[h5md-user] Strings again / parallel issue

[Pierre de Buyl]

Hi all,

I just discovered a serious annoyance with HDF5 variable-length types. You
cannot use them in parallel [1].

This may have slipped through because nobody is doing parallel H5MD right now,
however for large simulations in parallel (with existing code like ESPResSo or
ESPResSo++) this will become a problem really fast.

I became interested in this because I was toying with topologies (not yet part
of H5MD so no problem for now) but all the strings in H5MD are variable-length
currently. I thus started to check the behaviour for our string data.

Unless someone has a solution to this problem (because I misunderstood
something), we probably need to change all VL strings to fixed-length strings.
The only real annoyance is for arrays of strings (such as the box boundary that
may hold strings of different lengths) were the maximum length must be used for
the string type.

To put the timeframe into context, our paper [2] (me, peter and felix) is 
accepted
now and we are waiting for the proofs. So this should be set within the next few
days.

I attach parallel_string_attribute.f90 (fixed length attribute, works in
parallel) and parallel_vl_string_attribute.f90 (vl strings, doesn't work as far
as I can tell). They require parallel hdf5, indeed.

Best,

Pierre

[1] http://www.hdfgroup.org/hdf5-quest.html#pvl
[2] http://arxiv.org/abs/1308.6382