[gmx-users] job failed. Too many CPU?

[Justin Lemkul]

On 6/17/16 5:32 PM, Albert wrote:
>
> Hello:
>
> I am trying to run a Gromacs job with command line:
>
> mpirun -np 1 gmx_mpi grompp -f step6.0_minimization.mdp -o 60.tpr -n -c
> step5_charmm2gmx.pdb -maxwarn -1
> mpirun -np 56 mdrun_mpi -s 60.tpr -g  60.log -c 60.gro >& 60.info
>
>
> I am using Charmm36 FF for my system which contains 60,000 atoms.
>
> The box size is:
>
> CRYST1  73.607065  73.607065  109.376  90.0  90.0  90.0
>
>
> Here is the log file. I googled similar errors and found that this normally
> happen to a small system with large no. of CPU. However, I don't think 56 cores
> CPU are too many for my system....
>
>
>
> Reading file 60.tpr, VERSION 5.1.1 (single precision)
>
> Will use 40 particle-particle and 16 PME only ranks
> This is a guess, check the performance at the end of the log file
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.1.1
> Source code file:
> /icm/home/memar/topola/gromacs-5.1.1/src/gromacs/domdec/domdec.cpp, line: 6987
>
> Fatal error:
> There is no domain decomposition for 40 ranks that is compatible with the given
> box and a minimum cell size of 6.76123
>  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
> -------------------------------------------------------
>
>
>
> THX a lot

Look in the log file for why you have such long distances.  Normal bonded 
interactions should be significantly shorter.  I suspect something is wrong with 
the topology or you're applying some sort of long-distance restraints that you 
haven't mentioned.

-Justin

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

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
http://mackerell.umaryland.edu/~jalemkul

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