[gmx-developers] pme in release-4-6 with domain decomposition

[Dommert Florian]

On Thu, 2012-04-12 at 01:10 -0400, Roland Schulz wrote:
> 
> 
> On Mon, Apr 9, 2012 at 11:11 AM, Dommert Florian
> <dommert at icp.uni-stuttgart.de> wrote:
>         On Mon, 2012-04-09 at 10:45 -0400, Roland Schulz wrote:
>         > Hi,
>         >
>         >
>         > we need a bit more detail. What architecture (/what nb
>         kernel)? What
>         > compiler?
>         >
>         >
>         
>         
>         Hi,
>         
>         the architecture is X86_64 and the compiler is gcc4.4 shipped
>         with
>         Ubuntu 10.4. OpenMPI1.4.3 compiled with gcc4.4 has been used
>         to build
>         Gromacs in double precision. The error arises with the
>         NB_GENERIC and
>         the standard ASM kernels for x86_64. 
> 
> 
> Is this with an unmodified version? Do you get valgrind errors? I
> suppose if the forces are that large  the simulation crashes, correct?
> I suggest you open a bug and attach the tpr.
> 

Hi,

today I got an update of the following bug report:

http://redmine.gromacs.org/issues/767

Now  I remember, that the same problems occurred earlier. So it seems
Berk already takes care about this problem.

Sorry for the inconvenience.

/Flo

> 
> Roland
>  
>         
>         
>         Cheers,
>         
>         Flo 
>         
>         > Roland
>         >
>         > On Mon, Apr 9, 2012 at 8:54 AM, Dommert Florian
>         > <dommert at icp.uni-stuttgart.de> wrote:
>         >         Hi,
>         >
>         >         today I tested the new release-4-6 branch, but
>         inconsistent
>         >         electrostatic forces arise.
>         >
>         >         As test system I used the spc216 water box and
>         calculated the
>         >         forces
>         >         with ewald and pme. If only a single processor is
>         used the
>         >         forces are
>         >         consistent. Also for multiple processes and particle
>         >         decomposition the
>         >         forces are correct. However if domain decomposition
>         used, the
>         >         forces are
>         >         sometimes in the order of 10^102 (correct average
>         maximum
>         >         force 2402
>         >         kJ/mol/nm).
>         >
>         >         If the test systems consists of 500 positive and
>         negative
>         >         atomic ions or
>         >         molecular ions, everything is fine, too, indepenent
>         of the
>         >         decomposition
>         >         scheme.
>         >
>         >         Only the model systems with water make trouble (I
>         tried SPC/E
>         >         and
>         >         TIP-4P).
>         >         Does anyone has an idea, what the reason for this
>         problem
>         >         might be ?
>         >
>         >         Cheers,
>         >         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
>         
> 
> 
> 
> 
> -- 
> 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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