[h5md-user] Multiple H5MD root groups per file

[Peter Colberg]

Hi all,

We received an in-depth review of the H5MD specification as part of
an article intended to introduce H5MD to the broader scientific
community. The reviewer provides many valuable suggestions, of which
I would like to bring up for discussion the one with a major impact
on the specification.

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.

Examples:

  file root
  \-- h5md
  \-- ...


  file root
  \-- <group1>
  |    \-- h5md
  |    \-- ...
  \-- <group2>
  |    \-- h5md
  |    \-- ...
  \-- <group3>
  |    \-- <subgroup>
  |         \-- h5md
  |         \-- ...
  \-- ...

-------------------------------------------------------------------

This allows storing multiple H5MD trajectories in the same file; or
mixing one or more H5MD data structures with other non-H5MD data
structures, and thus making use of the hierarchical nature of HDF5 to
the fullest extent possible.

I think this is a very useful proposal. The topic of merging files
was brought up already during the debate on units, and the above
would provide a solution.

Multiple H5MD root groups need not necessarily mean that one HDF5 file
contains all data. HDF5 supports linking an object in an external file
to a location within another file. This could for example be used to
present a unified view of many realizations of a single parameter set,
without actually merging the data files.

Peter