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

[David van der Spoel]

On 2015-05-12 08:21, Robert McGibbon 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
>
Is the patch somewhere? I'd be happy to apply some more patches and then 
release a new version of the library.

> -Robert
>
> On Mon, May 11, 2015 at 11:16 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto: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
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
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-- 
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