Hello,
>From your cmake.log, it seems you have 2 different C compilers: gcc and
mpicc. Same for Fortran.
Does your MPI implementation (mpt here) use gcc 8.2.0 as a backend? If not,
may be using the flag -DCOMPILER=GNU is not appropriate here.
I don't know if anyone has ever compiled Amber with this proprietary mpt
implementation of MPI.
Best regards,
Greald.
On Tue, Apr 27, 2021 at 7:57 PM Gabriel Cretin <gabriel.cretin.inserm.fr>
wrote:
> Hi,
>
> I am trying to install Amber20 on my SGI cluster with mpt/2.20 as MPI
> compiler.
> When I run the following cmake command:
>
> cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=/opt/apps/software/Core/amber/20 \
> -DCOMPILER=GNU \
> -DMPI=TRUE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
> 2>&1 | tee cmake.log
>
> I get the error below:
>
> --
> **************************************************************************
> -- Starting configuration of Amber version 20.0.0...
> -- CMake Version: 3.11.4
> -- For how to use this build system, please read this wiki:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> -- For a list of important CMake variables, check here:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> --
> **************************************************************************
> -- Setting C compiler to gcc
> -- Setting CXX compiler to g++
> -- Setting Fortran compiler to gfortran
> -- Amber source found, building AmberTools and Amber
> -- The C compiler identification is GNU 8.2.0
> -- The CXX compiler identification is GNU 8.2.0
> -- The Fortran compiler identification is GNU 8.2.0
> -- Check for working C compiler: /opt/apps/software/pkg/gcc/8.2.0/bin/gcc
> -- Check for working C compiler: /opt/apps/software/pkg/gcc/8.2.0/bin/gcc
> -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /opt/apps/software/pkg/gcc/8.2.0/bin/g++
> -- Check for working CXX compiler:
> /opt/apps/software/pkg/gcc/8.2.0/bin/g++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Check for working Fortran compiler:
> /opt/apps/software/pkg/gcc/8.2.0/bin/gfortran
> -- Check for working Fortran compiler:
> /opt/apps/software/pkg/gcc/8.2.0/bin/gfortran -- works
> -- Detecting Fortran compiler ABI info
> -- Detecting Fortran compiler ABI info - done
> -- Checking whether /opt/apps/software/pkg/gcc/8.2.0/bin/gfortran supports
> Fortran 90
> -- Checking whether /opt/apps/software/pkg/gcc/8.2.0/bin/gfortran supports
> Fortran 90 -- yes
> -- Testing if stdlib.h can be included...
> -- Testing if stdlib.h can be included... yes
> -- Found MPI_C: /usr/lib64/libpthread.so (found version "3.1")
> -- Found MPI_CXX: /usr/lib64/libpthread.so (found version "3.1")
> -- Found MPI_Fortran: /usr/lib64/libpthread.so (found version "3.1")
> -- Found MPI: TRUE (found version "3.1")
> -- MPI C Compiler: /opt/apps/sgi/mpt-2.20/bin/mpicc
> -- MPI CXX Compiler: /opt/apps/sgi/mpt-2.20/bin/mpicxx
> -- MPI Fortran Compiler: /opt/apps/sgi/mpt-2.20/bin/mpif90
> -- If these are not the correct MPI wrappers, then set
> MPI_<language>_COMPILER to the correct wrapper and reconfigure.
> RegularExpression::compile(): Nested *?+.
> RegularExpression::compile(): Error in compile.
> CMake Error at cmake/LibraryTracking.cmake:38 (if):
> if given arguments:
>
> "NOT" "("
> "/usr/lib64/libpthread.so;/opt/apps/sgi/mpt-2.20/lib/libmpi.so" "MATCHES"
> "/opt/apps/sgi/mpt-2.20/lib/libmpi++.so" "OR"
> "/usr/lib64/libpthread.so;/opt/apps/sgi/mpt-2.20/lib/libmpi.so" "MATCHES"
> "/opt/apps/sgi/mpt-2.20/lib/libmpi++.so" ")"
>
> Regular expression "/opt/apps/sgi/mpt-2.20/lib/libmpi++.so" cannot
> compile
> Call Stack (most recent call first):
> cmake/LibraryTracking.cmake:196 (using_external_library)
> cmake/MPIConfig.cmake:122 (import_libraries)
> CMakeLists.txt:118 (include)
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/opt/apps/software/src/amber/amber20_src/build/CMakeFiles/CMakeOutput.log".
>
> If the cmake build report looks OK, you should now do the following:
>
> make install
> source /opt/apps/software/src/amber/amber20/amber.sh
>
> Consider adding the last line to your login startup script, e.g. ~/.bashrc
>
> --
> Gabriel Cretin
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 27 2021 - 05:00:02 PDT
