[gmx-developers] electrostatic forces and domain decomposition

[Dommert Florian]

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.

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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> 
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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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