Glad you figured it out. Just for some additional color:
https://www.open-mpi.org/faq/?category=building#install-overwrite
> On Sep 3, 2018, at 4:17 AM, Patrick Begou
> <[email protected]> wrote:
>
> Solved.
> Strange conflict (not explained) after several compilation test of OpenMPI
> with gcc7. Solved by removing the destination directory before any new "make
> install" command.
>
> Patrick
>
> Patrick Begou wrote:
>> I am compiling openmpi-3.1.2 on CentOS 7 with GCC 7.3 installed in
>> /opt/GCC7. My setup is "debug" as I had some trouble with MPI lib.
>> When I run a ldd command on libmpi_usempi.so it shows that it load
>> libgfortran.so.4 (from GCC 7.3) but also libgfortran.so.3 (from system GCC
>> 4.8.5) and there is a conflict message when linking MPI applications.
>> I do not know how to remove this dependancie on libgfortran.so.3.
>>
>> Thanks for your advices
>>
>> Patrick
>>
>> $ldd /opt/openmpi-GCC73/3.1.2/lib/libmpi_usempi.so
>> linux-vdso.so.1 => (0x00007fffd9b33000)
>> libmpi_mpifh.so.40 => /opt/openmpi-GCC73/3.1.2/lib/libmpi_mpifh.so.40
>> (0x00007f3efb75f000)
>> libmpi.so.40 => /opt/openmpi-GCC73/3.1.2/lib/libmpi.so.40
>> (0x00007f3efb1d9000)
>> libopen-rte.so.40 => /opt/openmpi-GCC73/3.1.2/lib/libopen-rte.so.40
>> (0x00007f3efadf6000)
>> libopen-pal.so.40 => /opt/openmpi-GCC73/3.1.2/lib/libopen-pal.so.40
>> (0x00007f3efa8d4000)
>> libnuma.so.1 => /lib64/libnuma.so.1 (0x00007f3efa6c8000)
>> libudev.so.1 => /lib64/libudev.so.1 (0x00007f3efa4b2000)
>> libdl.so.2 => /lib64/libdl.so.2 (0x00007f3efa2ae000)
>> librt.so.1 => /lib64/librt.so.1 (0x00007f3efa0a6000)
>> libutil.so.1 => /lib64/libutil.so.1 (0x00007f3ef9ea3000)
>> libz.so.1 => /lib64/libz.so.1 (0x00007f3ef9c8d000)
>> libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f3ef996b000)
>> <<== system GCC 4.8.5
>> libm.so.6 => /lib64/libm.so.6 (0x00007f3ef9669000)
>> libquadmath.so.0 => /opt/GCC73/lib64/libquadmath.so.0
>> (0x00007f3ef942a000)
>> libc.so.6 => /lib64/libc.so.6 (0x00007f3ef905d000)
>> libgcc_s.so.1 => /opt/GCC73/lib64/libgcc_s.so.1 (0x00007f3ef8e46000)
>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f3ef8c2a000)
>> libgfortran.so.4 => /opt/GCC73/lib/../lib64/libgfortran.so.4
>> (0x00007f3ef8858000) <<== /opt GCC 7.3.0
>> /lib64/ld-linux-x86-64.so.2 (0x00007f3efbbbe000)
>> libcap.so.2 => /lib64/libcap.so.2 (0x00007f3ef8653000)
>> libdw.so.1 => /lib64/libdw.so.1 (0x00007f3ef840c000)
>> libattr.so.1 => /lib64/libattr.so.1 (0x00007f3ef8207000)
>> libelf.so.1 => /lib64/libelf.so.1 (0x00007f3ef7fef000)
>> liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f3ef7dc9000)
>> libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f3ef7bb9000)
>>
>> I've run several configurations for building OpenMPI, below is the last one
>> which fails too.
>>
>> module load Compilers-GCC73
>> export BASE=/opt
>> export MPIVERS=3.1.2
>> export DESTMPI=$BASE/openmpi-GCC73/$MPIVERS
>> tar xvfz openmpi-$MPIVERS.tar.gz
>> cd openmpi-$MPIVERS
>> mkdir build
>> cd build/
>> CC=$(which gcc) CXX=$(which g++) FC=$(which gfortran)
>> LDFLAGS="-L/opt/GCC73/lib64 -L/opt/GCC73/lib" \
>> ../configure --prefix=$DESTMPI --enable-mpirun-prefix-by-default
>> --disable-dlopen \
>> --enable-mca-no-build=openib --without-verbs --enable-mpi-cxx --enable-debug
>> --enable-mem-debug --without-slurm
>> make -j 8
>> make check
>> make install
>>
>> Gfortran is in the PATH and LD_LIBRARY_PATH is set when module is loaded.
>> $which gfortran
>> /opt/GCC73/bin/gfortran
>> $echo $LD_LIBRARY_PATH
>> /opt/GCC73/lib64:/opt/GCC73/lib
>>
>> Building a basic fortran application with gfortran 7.3.0 do no show any
>> reference to libgfortran.so.3:
>> $ldd a.out
>> linux-vdso.so.1 => (0x00007fff620e8000)
>> libgfortran.so.4 => /opt/GCC73/lib64/libgfortran.so.4
>> (0x00007f5e7b573000)
>> libm.so.6 => /lib64/libm.so.6 (0x00007f5e7b271000)
>> libgcc_s.so.1 => /opt/GCC73/lib64/libgcc_s.so.1 (0x00007f5e7b05a000)
>> libquadmath.so.0 => /opt/GCC73/lib64/libquadmath.so.0
>> (0x00007f5e7ae1b000)
>> libc.so.6 => /lib64/libc.so.6 (0x00007f5e7aa4e000)
>> /lib64/ld-linux-x86-64.so.2 (0x00007f5e7b945000)
>>
>> --
>> ===================================================================
>> | Equipe M.O.S.T. | |
>> | Patrick BEGOU |
>> mailto:[email protected]
>> |
>> | LEGI | |
>> | BP 53 X | Tel 04 76 82 51 35 |
>> | 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 |
>> ===================================================================
>>
>>
>>
>> _______________________________________________
>> users mailing list
>>
>> [email protected]
>> https://lists.open-mpi.org/mailman/listinfo/users
>
>
> --
> ===================================================================
> | Equipe M.O.S.T. | |
> | Patrick BEGOU |
> mailto:[email protected]
> |
> | LEGI | |
> | BP 53 X | Tel 04 76 82 51 35 |
> | 38041 GRENOBLE CEDEX | Fax 04 76 82 52 71 |
> ===================================================================
>
> _______________________________________________
> users mailing list
> [email protected]
> https://lists.open-mpi.org/mailman/listinfo/users
--
Jeff Squyres
[email protected]
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