Re: [h5md-user] Fortran bindings for H5MD

[Pierre de Buyl]

Hi,

I am aware that H5Part exists but I have never used it. From the description, it
seems that it is appropriate for Molecular Dynamics. There is a notice on their
page that it is replaced by H5hut http://vis.lbl.gov/Research/H5hut/

Your comment that parallel HDF5 is fairly short to set up is right. Managing
properly all the data (chunk sizes, particle IDs, etc) is less simple and making
a generic interface in a library is a complex task.

Regards,

Pierre

On Mon, Aug 10, 2015 at 10:43:31PM +0100, W. Miah wrote:
> Hi again Pierre,
> 
> sorry to bother you again, but I also came across H5Part
> (http://vis.lbl.gov/Research/H5Part/) which is a file format for
> particle physics which does support parallel I/O. If you are familiar
> with H5Part, do you know if it can be used for molecular dynamics?
> 
> Regards,
> Wadud.
> 
> On 10 August 2015 at 22:22, W. Miah <address@hidden> wrote:
> > Hi Pierre,
> >
> > I'm not an expert in HDF5, but isn't the only difference between
> > serial and parallel is in opening the HDF5 file? In the parallel
> > version, you provide it the MPI communicator.
> >
> > Regards,
> > Wadud.
> >
> > On 10 August 2015 at 21:56, Pierre de Buyl
> > <address@hidden> wrote:
> >> Hi,
> >>
> >> On Mon, Aug 10, 2015 at 04:25:40PM +0100, W. Miah wrote:
> >>> Do you have a version that runs in parallel, namely MPI?
> >>
> >> The code is not working in parallel currently. The efforts required would 
> >> be
> >> moderate but I do not have the time to work on this currently. I am 
> >> available
> >> for advice if you wish though.
> >>
> >> Regards,
> >>
> >> Pierre
> >>
> >>
> >>>
> >>> Regards,
> >>> Wadud
> >>>
> >>> --------------------
> >>> Wadud Miah
> >>> http://miahw.wordpress.com
> >>> On 10 Aug 2015 16:23, "Pierre de Buyl" <address@hidden>
> >>> wrote:
> >>>
> >>> > Dear Wadud,
> >>> >
> >>> > We have collected resources for H5MD software here:
> >>> > http://nongnu.org/h5md/software.html
> >>> >
> >>> > I have written a fortran module that can be found here:
> >>> > https://github.com/pdebuyl/fortran_h5md
> >>> >
> >>> > It works with serial HDF5 and is poorly documented, sadly. The simplest
> >>> > method
> >>> > to start using it is to look at the example directory.
> >>> >
> >>> > Regards,
> >>> >
> >>> > Pierre
> >>> >
> >>> > On Mon, Aug 10, 2015 at 11:41:10AM +0100, W. Miah wrote:
> >>> > > Hello,
> >>> > >
> >>> > > Do you have Fortran bindings for H5MD? If so, where can I download it
> >>> > from?
> >>> > >
> >>> > > Regards,
> >>> > > Wadud
> >>> >
> >>> >
> >>
> >> --
> >> -----------------------------------------------------------
> >> Pierre de Buyl
> >> KU Leuven - Institute for Theoretical Physics
> >> T +32 16 3 27355
> >> W http://pdebuyl.be/
> >> -----------------------------------------------------------
> >>
> >
> >
> >
> > --
> > web: http://miahw.wordpress.com
> > mobile: 07905 755604
> > gnupg: 2E29 B22F
> 
> 
> 
> -- 
> web: http://miahw.wordpress.com
> mobile: 07905 755604
> gnupg: 2E29 B22F
> 

-- 
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Pierre de Buyl
KU Leuven - Institute for Theoretical Physics
T +32 16 3 27355
W http://pdebuyl.be/
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