlite3_backend.cpp
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/utils.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=".so" -DCPPDB_LIBRARY_PREFIX="lib" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION="0" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION="0.3.0" -DCPPDB_WITH_SQLITE3 -Ibuild/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3 -Iexternal/dbio/sqlite3 external/dbio/cppdb/utils.cpp
sh: mpiCC: command not found
mpicc -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3/sqlite3.os -c -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -Wno-error -fno-fast-math -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -DSQLITE_THREADSAFE=0 -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_DISABLE_LFS external/dbio/sqlite3/sqlite3.c
sh: mpicc: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/BlockIO.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/BlockIO.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifDataInfo.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifDataInfo.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifExcept.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifExcept.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifFile.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifFile.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifFileReadDef.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifFileReadDef.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifParentChild.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifParentChild.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifParserBase.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifParserBase.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifScannerBase.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifScannerBase.C
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifString.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifString.C
sh: mpiCC: command not found
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DataInfo.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/DataInfo.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DicFile.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/DicFile.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DICParserBase.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/DICParserBase.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DICScannerBase.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/DICScannerBase.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/Exceptions.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/Exceptions.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/GenCont.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/GenCont.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/GenString.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/GenString.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ISTable.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/ISTable.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ITTable.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/ITTable.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/mapped_ptr_vector.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/mapped_ptr_vector.C
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/mapped_vector.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/mapped_vector.C
sh: mpiCC: command not found
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ParentChild.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/ParentChild.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/RcsbFile.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/RcsbFile.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/RcsbPlatform.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/RcsbPlatform.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/Serializer.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/Serializer.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/TableFile.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/TableFile.C
sh: mpiCC: command not found
mpiCC -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/TTable.os -c -std=c++0x -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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/TTable.C
sh: mpiCC: command not found
mpicc -o build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifParser.c
sh: mpicc: command not found
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dummy_zlib.os] Error 127
mpicc -o build/external/release/linux/4.18/64/x86/gcc/9.4/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 -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -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 -DNDEBUG -DUSEMPI -DOMPI_SKIP_MPICXX -Iexternal/include external/cifparse/CifScanner.c
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/atomic_counter.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/conn_manager.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/driver_manager.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/frontend.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/backend.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/mutex.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/pool.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/shared_object.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/sqlite3_backend.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/cppdb/utils.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/dbio/sqlite3/sqlite3.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/BlockIO.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifDataInfo.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifExcept.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifFile.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifFileReadDef.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifParentChild.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifParserBase.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifScannerBase.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifString.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DataInfo.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DicFile.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DICParserBase.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/DICScannerBase.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/Exceptions.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/GenCont.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/GenString.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ISTable.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ITTable.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/mapped_ptr_vector.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/mapped_vector.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/ParentChild.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/RcsbFile.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/RcsbPlatform.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/Serializer.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/TableFile.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/TTable.os] Error 127
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifParser.os] Error 127
sh: mpicc: command not found
scons: *** [build/external/release/linux/4.18/64/x86/gcc/9.4/mpi/cifparse/CifScanner.os] Error 127
scons: building terminated because of errors.
(base) [tlarnd2@edam source]$ whereis mpicc
mpicc: /usr/local/mpich-4.0.3/bin/mpicc /home/tlarnd2/bin/mpicc
(base) [tlarnd2@edam source]$

[roccomoretti]

You may need to copy the source/build/tools/site.settings.release file to source/build/tools/site.settings That has some build system changes which means that Scons is better able to figure out where to find the compilers.

Failing that, you may be able to edit the site.settings file to explicitly point to the compiler you want to use. (There's commented-out lines in the site.settings.release file which gives examples of the syntax.)

