[gmx-users] error in parallel mdrun

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 22 18:00:34 CEST 2010

Gavin Melaugh 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*

Please search the list archive for this error.  There are dozens of posts, 
including one from just a day or two ago.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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