[gmx-developers] electrostatic forces and domain decomposition

[Dommert Florian]

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


> /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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