compiling parallel hdf5

Hdf-forum archives
1

Hi:

I am getting the following error message when compiling hdf5 with a parallel option:

checking whether to clear file buffers... yes
checking whether a memory checking tool will be used... no
checking for parallel support files... provided by compiler
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
checking for
            include 'mpif.h'
            integer:: ierr
            call mpi_file_open( ierr ) in -lmpi... ./configure: line 27480: ${ac_cv_lib_mpi_ ____________include__mpif_h_ ____________integer___ierr ____________call_mpi_file_open__ierr__+:}: bad substitution
./configure: line 27496: ac_cv_lib_mpi_: command not found
./configure: line 27497: ____________include__mpif_h_: command not found
./configure: line 27498: ____________integer___ierr: command not found
./configure: line 27502: ____________include__mpif_h_: command not found
yes
checking prefix for running on one processor...
checking prefix for running in parallel...
checking whether a simple MPI-IO program can be linked... no
configure: error: unable to link a simple MPI-IO application

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

Can somebody help?
Thanks,
Laura

!=====================================================
! Laura D. Fowler
! e-mail: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================

2

hm. looks right except 'sudo' for configure seems odd. sudo might
inherit CC and FC from the parent shell.

I'd suggest configuring and building as a regular user. use sudo
for "make install"

==rob

···

On Wed, Sep 05, 2012 at 11:23:59AM -0600, ldfowler wrote:

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

3

Hi Rob:
Thanks for the quick reply. I got the same error message when I tried to "configure" locally without sudo? Any other idea?
Thanks,
Laura

···

On Sep 5, 2012, at 12:06 PM, Rob Latham wrote:

On Wed, Sep 05, 2012 at 11:23:59AM -0600, ldfowler wrote:

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

hm. looks right except 'sudo' for configure seems odd. sudo might
inherit CC and FC from the parent shell.

I'd suggest configuring and building as a regular user. use sudo
for "make install"

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

4

do you have MPI installed on your machine?
does compiling a simple MPI program using mpicc work?

I do not see anything wrong with your configure line if you did not use sudo..

Mohamad

···

On 9/5/2012 1:31 PM, ldfowler wrote:

Hi Rob:
Thanks for the quick reply. I got the same error message when I tried to "configure" locally without sudo? Any other idea?
Thanks,
Laura

On Sep 5, 2012, at 12:06 PM, Rob Latham wrote:

On Wed, Sep 05, 2012 at 11:23:59AM -0600, ldfowler wrote:

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

hm. looks right except 'sudo' for configure seems odd. sudo might
inherit CC and FC from the parent shell.

I'd suggest configuring and building as a regular user. use sudo
for "make install"

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

5

Hi Rob:
One thing that I noticed is that in the errors below, configure is looking for mpi_file_open in mpif.h. Checking my installation of mpich2, the subroutine mph_file_open is located in mpio.h and not in mpif.h. Do you think that this could explain the error I get?

Thanks,
Laura

checking for
            include 'mpif.h'
            integer:: ierr
            call mpi_file_open( ierr ) in -lmpi... ./configure: line 27480: ${ac_cv_lib_mpi_ ____________include__mpif_h_ ____________integer___ierr ____________call_mpi_file_open__ierr__+:}: bad substitution
./configure: line 27496: ac_cv_lib_mpi_: command not found
./configure: line 27497: ____________include__mpif_h_: command not found

···

On Sep 5, 2012, at 12:06 PM, Rob Latham wrote:

On Wed, Sep 05, 2012 at 11:23:59AM -0600, ldfowler wrote:

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

hm. looks right except 'sudo' for configure seems odd. sudo might
inherit CC and FC from the parent shell.

I'd suggest configuring and building as a regular user. use sudo
for "make install"

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

6

Hi Mohamad:
Thanks for the reply. Yes, I installed mpich2 on my machine. I tested that mpi worked using the c and f90 examples that was provided, and it worked well. I do not understand the line:

            call mpi_file_open( ierr ) in -lmpi... ./configure: line 27480: ${ac_cv_lib_mpi_ ____________include__mpif_h_ ____________integer___ierr ____________call_mpi_file_open__ierr__+:}: bad substitution
./configure: line 27496: ac_cv_lib_mpi_: command not found

Is it trying to substitute something that it does not find?

Laura

···

On Sep 5, 2012, at 12:35 PM, Mohamad Chaarawi wrote:

do you have MPI installed on your machine?
does compiling a simple MPI program using mpicc work?

I do not see anything wrong with your configure line if you did not use sudo..

Mohamad

On 9/5/2012 1:31 PM, ldfowler wrote:

Hi Rob:
Thanks for the quick reply. I got the same error message when I tried to "configure" locally without sudo? Any other idea?
Thanks,
Laura

On Sep 5, 2012, at 12:06 PM, Rob Latham wrote:

On Wed, Sep 05, 2012 at 11:23:59AM -0600, ldfowler wrote:

Initially, I did:
CC=mpicc
FC=mpif90
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran.parallel --with-zlib=/usr/local/zlib-1.2.7-gfortran

hm. looks right except 'sudo' for configure seems odd. sudo might
inherit CC and FC from the parent shell.

I'd suggest configuring and building as a regular user. use sudo
for "make install"

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org