[gmx-developers] electrostatic forces and domain decomposition

Dommert Florian dommert at icp.uni-stuttgart.de
Sun Jun 26 14:31:48 CEST 2011


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

When I got back to the commit with SHA1 ID e5eb052ebf35e4b778f7a3908463a68a2ef6faee, merge by merge,
everything is fine again.

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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