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

[Robert McGibbon]

Here's a patch file for the changes in MDTraj against xdrfile-1.1.4.tar.gz
from http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library:

https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc

Most of the patch file is noise from changing some error messages, but
there are a couple of meaningful things, like the check here
<https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc#file-xdrfile-1-1-4-src-patch-L68-L73>.
If I recall correctly, that originated because some trajectories collected
on Folding at Home had become corrupted in such a way that reading them
segfaulted the python interpreter.

-Robert

On Mon, May 11, 2015 at 11:57 PM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> 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
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