serial and parallel hdf5
Eric A. Borisch
eborisch at macports.org
Wed Jan 20 11:03:43 PST 2016
I think I see what you mean; H5_HAVE_PARALLEL=1 will be defined in
H5pubconf.h, which will then want to include mpi.h.
Just letting HDF5 pull in mpi.h, however, *should hopefully* not break
other things. Be sure you're including the same include directory for
mpi headers that hdf5 used (/opt/local/include/mpich-mp for +mpich,
I'd say this is still likely the preferred (only practical?) way for
an executable to use both parallel and serial HDF5 calls; I can't
begin to think about the conflicts if you tried to link to two
different libhdf5 (one built with parallel support, one without)
On Wed, Jan 20, 2016 at 11:39 AM, Francesco Miniati <fm at phys.ethz.ch> wrote:
> the first problem i see (after trying) is that the parallel libraries need the mpi headers,
> which I don’t necessarily specify when I compile in serial.
> I can provide those headers with an path to the proper include directory, but then I get a long list of compilation fails.
> it doesn’t seem to work, did you try yourself successfully ?
>> On 20 Jan 2016, at 18:17, Eric A. Borisch <eborisch at ieee.org> wrote:
>> The 'parallel' version of HDF5 still supports all of the serial
>> features; it additionally provides the ability to use MPI I/O for
>> distributed HDF5 R/W. You need to select parallel IO explicitly in
>> your code with all call to H5Pset_fapl_mpio(...) (for example) with
>> the 'parallel' version -- otherwise you get the standard serial
>> Said differently: install the parallel version of HDF5; if you run
>> into something you feel you can't do with it that you could with the
>> 'non-parallel' version, let me know.
>> - Eric
>> On Wed, Jan 20, 2016 at 11:07 AM, David Strubbe <dstrubbe at macports.org> wrote:
>>> Right, you can only use one at a time. I think the options are (1) rewrite
>>> the application to use only parallel (can't the parallel library do serial
>>> operations too?); (2) make a second installation of macports with a
>>> different prefix (not /opt/local), and install hdf5 serial in one and
>>> parallel in the other.
>>> On Wed, Jan 20, 2016 at 11:48 AM, Francesco Miniati <fm at phys.ethz.ch> wrote:
>>>> I am using an application that requires both serial and parallel versions
>>>> of hdf5.
>>>> as far as I understand i can only install one version in /opt/local/ with
>>>> and cannot specify a different installation directory, am I correct?
>>>> In any case, is there a way to install both versions with macports in
>>>> separate directories
>>>> somewhere under /opt/local ?
>>>> thanks a lot for your support,
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