[gmx-developers] MDAnalysis' libxdrfile2 vs. GROMACS' xdrfile
Robert McGibbon
rmcgibbo at gmail.com
Tue May 12 10:38:00 CEST 2015
Honestly, I'm not too sure. I always have trouble with patch files. Maybe I
generated it incorrectly.
If it were me, I would just download the three C files from
https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src and
overwrite the corresponding files in your source tree, and then check
git-diff.
-Robert
On Tue, May 12, 2015 at 1:33 AM, David van der Spoel <spoel at xray.bmc.uu.se>
wrote:
> On 2015-05-12 09:14, Robert McGibbon wrote:
>
>> 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
>>
>
> Pardon my ignorance, but I tried a few things without success. How do I
> apply this patch to a freshly checked out xdrfile src tree?
>
>
>> 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 <mailto: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>
>> <mailto: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>
>> <tel:%2B46184714205>.
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>> <mailto: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
>> <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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