[gmx-users] error in parallel mdrun

Gavin Melaugh gmelaugh01 at qub.ac.uk
Tue Jun 22 17:58:40 CEST 2010

Hi all

I have a ran a simulation of 64 molecules in a cubic box with side 6 nm,
using nose-hoover thermostat, parinello-rahman pressure coupling, and
pme. Runnin the simulation in parallel is no problem (using 16 CPUs).
However when I want to run an almost identical molecule using the exact
same conditions as the previous case I get the following error (below),
until eventual I reduce the number of CPUs to 4 and then everything is
fine. I would however like to run the simulation using more processors
if anyone can give me some advise. Note the following error is from the
log file.

*Program mdrun, VERSION 4.0.7
Source code file: domdec.c, line: 5888

Fatal error:
There is no domain decomposition for 13 nodes that is compatible with
the given box and a minimum cell size of 1.25784 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition*

More information about the gromacs.org_gmx-users mailing list