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

[Magnus Lundborg]

On 05/12/2015 10:32 AM, David van der Spoel wrote:
> 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.
Not until most viewers can open tngs, I'd say. Currently there is a 
plugin for vmd, but it's not yet included in the standard distribution. 
I think it'll be realistic to use xtc as default for quite a while and 
certainly include the xdrfile library it for a lot longer.

Cheers,

Magnus
>
>
>>
>> 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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>>
>>
>>
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>
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