[gmx-developers] electrostatic forces and domain decomposition
Dommert Florian
dommert at icp.uni-stuttgart.de
Mon Jun 27 14:21:48 CEST 2011
On Mon, 2011-06-27 at 11:59 +1000, Mark Abraham wrote:
> On 27/06/2011 2:15 AM, Dommert Florian wrote:
> > On Sun, 2011-06-26 at 17:44 +0200, Dommert Florian wrote:
> > > On Sun, 2011-06-26 at 16:54 +0200, Dommert Florian wrote:
> > > > On Sun, 2011-06-26 at 08:45 -0400, Roland Schulz wrote:
> > > > > Hi,
> > > > >
> > > > > On Sun, Jun 26, 2011 at 8:31 AM, Dommert Florian
> > > > > <dommert at icp.uni-stuttgart.de> 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?
> > > > 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 ?
> > > >
> > > 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
> > >
> > 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.
>
> I don't understand what version you regard as "obviously" working, or
> even working.
>
> 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.
>
> 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 http://redmine.gromacs.org, where you can make suitable
> attachments.
>
> 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.
Hello,
I tried statically compiled builds, but the effect is still the same.
When I run mdrun different times I got strongly varying forces.
The reason, why git bisect did not work was that this effect occurs
completely random, if DD is used. As mentioned, for PD everything work
perfect. I will file a Redmine issue.
/Flo
>
> Mark
>
> > Any idea where this comes from ?
> >
> > /Flo
> >
> > > > /Flo
> > > > >
> > > > > Roland
> > > > >
> > > > >
> > > > > /Flo
> > > > > --
> > > > > Florian Dommert
> > > > > Dipl. - Phys.
> > > > >
> > > > > Institute for Computational Physics
> > > > > University Stuttgart
> > > > >
> > > > > Pfaffenwaldring 27
> > > > > 70569 Stuttgart
> > > > >
> > > > > EMail: dommert at icp.uni-stuttgart.de
> > > > > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> > > > >
> > > > > 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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--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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