[gmx-users] There is no domain decomposition

[Justin Lemkul]

On 1/5/16 7:40 PM, Ahmet Yıldırım wrote:
> Dear users,
>
> I get "domain decomposition error" in the energy minimization step of an
> apo-protein. The last part of the log file is below.
>
> log file:
> ...
> Initializing Domain Decomposition on 24 ranks
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>      two-body bonded interactions: 5.122 nm, LJ-14, atoms 3888 3896
>    multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 3888 3896
> Minimum cell size due to bonded interactions: 5.634 nm
> Guess for relative PME load: 0.18
> Will use 18 particle-particle and 6 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 6 separate PME ranks, as guessed by mdrun
> Optimizing the DD grid for 18 cells with a minimum initial size of 5.634 nm
> The maximum allowed number of cells is: X 1 Y 1 Z 1
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.5
> Source code file:
> ../gromacs/5.0.5/src/gromacs-5.0.5/src/gromacs/mdlib/domdec.c, line: 6902
>
> Fatal error:
> There is no domain decomposition for 18 ranks that is compatible with the
> given box and a minimum cell size of 5.63385 nm
> Change the number of ranks or mdrun option -rdd
>
>
> After I got that error, I tried -dd  3 3 2 -npme 6 options with mdrun. This
> times I got the following error:
>
> Fatal error:
> The initial cell size (3.047267) is smaller than the cell size limit
> (5.633849), change options -dd, -rdd or -rcon, see the log file for details
> For more information and tips for troubleshooting, please check the GROMACS
>
> Later I used -rdd 0.7 option with mdrun but it didn't help also. Lastly I
> excluded some bonds that have long distance (for instance: 5.122 nm, LJ-14,
> atoms 3888 3896) in itp file but it couldn't fixed the problem.
>
> Could you give me any clue about how to solve the error?
>

You have a 1-4 interaction with a distance of over 5 nm, which is nonsense. 
Something is wrong with your topology.

-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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