[gmx-developers] Re: TNG format in Gromacs

Peter Kasson kasson at stanford.edu
Tue Apr 17 19:12:42 CEST 2012

>I think including a lightweight version is the worst option. It combines
the main disadvantage of an own format (a large code base to maintain
without many optional features (because lightweight))
with a few extra disadvantages (extra code for HDF5 compatibility, less
design choices).

Unfortunately, if it becomes an all-or-nothing question, then my
strong vote is to ditch HDF5 and go with our own format.  We want to
avoid large external dependencies as much as possible.

(An example of annoying problems with such dependencies is as follows:
 eager developers for a package I use enabled BLOSC compression for
HDF5 as the default, and the default used in their unit tests.  The
versions of HDF5 that come with Ubuntu 10.04 LTS, which is pretty
standard for stable servers, don't support BLOSC, as that was added
more recently.  So I #1 had to hack the package to step down to
alternate compression rather than failing outright and #2 am
consequently unable to run unit tests on most of my servers.  Apart
from portability, this is one of the scenarios we want to avoid.)


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