Re: [h5md-user] Another HDF5-based trajector format

[Konrad Hinsen]

Felix Höfling writes:

 > which require a chunked dataspace layout. The relevant filters are
 > "shuffle" in combination with "deflate" (GZIP) or szip. You can nicely
 > play around with
 > 
 >      h5repack -f SHUF -f GZIP=6 input.h5 output.h5

Thanks for those hints, I will produce some trajectories and play with these
options when I find the time. It's encouraging to see that this does give
interesting compression rates.

 > Dataset layout and the chunk size are relatively important. Switching from
 > chunks of 1xNxD to 1xNx1 by
 > 
 >      h5repack -l particles/A/position:CHUNK=1x204800x1 input.h5 output.h5
 > 
 > packs all x-coordinates separately etc. and improves the compression ratio
 > considerably from 39% to 59% (for my specific example).

That makes sense.

Thanks,
  Konrad.
-- 
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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