[Mikukub]

now i have this error
inlined from 'void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(core::pose::Pose&)' at src/protocols/forge/remodel/RemodelGlobalFrame.cc:195:23:
/home/tlarnd2/miniconda3/envs/rosetta310/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/xmmintrin.h:937:23: warning: array subscript '__m128_u[0]' is partly outside array bounds of 'Eigen::Vector3f [1]' {aka 'Eigen::Matrix<float, 3, 1> [1]'} [-Warray-bounds]
937 | return (__m128_u )__P;
| ^~~
src/protocols/forge/remodel/RemodelGlobalFrame.cc: In member function 'void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(core::pose::Pose&)':
src/protocols/forge/remodel/RemodelGlobalFrame.cc:189:18: note: object 'c_B' of size 12
189 | Vector3f c_B(B.row(0).mean(), B.row(1).mean(), B.row(2).mean());
| ^~~
In function '__m128 _mm_loadu_ps(const float)',
inlined from 'Packet Eigen::internal::ploadu(const typename unpacket_traits::type) [with Packet = __vector(4) float]' at external/include/Eigen/src/Core/arch/SSE/PacketMath.h:537:22,
inlined from 'Packet Eigen::internal::ploadt(const typename unpacket_traits::type*) [with Packet = __vector(4) float; int Alignment = 0]' at external/include/Eigen/src/Core/GenericPacketMath.h:663:26,
inlined from 'PacketType Eigen::internal::evaluator<Eigen::PlainObjectBase >::packet(Eigen::Index) const [with int LoadMode = 0; PacketType = __vector(4) float; Derived = Eigen::Matrix<float, 3, 1>]' at external/include/Eigen/src/Core/CoreEvaluators.h:245:40,
inlined from 'PacketType Eigen::internal::binary_evaluator<Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>, Eigen::internal::IndexBased, Eigen::internal::IndexBased>::packet(Eigen::Index) const [with int LoadMode = 0; PacketType = __vector(4) float; BinaryOp = Eigen::internal::scalar_difference_op<float, float>; Lhs = const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; Rhs = const Eigen::Matrix<float, 3, 1>]' at external/include/Eigen/src/Core/CoreEvaluators.h:790:80,
inlined from 'void Eigen::internal::generic_dense_assignment_kernel<DstEvaluatorTypeT, SrcEvaluatorTypeT, Functor, Version>::assignPacket(Eigen::Index) [with int StoreMode = 16; int LoadMode = 0; PacketType = __vector(4) float; DstEvaluatorTypeT = Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true> >; SrcEvaluatorTypeT = Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> > >; Functor = Eigen::internal::assign_op<float, float>; int Version = 0]' at external/include/Eigen/src/Core/AssignEvaluator.h:663:114,
inlined from 'static void Eigen::internal::dense_assignment_loop<Kernel, 3, 0>::run(Kernel&) [with Kernel = Eigen::internal::generic_dense_assignment_kernel<Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true> >, Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> > >, Eigen::internal::assign_op<float, float>, 0>]' at external/include/Eigen/src/Core/AssignEvaluator.h:420:75,
inlined from 'void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; SrcXprType = Eigen::CwiseBinaryOp<scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >; Functor = assign_op<float, float>]' at external/include/Eigen/src/Core/AssignEvaluator.h:767:37,
inlined from 'static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; SrcXprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >; Functor = Eigen::internal::assign_op<float, float>; Weak = void]' at external/include/Eigen/src/Core/AssignEvaluator.h:926:31,
inlined from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; Src = Eigen::CwiseBinaryOp<scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >; Func = assign_op<float, float>]' at external/include/Eigen/src/Core/AssignEvaluator.h:862:49,
inlined from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename enable_if<(! evaluator_assume_aliasing::value), void*>::type) [with Dst = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; Src = Eigen::CwiseBinaryOp<scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >; Func = assign_op<float, float>]' at external/include/Eigen/src/Core/AssignEvaluator.h:830:27,
inlined from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>; Src = Eigen::CwiseBinaryOp<scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >]' at external/include/Eigen/src/Core/AssignEvaluator.h:808:18,
inlined from 'Derived& Eigen::MatrixBase::operator=(const Eigen::DenseBase&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_difference_op<float, float>, const Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>, const Eigen::Matrix<float, 3, 1> >; Derived = Eigen::Block<Eigen::Matrix<float, -1, -1>, -1, 1, true>]' at external/include/Eigen/src/Core/Assign.h:66:28,
inlined from 'void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(core::pose::Pose&)' at src/protocols/forge/remodel/RemodelGlobalFrame.cc:194:23:
/home/tlarnd2/miniconda3/envs/rosetta310/lib/gcc/x86_64-conda-linux-gnu/12.3.0/include/xmmintrin.h:937:23: warning: array subscript '__m128_u[0]' is partly outside array bounds of 'Eigen::Vector3f [1]' {aka 'Eigen::Matrix<float, 3, 1> [1]'} [-Warray-bounds]
937 | return *(__m128_u *)__P;
| ^~~
src/protocols/forge/remodel/RemodelGlobalFrame.cc: In member function 'void protocols::forge::remodel::RemodelGlobalFrame::get_helical_params(core::pose::Pose&)':
src/protocols/forge/remodel/RemodelGlobalFrame.cc:188:18: note: object 'c_A' of size 12
188 | Vector3f c_A(A.row(0).mean(), A.row(1).mean(), A.row(2).mean());
| ^~~
scons: building terminated because of errors.

