Hello everybody,
I have a problem installing hdf5 :
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application
but I am using mpicc for the compiler :
How can I fix the problem ?
I read
http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
and it says :
he HDF5 Library can be configured to use MPI and MPI-IO for parallelism on
a distributed multi-processor system. The easiest way to do this is to have
a properly installed parallel compiler (for example, MPICH's mpicc or
IBM's mpcc_r) and supply the compiler name as the value of the CC
environment variable.
which is what I have :
echo $CC
/scinet/bgq/compilers/gcc-4.8.1/mpi/bin/mpicc
Do you have any suggestions ?
Thank you for your help,
Cheers,
Bertrand
Hi Bertrand,
Have you checked mpicc installed on your system? I would start there. Please try to compile and run the attached program to check if mpicc works. If it does, we should probably take a closer look at the config.log file created by configure.
It will also help to know on which system you are trying to build HDF5 and which version of MPI IO library you are using.
Thank you and good luck!
Elena
Sample_mpio.c (5.87 KB)
···
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Dec 20, 2013, at 4:38 PM, Bertrand B. <bertrand25mtl@gmail.com> wrote:
Hello everybody,
I have a problem installing hdf5 :
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application
but I am using mpicc for the compiler :
How can I fix the problem ?
I read http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
and it says :
he HDF5 Library can be configured to use MPI and MPI-IO for parallelism on
a distributed multi-processor system. The easiest way to do this is to have
a properly installed parallel compiler (for example, MPICH's mpicc or
IBM's mpcc_r) and supply the compiler name as the value of the CC
environment variable.
which is what I have :
echo $CC
/scinet/bgq/compilers/gcc-4.8.1/mpi/bin/mpicc
Do you have any suggestions ?
Thank you for your help,
Cheers,
Bertrand
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Hello everybody,
The problem was coming from the zlib dependency which was not correctly
installed. Fixing the compilation of zlib let me configure and compile hdf5
without any issue.
Thanks for your help,
Cheers,
Bertrand
···
2013/12/20 Bertrand B. <bertrand25mtl@gmail.com>
Hello everybody,
I have a problem installing hdf5 :
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application
but I am using mpicc for the compiler :
How can I fix the problem ?
I read
http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
and it says :
he HDF5 Library can be configured to use MPI and MPI-IO for parallelism on
a distributed multi-processor system. The easiest way to do this is to have
a properly installed parallel compiler (for example, MPICH's mpicc or
IBM's mpcc_r) and supply the compiler name as the value of the CC
environment variable.
which is what I have :
echo $CC
/scinet/bgq/compilers/gcc-4.8.1/mpi/bin/mpicc
Do you have any suggestions ?
Thank you for your help,
Cheers,
Bertrand
Hello Elena,
Thank you very much for your help, I really appreciate.
mpicc is installed (installed with gcc 4.8.1) and works correctly.
I compiled the code you sent me and ran it with 1 MPI process :
Testing simple C MPIO program with 1 processes accessing file ./mpitest.data
(Filename can be specified via program argument)
Proc 0: hostname=bgqdev-ionode4
Proc 0: all tests passed
Looking at the config.log (attached to this email), I have the following
error messages :
checking for MPI_Init in -lmpich... no
checking prefix for running on one processor...
checking prefix for running in parallel...
checking whether a simple MPI-IO program can be linked... no
But I was able to compile your test with :
mpicc Sample_mpio.c -o Sample_mpio -lmpich
So I do not understand what is wrong with the test done by the configure.
Thank you for your advice,
Cheers,
Bertrand
log_configure (12.7 KB)
···
2013/12/22 Elena Pourmal <epourmal@hdfgroup.org>
Hi Bertrand,
Have you checked mpicc installed on your system? I would start
there. Please try to compile and run the attached program to check if mpicc
works. If it does, we should probably take a closer look at the config.log
file created by configure.
It will also help to know on which system you are trying to build HDF5 and
which version of MPI IO library you are using.
Thank you and good luck!
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Dec 20, 2013, at 4:38 PM, Bertrand B. <bertrand25mtl@gmail.com> wrote:
Hello everybody,
I have a problem installing hdf5 :
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application
but I am using mpicc for the compiler :
How can I fix the problem ?
I read
http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
and it says :
he HDF5 Library can be configured to use MPI and MPI-IO for parallelism on
a distributed multi-processor system. The easiest way to do this is to have
a properly installed parallel compiler (for example, MPICH's mpicc or
IBM's mpcc_r) and supply the compiler name as the value of the CC
environment variable.
which is what I have :
echo $CC
/scinet/bgq/compilers/gcc-4.8.1/mpi/bin/mpicc
Do you have any suggestions ?
Thank you for your help,
Cheers,
Bertrand
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Hi Bertrand,
Could you please send the config.log file (it should be in the top build directory or in the top HDF5 distribution directory if you are building in place). It may provide more hints than configure output.
Thank you!
Elena
···
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Dec 23, 2013, at 8:16 AM, Bertrand B. <bertrand25mtl@gmail.com> wrote:
<log_configure>
