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

[David van der Spoel]

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