this is what i have

(rosetta310) [tlarnd2@edam source]$ gcc --version # For compiler
gcc (conda-forge gcc 12.3.0-7) 12.3.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Should be 2.7 if installed
mpirun --version # For(rosetta310) [tlarnd2@edam source]$ python --version # Should be 2.7 if installed
OpenMPI
scons --version # For SCons
Python 3.10.14
(rosetta310) [tlarnd2@edam source]$ mpirun --version # For OpenMPI
HYDRA build details:
Version: 4.0.3
Release Date: Tue Nov 8 09:51:06 CST 2022
CC: gcc
Configure options: '--disable-option-checking' '--prefix=/usr/local/mpich-4.0.3' 'CC=gcc' 'CXX=g++' 'FC=gfortran' '--cache-file=/dev/null' '--srcdir=.' 'CFLAGS= ' 'LDFLAGS=' 'LIBS=' 'CPPFLAGS= '
Process Manager: pmi
Launchers available: ssh rsh fork slurm ll lsf sge manual persist
Topology libraries available: hwloc
Resource management kernels available: user slurm ll lsf sge pbs cobalt
Demux engines available: poll select
(rosetta310) [tlarnd2@edam source]$ scons --version # For SCons
SCons by Steven Knight et al.:
SCons: v4.8.1.08661ed4c552323ef3a7f0ff1af38868cbabb05e, Tue, 03 Sep 2024 17:46:32 -0700, by bdbaddog on M1Dog2021
SCons path: ['/home/tlarnd2/.local/lib/python3.10/site-packages/SCons']
Copyright (c) 2001 - 2024 The SCons Foundation

[roccomoretti]

I'm not sure if the warnings being printed are the actual reason for the error. (The actual error may be buried further up in the output.)

Try re-running the scons build command. Once the normal way you've done it, and then the second time add (or switch to) -j 1. The full output from the second time around should give a clearer description of what the actual error is.

[Mikukub]

this is error but have no idea how to fix it, is related to dependency?

