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

[Robert McGibbon]

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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