[gmx-users] mdrun -rdd and -dds flag
jalemkul at vt.edu
Thu Apr 11 12:44:25 CEST 2013
On Thu, Apr 11, 2013 at 6:17 AM, manara r. (rm16g09) <rm16g09 at soton.ac.uk>wrote:
> Dear gmx-users,
> I am having a problem with a periodic molecule and the domain
> decomposition, I wish to use a high number of processors (circa 180, but
> can obviously be reduced) and therefore need to use the -rdd or -dds flags
> (I believe), how do these value effect the simulation?
> The box size is 11.5 x 11.5 x 45.
> The polymer contains charged groups every repeating unit.
> The error I'm getting is (note this is a test run on my home machine, not
> the cluster):
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with the
> given box and a minimum cell size of 61.7923 nm
> Change the number of nodes or mdrun option -rdd or -dds
There is no amount of hacking of -rdd or -dds that will "solve" this
problem. DD cell size should be on the order of the longest cutoff. Your
minimum size is huge, indicating you probably have either a bad topology or
incorrect .mdp settings.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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