mpiCC -o build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.os -c -std=c++0x -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 -Wno-error=array-bounds -Wno-error=restrict -Wno-error=use-after-free -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 -DOMPI_SKIP_MPICXX -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/12.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc
In file included from /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/string:40,
from src/utility/backtrace.hh:30,
from src/utility/assert.hh:19,
from src/utility/vectorL.hh:22,
from src/utility/vector1.hh:23,
from src/protocols/jd2/JobsContainer.hh:31,
from src/protocols/jd2/JobDistributor.hh:27,
from src/protocols/jd2/MPIWorkPoolJobDistributor.hh:21,
from src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh:21,
from src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:20:
In static member function 'static void std::char_traits::assign(char_type&, const char_type&)',
inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1537:21,
inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1359:17,
inlined from 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)' at src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:126:43:
/home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/char_traits.h:358:14: error: 'slave_tlc_vector[0]' may be used uninitialized [-Werror=maybe-uninitialized]
358 | __c1 = __c2;
| ~~~~~^~~~~~
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc: In member function 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)':
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:80:14: note: 'slave_tlc_vector[0]' was declared here
80 | char slave_tlc_vector[LENGTH_TLC];
| ^~~~~~~~~~~~~~~~
In static member function 'static void std::char_traits::assign(char_type&, const char_type&)',
inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1537:21,
inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1359:17,
inlined from 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)' at src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:126:43:
/home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/char_traits.h:358:14: error: 'slave_tlc_vector[1]' may be used uninitialized [-Werror=maybe-uninitialized]
358 | __c1 = __c2;
| ~~~~~^~~~~~
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc: In member function 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)':
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:80:14: note: 'slave_tlc_vector[1]' was declared here
80 | char slave_tlc_vector[LENGTH_TLC];
| ^~~~~~~~~~~~~~~~
In static member function 'static void std::char_traits::assign(char_type&, const char_type&)',
inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::push_back(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1537:21,
inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator+=(_CharT) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/basic_string.h:1359:17,
inlined from 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)' at src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:126:43:
/home/tlarnd2/miniconda3/envs/rosetta310/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/char_traits.h:358:14: error: 'slave_tlc_vector[2]' may be used uninitialized [-Werror=maybe-uninitialized]
358 | __c1 = __c2;
| ~~~~~^~~~~~
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc: In member function 'virtual void protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor::master_go(protocols::moves::MoverOP)':
src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc:80:14: note: 'slave_tlc_vector[2]' was declared here
80 | char slave_tlc_vector[LENGTH_TLC];
| ^~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
scons: *** [build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.os] Error 1
scons: building terminated because of errors.

[Mikukub]

mpiCC -o build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/docking/DockingHighRes.os -c -std=c++0x -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 -Wno-error=array-bounds -Wno-error=restrict -Wno-error=use-after-free -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 -DOMPI_SKIP_MPICXX -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/12.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/docking/DockingHighRes.cc
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/docking/DockingHighResFactory.os -c -std=c++0x -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 -Wno-error=array-bounds -Wno-error=restrict -Wno-error=use-after-free -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 -DOMPI_SKIP_MPICXX -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/12.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/docking/DockingHighResFactory.cc
cc1plus: all warnings being treated as errors
mpiCC -o build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/docking/DockingHighResLegacy.os -c -std=c++0x -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 -Wno-error=array-bounds -Wno-error=restrict -Wno-error=use-after-free -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 -DOMPI_SKIP_MPICXX -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/12.3 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux src/protocols/docking/DockingHighResLegacy.cc
scons: *** [build/src/release/linux/4.18/64/x86/gcc/12.3/mpi/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.os] Error 1
scons: building terminated because of errors.

I add this but still have a problem
conda install -c conda-forge eigen=3.3.7

[roccomoretti]

The only external dependency Rosetta explicitly relies on is zlib (and the C/C++ standard libraries). You shouldn't need to install your own Eigen - Rosetta will use the version of Eigen it comes with.

[Mikukub]

I think the problem came from dependency, it is possible to share me a .yml file to I can make correct conda env to install rosetta, I don't have sudo and i try to install program locally but it doesn't work fro OpenMPI

[roccomoretti]

You should not need sudo to compile Rosetta. You probably also don't need to use a Conda environment. As mentioned, the only dependency typically used by Rosetta is zlib.

... except if you want to compile with MPI, then you do need to have a functional MPI install on your computer. That's typically more complicated, and would likely require sudo access. It's also not something that's easy to use a Conda environment for, as to properly run MPI on the machine needs background services running, which normally takes system-level access. If you aren't the computer admin (i.e. you don't have sudo access), then what you really should do is ask the person administering the machine to install OpenMPI for you.

When you build Rosetta with MPI, you need to use the version of MPI that's hooked into your system setup. (The one with the background services running.) The details of which tend to vary system-to-system, so it's hard to come up with a one-size-fits-all instruction for it.