[OMPI users] openmpi-3.1.2 libgfortran conflict

[Patrick Begou]

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)

[Patrick Begou]

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

Post by Patrick Begou
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
$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. | |
| LEGI | |
| BP 53 X | Tel [phone] |
| 38041 GRENOBLE CEDEX | Fax [phone] |
===================================================================
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

[Jeff Squyres (jsquyres) via users]

Glad you figured it out. Just for some additional color:

https://www.open-mpi.org/faq/?category=building#install-overwrite

Post by Patrick Begou
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

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
$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 |
|
| LEGI | |
| BP 53 X | Tel [phone] |
| 38041 GRENOBLE CEDEX | Fax [phone] |
===================================================================
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users

--
===================================================================
| Equipe M.O.S.T. | |
| Patrick BEGOU |
|
| LEGI | |
| BP 53 X | Tel [phone] |
| 38041 GRENOBLE CEDEX | Fax [phone] |
===================================================================
_______________________________________________
users mailing list
https://lists.open-mpi.org/mailman/listinfo/users