[gmx-users] grompp for minimization: note & warning

[Justin Lemkul]

On 9/15/13 8:17 AM, shahab shariati wrote:
> Dear gromacs users
>
> I used -maxwarn option, but after using this command:
>
> mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
>
> I encountered with:
>
>
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with the
> given box and a minimum cell size of 6.61528 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition
>
>
> Based on above suggestion, I should use option -rdd with mdrun, but I dont
> what argument with -rdd? What value is appropriate for -rdd? 0 or other?
>

Not all systems can be decomposed to run on any arbitrary number of cores/threads.

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

See my previous message for my thoughts on the error grompp gave you, as it 
relates to this one.  Regardless, running with -nt 1 will work and should 
complete reasonably quickly (EM shouldn't take too long).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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