<div dir="ltr">Honestly, I'm not too sure. I always have trouble with patch files. Maybe I generated it incorrectly.<div><br></div><div>If it were me, I would just download the three C files from <a href="https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src">https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src</a> and overwrite the corresponding files in your source tree, and then check git-diff.</div><div><div><br></div><div>-Robert</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 12, 2015 at 1:33 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 2015-05-12 09:14, Robert McGibbon wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Here's a patch file for the changes in MDTraj against<br>
xdrfile-1.1.4.tar.gz from<br>
<a href="http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library" target="_blank">http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library</a>:<br>
<br>
<a href="https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc" target="_blank">https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc</a><br>
</blockquote>
<br></span>
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?<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
<br>
Most of the patch file is noise from changing some error messages, but<br>
there are a couple of meaningful things, like the check here<br></span>
<<a href="https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc#file-xdrfile-1-1-4-src-patch-L68-L73" target="_blank">https://gist.github.com/rmcgibbo/ed7be1fff89e3467f1bc#file-xdrfile-1-1-4-src-patch-L68-L73</a>>.<span class=""><br>
If I recall correctly, that originated because some trajectories<br>
collected on Folding@Home had become corrupted in such a way that<br>
reading them segfaulted the python interpreter.<br>
<br>
-Robert<br>
<br>
On Mon, May 11, 2015 at 11:57 PM, David van der Spoel<br></span><span class="">
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br>
On 2015-05-12 08:21, Robert McGibbon wrote:<br>
<br>
For what it's worth, the MDTraj python package (similar to<br>
MDAnalysis)<br>
also includes a modified version of xdrfile, which fixes a few small<br>
bugs. The changes are described here:<br>
<a href="https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src" target="_blank">https://github.com/mdtraj/mdtraj/tree/master/mdtraj/formats/xtc/src</a>.<br>
<br>
One of the bugs (a segfault on reading certain malformed xtc<br>
files) was<br>
reported to the gromacs-dev list a while ago, but nobody seemed<br>
interested:<br>
<a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html" target="_blank">https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html</a><br>
<br>
Is the patch somewhere? I'd be happy to apply some more patches and<br>
then release a new version of the library.<br>
<br>
-Robert<br>
<br>
On Mon, May 11, 2015 at 11:16 PM, David van der Spoel<br>
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br></span><div><div class="h5">
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>>> wrote:<br>
<br>
On 2015-05-11 23:23, Dominik 'Rathann' Mierzejewski wrote:<br>
<br>
Dear developers,<br>
there seems to be a fork of GROMACS' xdrfile by the<br>
MDAnalysis<br>
project:<br>
<a href="https://github.com/MDAnalysis/mdanalysis/tree/develop/package/src/xdrfile" target="_blank">https://github.com/MDAnalysis/mdanalysis/tree/develop/package/src/xdrfile</a><br>
<br>
What are the plans for xdrfile? Would you be open to<br>
incorporating<br>
MDAnalysis' fork changes into your library?<br>
<br>
They have added proper python bindings (via swig) and<br>
some new C<br>
APIs.<br>
There are also small changes in API, for example in<br>
read_trr (new<br>
parameter) and xdrstdio_(get|set)pos() functions<br>
(parameter types).<br>
I'm attaching a sanitized diff of the C code. Python<br>
changes are too<br>
extensive to make a diff of.<br>
<br>
The reason I'm asking is that I'm trying to package<br>
MDAnalysis for<br>
Fedora (and I became the GROMACS maintainer in Fedora<br>
recently<br>
as well).<br>
Our guidelines forbid bundling of third-party libraries<br>
- system<br>
versions are to be used. xdrfile is already packaged in<br>
Fedora, but<br>
MDAnalysis bundles its fork - libxdrfile2 which I have<br>
to unbundle<br>
and package separately. It would make everyone's life<br>
much easier if<br>
xdrfile could be simply updated to include the new python<br>
bindings and<br>
APIs so that MDAnalysis could use them.<br>
<br>
Regards,<br>
Dominik<br>
<br>
<br>
<br>
Are these changes compatible with the latest xdrfile<br>
changes? There<br>
has not been a release recently though.<br>
<br>
<br>
--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a><br>
<tel:%2B46184714205><br>
<tel:%2B46184714205>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>><br></div></div>
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Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
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