[gmx-developers] MDAnalysis' libxdrfile2 vs. GROMACS' xdrfile

Roland Schulz roland at utk.edu
Tue May 12 08:27:35 CEST 2015

Should we add xdrfile to gerrit so that we can easily accepts patches our
standard way?

On Tue, May 12, 2015 at 2:21 AM, Robert McGibbon <rmcgibbo at gmail.com> wrote:

>  For what it's worth, the MDTraj python package (similar to MDAnalysis)
> also includes a modified version of xdrfile, which fixes a few small bugs.
> The changes are described here:
> https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src.
>  One of the bugs (a segfault on reading certain malformed xtc files) was
> reported to the gromacs-dev list a while ago, but nobody seemed interested:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html
>  -Robert
> On Mon, May 11, 2015 at 11:16 PM, David van der Spoel <
> spoel at xray.bmc.uu.se> wrote:
>> On 2015-05-11 23:23, Dominik 'Rathann' Mierzejewski wrote:
>>> Dear developers,
>>> there seems to be a fork of GROMACS' xdrfile by the MDAnalysis project:
>>> https://github.com/MDAnalysis/mdanalysis/tree/develop/package/src/xdrfile
>>> What are the plans for xdrfile? Would you be open to incorporating
>>> MDAnalysis' fork changes into your library?
>>> They have added proper python bindings (via swig) and some new C APIs.
>>> There are also small changes in API, for example in read_trr (new
>>> parameter) and xdrstdio_(get|set)pos() functions (parameter types).
>>> I'm attaching a sanitized diff of the C code. Python changes are too
>>> extensive to make a diff of.
>>> The reason I'm asking is that I'm trying to package MDAnalysis for
>>> Fedora (and I became the GROMACS maintainer in Fedora recently as well).
>>> Our guidelines forbid bundling of third-party libraries - system
>>> versions are to be used. xdrfile is already packaged in Fedora, but
>>> MDAnalysis bundles its fork - libxdrfile2 which I have to unbundle
>>> and package separately. It would make everyone's life much easier if
>>> xdrfile could be simply updated to include the new python bindings and
>>> APIs so that MDAnalysis could use them.
>>> Regards,
>>> Dominik
>>>  Are these changes compatible with the latest xdrfile changes? There
>> has not been a release recently though.
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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