Re: [h5md-user] Strings again / parallel issue

[Peter Colberg]

Hi Pierre,

On Tue, Feb 04, 2014 at 04:05:26PM +0100, Pierre de Buyl wrote:
> I just discovered a serious annoyance with HDF5 variable-length types. You
> cannot use them in parallel [1].
> 
> This may have slipped through because nobody is doing parallel H5MD right now,
> however for large simulations in parallel (with existing code like ESPResSo or
> ESPResSo++) this will become a problem really fast.
> 
> I became interested in this because I was toying with topologies (not yet part
> of H5MD so no problem for now) but all the strings in H5MD are variable-length
> currently. I thus started to check the behaviour for our string data.

Could you describe the data layout of your topology?

Maybe you could use an enumeration for the datasets in question?

The variable-length string type is currently used with attributes,
which cannot be written in parallel. So I would not expect any
problem for the H5MD specification.

> I attach parallel_string_attribute.f90 (fixed length attribute, works in
> parallel) and parallel_vl_string_attribute.f90 (vl strings, doesn't work as 
> far
> as I can tell).

The attachments are missing ;-).

Regards,
Peter