Re: [h5md-user] Minor revisions before H5MD v1.0

[Felix Höfling]

Am 03.05.2013, 16:27 Uhr, schrieb Peter Colberg  
<address@hidden>:

> Hi Felix,
>
> On Fri, May 03, 2013 at 04:03:26PM +0200, Felix Höfling wrote:
> > Am 02.05.2013, 22:57 Uhr, schrieb Peter Colberg
> > <address@hidden>:

> > On the other hand, attributes are the most efficient way for
> > small pieces of information as you noted earlier.
> >
> > This ambiguity is already inherent in the HDF5 Manual, see the first
> > sentences of Chapter 8.1:
> > http://www.hdfgroup.org/HDF5/doc/UG/UG_frame13Attributes.html
> > Further down in this chapter, the maximum reasonable size of an
> > attribute is given as 64k. So in conclusion, storing the fixed box
> > data as attribute would be fine with me.
>
> Should we mention the 64k in a small section on HDF5 implementation?
>
> That could serve as a guideline for future decisions on small (meta)data.
Good idea.

> > >The "parameters" group is intended as a program-dependent group.
> > >I suggest to remove the "parameters/dimension" attribute, as it
> > >is in contrast to the purpose of this group. The dimension can
> > >be derived from, e.g., the "edges" attributes or "edges/value"
> > >dataset, similar to the number of particles being derived from
> > >"position/value" dataset(s).
> > >
> > I think we should not turn the clock back. There were good reasons
> > to include the dimension parameter explicitly, mainly it cannot be
> > inferred from scalar datasets in /observables. Recall that the box
> > group is not mandatory.
>
> (It was a recent proposal, so it can be reverted without causing  
> trouble.)
>
> I am definitely opposed to defining anything within the “parameters”
> group. That group has been, as said, intended as program-specific.
>
> As for the spatial dimension attribute: The idea of self-describing
> datasets is one of the main benefits of using a structural format for
> storing molecular data. I would rather not violate that principle.
>
> If you need to split up your files, you could store the box group as
> well, or add a custom attribute "dimension" to your observables. The
> tool h5copy is quite useful for such splitting operations.
>
> Peter

I do not adhere to the /parameters group, but one needs a definite place  
were an H5MD reader can get the space dimension from in a simple and  
reliable way. In particular, it must not depend on the presence of any  
group, be it /trajectory or /observables or /observables/box. The point is  
that the scalar observable data sets are incomplete without the dimension  
thus breaking the self-descriptiveness of the data format.

Felix