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[h5md-user] Multiple H5MD root groups per file

From: Konrad Hinsen
Subject: [h5md-user] Multiple H5MD root groups per file
Date: Fri, 20 Sep 2013 09:50:47 +0200

Peter Colberg writes:

 > The proposal is as follows:
 > -------------------------------------------------------------------
 > Any group within an HDF5 file may be an H5MD root group, with
 > the exclusion of groups contained within an H5MD root group.

Sounds good. The only downside is that it makes reading trajectory
files a bit more complicated, since the full specification of a
trajectory is filename plus path to the group. But the benefits
are worth it in my opinion.

I have one immediate application for this (in addition to the one you
mentioned). I have been working on a framework for reproducible
research for which I just made a first public announcement on the h5py
mailing list. All the details are on Bitbucket:


In this framework, each publishable and shareable unit, containing
both code and data, is a single HDF5 file. The root group for this
file contains administrative information, whereas all data has to
reside in the group /data. With the proposed extension, I could have a
H5MD trajectory inside an ActivePaper, which is very attractive for my
plans. In fact, I would probably have done this sooner or later even if
the H5MD specification did not allow it :-)

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
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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