[gmx-users] decomposition error

[Justin Lemkul]

On 7/22/16 6:50 PM, Chang Woon Jang wrote:
> Dear Grimaces Users,
>
> I have the decomposition error. I have tried to reduce the number of cores
> but still have the same problem. In my conf.gro, the cell size is about
> 5.5x5.5x5.5 but I do not know what the minimum cell size of 1.875nm.
>
>  Would you please give me some comments or relevant topics addressed?
>

The .log file tells you how DD is being set up and what the the limiting 
interactions are.  Verify that your topology is sound from what the .log tells you.

> -------------------------------------------------------
>
> Program gmx, VERSION 5.0.7-dev-20151003-1909f2f
>
> Source code file:
> /home1/02271/huddack/votca_install/src/gromacs/src/gromacs/mdlib/domdec.c,
> line: 6902
>

Also make sure your run isn't failing because of something due to hacked code. 
Development versions generally shouldn't be used for production-level science.

-Justin

>
> Fatal error:
>
> There is no domain decomposition for 16 ranks that is compatible with the
> given box and a minimum cell size of 1.875 nm
>
> Change the number of ranks or mdrun option -rdd or -dds
>
> 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
>
> -------------------------------------------------------
>

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

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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