Comping with enable-parallel, gfortran error

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Comping with enable-parallel, gfortran error

Paul Arias
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

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Re: Comping with enable-parallel, gfortran error

Paul Arias
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 <[hidden email]> 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


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Re: Comping with enable-parallel, gfortran error

Scot Breitenfeld
In reply to this post by Paul Arias
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 <[hidden email]> 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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
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Re: Comping with enable-parallel, gfortran error

Paul Arias
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 <[hidden email]> 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 <[hidden email]> 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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


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


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
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Twitter: https://twitter.com/hdf5

config.log (247K) Download Attachment
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Re: Comping with enable-parallel, gfortran error

Paul Arias
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5


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



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