Re: [netcdf-hdf] script to compile parallel hdf5

• To: ldfowler <ldfowler58@xxxxxx>
• Subject: Re: [netcdf-hdf] script to compile parallel hdf5
• From: Elena Pourmal <epourmal@xxxxxxxxxxxx>
• Date: Thu, 6 Sep 2012 17:22:12 -0500

Laura,

I was going to reply you on the hdf-forum list, but saw your mail here.

Could you please send me config.log file (in the top directory). Information 
you provide is not enough.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal  The HDF Group  http://hdfgroup.org   
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



On Sep 6, 2012, at 4:47 PM, ldfowler wrote:

> Hi:
> I have been trying for the longest time to compile the hdf5 library with the 
> --enable-parallel option so that I can then compile netCDF with HDF on my 
> MacBook Pro using Lion (10.7.4). I have been in touch with the hdf-forum 
> mailing list but I have not gotten any response. I assume that some of you 
> must have gone through the same steps to install hdf5 parallel. May be one of 
> you can help me figure out what I am doing wrong?
> 
> Here are my settings:
> FC=mpif90
> CC=mpicc
> sudo ./configure --prefix=/usr/local/hdf5-1.8.9-gfortran --enable-parallel 
> --enable-fortran --with-zlib=/usr/local/zlib-1.2.7-gfortran/
> 
> I have tested my mpich2 implementation and know that to works. I am getting 
> the following error message:
> 
> checking for API tracing... no
> checking for instrumented library... no
> 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
> 
> I checked my mpi implementation. The subroutine mpi_file_open is in mpio.h 
> and not in mpif.h. So I am not sure why configure points to mpif.h and not 
> mpio.h. I do not know how to proceed from there from folks on the netcdf 
> side. Any suggestion?
> 
> Thanks,
> Laura
> 
> !=====================================================
> !  Laura D. Fowler
> !  e-mail:  ldfowler58@xxxxxx
> !  Phone:  970-215-0516
> !=====================================================
> 
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• References:
  • [netcdf-hdf] script to compile parallel hdf5
    • From: ldfowler