netcdf4/hdf5/mpi (-dev) on Debian sid

[Sylwester Arabas]

Hi again,

On Jan 30, 2012, at 6:58 PM, Francesco P. Lovergine wrote:
> On Mon, Jan 30, 2012 at 04:16:40PM +0100, slayoo wrote:
>> I'm trying to get a development set-up of the netcdf4 package
>> on Debian sid with MPI-hdf5 support. Unfortunatelly, without sucess :(
>> 
>> $ sudo apt-get -V install libhdf5-mpi-dev libnetcdf-dev
>> ...
> Currently hdf5 does not provide an MPI version installable with the serial
> one, due to upstream bad habit of using the same name and sonames for all
> versions (serial,parallel and so on). So you have to use the serial version.
> One possibility would be providing parallel versions for all buildable
> chains of tools, as an alternative, but it would be very complicated.

Apparently, it seems that it's the only option - i.e. to provide
netcdf-openmpi, netcdf-mpich, ... etc packages. Here's an extract from
the netCDF source (libsrc4/nc4file.c):

>  164 /* Get the 4-byte blob from the beginning of the file. Don't use posix
>  165  * for parallel, use the MPI functions instead. */
>  166 #ifdef USE_PARALLEL
>  167    if (use_parallel)
>  168    {
>  169       MPI_File fh;
>  170       MPI_Status status;
>  171       int retval;
>  172       if ((retval = MPI_File_open(comm, (char *)path, MPI_MODE_RDONLY,
>  173                                   info, &fh)) != MPI_SUCCESS)
>  174          return NC_EPARINIT;
>  175       if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR,
>  176                                   &status)) != MPI_SUCCESS)
>  177          return NC_EPARINIT;
>  178       if ((retval = MPI_File_close(&fh)) != MPI_SUCCESS)
>  179          return NC_EPARINIT;
>  180    }
>  181    else
>  182 #endif /* USE_PARALLEL */


So, if I get it right: if netCDF uses MPI calls within such ifdefs,
it has to be compiled with mpicc-like compiler calls, and hence the
binary packages for serial, openmpi, and mpich versions of netCDF
have to be different?

HTH,
Sylwester

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