[gmx-developers] MDAnalysis' libxdrfile2 vs. GROMACS' xdrfile
magnus.lundborg at scilifelab.se
Tue May 12 16:57:59 CEST 2015
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.
>> 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:
>> 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
>> 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:
>> What are the plans for xdrfile? Would you be open to
>> 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
>> parameter) and xdrstdio_(get|set)pos() functions (parameter
>> 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 -
>> versions are to be used. xdrfile is already packaged in
>> Fedora, but
>> MDAnalysis bundles its fork - libxdrfile2 which I have to
>> 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.
>> 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
>> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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