[gpaw-users] HDF5 and parallel calculation support

[Nichols A. Romero]

Also, HDF5 can be tricky to compile. There are some configuration options that are mutually exclusive.

For GPAW, you need parallel enable with C bindings and serial enable with C bindings. You don't need C++ or Fortran bindings.

Here is my configure script for my Linux box.
http://en.pastebin.ca/2306562


----- Original Message -----
> From: "Jussi Enkovaara" <jussi.enkovaara at aalto.fi>
> To: gpaw-users at listserv.fysik.dtu.dk
> Sent: Wednesday, January 23, 2013 3:25:03 AM
> Subject: Re: [gpaw-users] HDF5 and parallel calculation support
> 
> On 2013-01-22 21:21, Gaël DONVAL wrote:
> > Hi everyone,
> >
> > I'm about to install gpaw on our computer cluster.
> >
> 
> >
> > The question is, is there any support for the HDF5 format in gpaw
> > without parallel compilation of the HDF5 library? I tried to
> > compile
> > HDF5 with parallel support but since the FS we used is not parallel
> > yet,
> > we don't even have the MPI/IO extension compiled in OpenMPI.
> 
> Hi,
> the short answer is that currently one cannot use parallel GPAW with
> serial HDF5 (it is, however, possible to use serial GPAW with serial
> HDF5).
> 
> When using .gpw files, all the data is collected to single process
> which
> does then the I/O, and while in principle similar thing could be done
> with HDF5, I do not think it is worth of implementing.
> 
> There are only two MPI I/O related HDF5 functions used in GPAW, and
> even
> tough the one of them (which enables collective I/O) can be
> disabled easily, the other one used for opening the file for parallel
> access is really required. At least very brief test on our Cray
> system
> showed that file write does not work correctly (with more than single
> CPU core) if file is not opened for parallel access.
> 
> Best regards,
> Jussi
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