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Re: [h5md-user] Multiple H5MD root groups per file

From: Felix Höfling
Subject: Re: [h5md-user] Multiple H5MD root groups per file
Date: Mon, 23 Sep 2013 15:57:54 +0200
User-agent: Opera Mail/12.15 (Linux)

Am 20.09.2013, 14:40 Uhr, schrieb Peter Colberg <address@hidden>:

On Fri, Sep 20, 2013 at 01:14:59PM +0200, Konrad Hinsen wrote:
Pierre de Buyl writes:

 > I propose one of these updates:
> 1. Mandate a list of H5MD paths somewhere at the root of the file (for
 > autodiscovery of H5MD containers).

If we want to be able to use H5MD inside a collection of data managed
by some other specification, then we cannot mandate anything to be at
the root level. Any prescription about the root level more or less
implies "we own the whole file".

It's actually not so difficult to let programs search for H5MD data
inside a file. The real difficulty is what to do when there are
multiple H5MD trajectories but the operation of the program requires a
single one.

 > 2. Allow the extension but mandate that H5MD data be communicated as
 > file.h5/path/to/some/h5md_root_group.

No problem with that but it's a bit outside of the specification of the
file format.

BTW, I'd use some other separator between filename and path, otherwise
it's difficult for Unix software to identify the filename. Of course anything
else could conflict with some other platform's path separator.

I don't think we need or should worry about communicating the path(s)
to H5MD roots. An H5MD root is intended to be a self-contained unit,
so by definition it cannot point to itself from outside the H5MD root.

Finding the H5MD roots in a file is a task to be solved by the program.
Simple programs can ask for a path+group instead of a just a path, and
more complex programs can locate root(s) by walking the HDF5 file.


Having an H5MD root distinct from the file root is a very nice suggestion.

I think we could allow for this by a careful rephrasing of the draft without promising too much. Mainly replacing "file root" by "H5MD root group" and indicating that H5MD does not specify the structure of the whole file but only a subtree. Thus, we automatically allow for multiple, independent H5MD roots in one file (which could even be of different H5MD versions or use different conventions!)

A suggestion for an according patch is attached.


Attachment: 0001-replace-H5MD-file-by-H5MD-structure.patch
Description: Text Data

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