[gmx-users] domain decomposition problems

Justin Lemkul jalemkul at vt.edu
Sun Jan 29 15:18:42 CET 2017

On 1/29/17 4:33 AM, Albert wrote:
> Hello,
> I am trying to run MD simulation for a system:
> box size: 105.166 x 105.166 x 105.166
> atoms: 114K
> FF: Amber99SB
> I submitted the job with command line:
> srun -n 1 gmx_mpi grompp -f mdp/01-em.mdp -o 60.tpr -n -c ion.pdb
> srun -n 12 gmx_mpi mdrun -s 60.tpr -v -g 60.log -c 60.gro -x 60.xtc
> but it always failed with messages:
> There is no domain decomposition for 12 ranks that is compatible with the given
> box and a minimum cell size of 4.99678 nm
> Change the number of ranks or mdrun option -rdd
> Look in the log file for details on the domain decomposition
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I google it, and the answer for above problem is that the system is too small to
> use a large number of CPU. However, I don't think 12 CPU is too big for my
> system which contains 114 K atoms in all.
> Does anybody have other suggestions?

Check the information in the .log file for the DD setup.  Your cell size is 
pretty large, which suggests long-range interactions that are limiting to the DD 
cell size, usually due to some kind of long distance restraints or otherwise 
unconventional interactions (explicit pairs/exclusions in a free energy 
calculation, etc.)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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