[gmx-users] error in parallel mdrun

Amir Marcovitz amarcovitz at gmail.com
Sun Jun 27 10:18:47 CEST 2010

Hi Gavin,

I had exactly the same problem a few days ago.
you have 2 options for parallel runs: domain decomposition (default) and
particle decomposition
you can either try to manipulate the parameters of your system such that
they fit domain decomposition or choose the easier way..that is using
particle decomposition (mdrun -pd)
i use it and it works fine, though I'm not sure  it the most efficient
algorithm for parallel runs.


On Tue, Jun 22, 2010 at 6:58 PM, Gavin Melaugh <gmelaugh01 at qub.ac.uk> wrote:

> 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*
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