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

[David van der Spoel]

On 2015-05-12 08:27, Roland Schulz wrote:
> Should we add xdrfile to gerrit so that we can easily accepts patches
> our standard way?

An alternative would be to hand over he whole xdrfile library to an 
outside developer.

A further thing to consider is whether the tng_io library should replace 
the xdrfile library.



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