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Re: [h5md-user] Strings again / parallel issue
From: |
Pierre de Buyl |
Subject: |
Re: [h5md-user] Strings again / parallel issue |
Date: |
Tue, 4 Feb 2014 18:19:20 +0100 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
On Tue, Feb 04, 2014 at 10:38:55AM -0500, Peter Colberg wrote:
> 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?
In another thread if you wish :-)
> 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.
Well, the code that I attach (for real now) writes an attribute in parallel. The
operation is collective (as it must).
Best,
Pierre
> > 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 ;-).
parallel_string_attribute.f90
Description: Text document
parallel_vl_string_attribute.f90
Description: Text document
- [h5md-user] Strings again / parallel issue, Pierre de Buyl, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue,
Pierre de Buyl <=
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue, Pierre de Buyl, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/04
- Re: [h5md-user] Strings again / parallel issue, Pierre de Buyl, 2014/02/05
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/05
- Re: [h5md-user] Strings again / parallel issue, Felix Höfling, 2014/02/06
- Re: [h5md-user] Strings again / parallel issue, Peter Colberg, 2014/02/06
- Re: [h5md-user] Strings again / parallel issue, Pierre de Buyl, 2014/02/06
- Re: [h5md-user] Strings again / parallel issue, Felix Höfling, 2014/02/07