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On 27/06/2011 2:15 AM, Dommert Florian wrote:
<blockquote cite="mid:1309104922.14696.107.camel@fermi" type="cite">
<pre wrap="">On Sun, 2011-06-26 at 17:44 +0200, Dommert Florian wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Sun, 2011-06-26 at 16:54 +0200, Dommert Florian wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Sun, 2011-06-26 at 08:45 -0400, Roland Schulz wrote:
</pre>
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<pre wrap="">Hi,
On Sun, Jun 26, 2011 at 8:31 AM, Dommert Florian
<a class="moz-txt-link-rfc2396E" href="mailto:dommert@icp.uni-stuttgart.de"><dommert@icp.uni-stuttgart.de></a> wrote:
with the current release-4-5-patches branch unexpected large
electrostatic forces arise when using PME and MPI in
combination with domain decomposition. I tried to attach a
small test case with a water box of about 4000 molecules and a
corresponding mdp, top, itp, and gro file, but it was too
large. For particle decomposition
with different numbers of processes everything is fine as well
as for a
run with a single process and DD. However using multiple
processes and
DD I obtain forces around 10^10, though they should be around
10^3.
For the testruns I compiled gromacs with cmake on a
Ubuntu 10.4 platform with a 2.6.39-rc6+ kernel using gcc4.4.3
and
OpenMPI 1.4.3 and fftw3.2.2
and a Rocks Cluster with a 2.6.18-164.6.1.el5 kernel and the
same
compiler, MPI and fftw3 version. On both systems I obtain the
strange
behaviour.
When I got back to the commit with SHA1 ID
e5eb052ebf35e4b778f7a3908463a68a2ef6faee, merge by merge,
everything is fine again.
What do you mean merge by merge? Could you do a git bisect?
</pre>
</blockquote>
<pre wrap="">
Hello,
after bisecting the release-4-5-patches branches, git tracked down the
error to commit:
[68ab9f6fa143fec070ffe60686cb8f9e397d0376] Expanded LINCS warning text
Is this what you asked me to do ?
</pre>
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<pre wrap="">
Now I did it again, but ended up with another result. The output of git
bisect good was:
2e4f7f300a284690ef2ad60359f3d7e40653724c is the first bad commit ...
/Flo
</pre>
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<pre wrap="">
As I tested the "oviously" working version, it turned out, that the
results is of random behaviour. Though I turned off fftw-measurement and
used the -reprod flag of mdrun, the average maximum force has values
that arise randomly and are in an interval from 10^3 to 10^10. Also for
the code I considered as "working" this behaviour can be observed.
</pre>
</blockquote>
<br>
I don't understand what version you regard as "obviously" working,
or even working. <br>
<br>
The commits with hashes you have mentioned can't be causing such
problems, so if you have used git bisect correctly, then the problem
is actually not in the code.<br>
<br>
Are you saying that a range of versions of release-4-5-patches give
you maximum force values up to 10^10? If so, please file a Redmine
issue <a href="http://redmine.gromacs.org/">http://redmine.gromacs.org</a>,
where you can make suitable attachments.<br>
<br>
My suspicion is that you are experiencing some kind of linking
error, perhaps between different available FFTW or GROMACS versions.
Perhaps you can try static linking.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:1309104922.14696.107.camel@fermi" type="cite">
<pre wrap="">Any idea where this comes from ?
/Flo
</pre>
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<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">/Flo
</pre>
<blockquote type="cite">
<pre wrap="">
Roland
/Flo
--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: <a class="moz-txt-link-abbreviated" href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>
Homepage: <a class="moz-txt-link-freetext" href="http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a>
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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<pre wrap="">
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<pre wrap="">
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<pre wrap="">
</pre>
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