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

[Roland Schulz]

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.

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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