Comping with enable-parallel, gfortran error

HDF5 Library
1

Hello,

I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu).

This is the error message that I get near the end:

checking whether a simple MPI-IO C program can be linked... yes
checking whether a simple MPI-IO Fortran program can be linked... no
configure: error: unable to link a simple MPI-IO Fortran program

This is my configuration script:

···

-------
export CC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpicc
export FC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F77=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F90=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort

export FFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export CFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export LDFLAGS="-L/usr/mpi/gcc/openmpi-1.10.4/lib64/"
export LIBS="-lmpi"

./configure --enable-parallel --enable-fortran --prefix=/home1/pgarias/
software/hdf5-mpich3.2-gcc4.9.4
----

I'm wondering what I might be missing when attempting to configure HDF5
with mpi-io.

Thanks you for your assistance!
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

2

I made a slight change to the file. Changed FFLAGS to FCFLAGS, and made the
directories of the compilers and library files consistent, but this did not
yet advance beyond the fortran linking stage.

Thanks in advance.

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

···

On Fri, Jan 26, 2018 at 4:57 PM, Paul Arias <paul.g.arias@gmail.com> wrote:

Hello,

I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu).

This is the error message that I get near the end:

checking whether a simple MPI-IO C program can be linked... yes
checking whether a simple MPI-IO Fortran program can be linked... no
configure: error: unable to link a simple MPI-IO Fortran program

This is my configuration script:
-------
export CC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpicc
export FC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F77=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F90=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort

export FFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export CFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export LDFLAGS="-L/usr/mpi/gcc/openmpi-1.10.4/lib64/"
export LIBS="-lmpi"

./configure --enable-parallel --enable-fortran
--prefix=/home1/pgarias/software/hdf5-mpich3.2-gcc4.9.4
----

I'm wondering what I might be missing when attempting to configure HDF5
with mpi-io.

Thanks you for your assistance!
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

3

Can you send the config.log file, it should contain the details of the error.

Scot

···

On Jan 26, 2018, at 3:57 PM, Paul Arias <paul.g.arias@gmail.com<mailto:paul.g.arias@gmail.com>> wrote:

Hello,

I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu).

This is the error message that I get near the end:

checking whether a simple MPI-IO C program can be linked... yes
checking whether a simple MPI-IO Fortran program can be linked... no
configure: error: unable to link a simple MPI-IO Fortran program

This is my configuration script:
-------
export CC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpicc
export FC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F77=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F90=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort

export FFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export CFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export LDFLAGS="-L/usr/mpi/gcc/openmpi-1.10.4/lib64/"
export LIBS="-lmpi"

./configure --enable-parallel --enable-fortran --prefix=/home1/pgarias/software/hdf5-mpich3.2-gcc4.9.4
----

I'm wondering what I might be missing when attempting to configure HDF5 with mpi-io.

Thanks you for your assistance!
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

4

Thank you Scot for the note.

I have attached the file here, and am also reviewing it.

Best,
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

config.log (181 KB)

···

On Mon, Jan 29, 2018 at 10:20 AM, Scot Breitenfeld <brtnfld@hdfgroup.org> wrote:

Can you send the config.log file, it should contain the details of the
error.

Scot

On Jan 26, 2018, at 3:57 PM, Paul Arias <paul.g.arias@gmail.com> wrote:

Hello,

I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu).

This is the error message that I get near the end:

checking whether a simple MPI-IO C program can be linked... yes
checking whether a simple MPI-IO Fortran program can be linked... no
configure: error: unable to link a simple MPI-IO Fortran program

This is my configuration script:
-------
export CC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpicc
export FC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F77=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F90=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort

export FFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export CFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export LDFLAGS="-L/usr/mpi/gcc/openmpi-1.10.4/lib64/"
export LIBS="-lmpi"

./configure --enable-parallel --enable-fortran
--prefix=/home1/pgarias/software/hdf5-mpich3.2-gcc4.9.4
----

I'm wondering what I might be missing when attempting to configure HDF5
with mpi-io.

Thanks you for your assistance!
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

5

Hi Scot,

Thanks for the suggestions. It turns out that the problem is that the
mpi.mod files are compiled with a different version of gcc than the one I
was using. I was able to make the change and can now configure and make
hdf5. I am running "make check-s" and "make check-p" now.

Thanks very much for the suggestion.

Best,
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

···

On Mon, Jan 29, 2018 at 10:28 AM, Paul Arias <paul.g.arias@gmail.com> wrote:

Thank you Scot for the note.

I have attached the file here, and am also reviewing it.

Best,
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute

On Mon, Jan 29, 2018 at 10:20 AM, Scot Breitenfeld <brtnfld@hdfgroup.org> > wrote:

Can you send the config.log file, it should contain the details of the
error.

Scot

On Jan 26, 2018, at 3:57 PM, Paul Arias <paul.g.arias@gmail.com> wrote:

Hello,

I am trying to compile HDF5 (1.8.20) with openmpi, fortran (gnu).

This is the error message that I get near the end:

checking whether a simple MPI-IO C program can be linked... yes
checking whether a simple MPI-IO Fortran program can be linked... no
configure: error: unable to link a simple MPI-IO Fortran program

This is my configuration script:
-------
export CC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpicc
export FC=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F77=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort
export F90=/usr/mpi/gcc/openmpi-1.10.4-hfi/bin/mpifort

export FFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export CFLAGS="-I/usr/mpi/gcc/openmpi-1.10.4/include/"
export LDFLAGS="-L/usr/mpi/gcc/openmpi-1.10.4/lib64/"
export LIBS="-lmpi"

./configure --enable-parallel --enable-fortran
--prefix=/home1/pgarias/software/hdf5-mpich3.2-gcc4.9.4
----

I'm wondering what I might be missing when attempting to configure HDF5
with mpi-io.

Thanks you for your assistance!
Paul

Paul Guillermo Arias, Ph.D.
Associate Research Scientist
Rutgers Discovery Informatics Institute
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5