[gmx-users] mdrun -rdd and -dds flag

[Justin Lemkul]

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.

http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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