[gmx-users] Error in domain decomposition

[Justin Lemkul]

On 9/25/12 12:20 PM, Dipankar Roy wrote:
> Hi,
>
> I am a newbie in Gromacs and is trying to simulate a small organic
> molecule in water. I got the following error message during a position
> restrained md run. I tried changing number of nodes but without success.
>
>
> Any help on this is appreciated.
>
>
>
>
>
> Initializing Domain Decomposition on 16 nodes
>
> Dynamic load balancing: auto
>
> Will sort the charge groups at every domain (re)decomposition
>
> Initial maximum inter charge-group distances:
>
>      two-body bonded interactions: 0.400 nm, LJ-14, atoms 10 14
>
>    multi-body bonded interactions: 0.400 nm, Ryckaert-Bell., atoms 10 14
>
> Minimum cell size due to bonded interactions: 0.440 nm
>
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.761
> nm
>
> Estimated maximum distance required for P-LINCS: 0.761 nm
>
> This distance will limit the DD cell size, you can override this with
> -rcon
>
> Guess for relative PME load: 0.21
>
> Will use 12 particle-particle and 4 PME only nodes
>
> This is a guess, check the performance at the end of the log file
>
> Using 4 separate PME nodes
>
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>
> Optimizing the DD grid for 12 cells with a minimum initial size of 0.951
> nm
>
> The maximum allowed number of cells is: X 2 Y 2 Z 2
>
>
>
> -------------------------------------------------------
>
> Program mdrun_mpi_d, VERSION 4.5.5
>
> Source code file: domdec.c, line: 6436
>
>
>
> Fatal error:
>
> There is no domain decomposition for 12 nodes that is compatible with
> the given box and a minimum cell size of 0.95125 nm
>
> Change the number of nodes or mdrun option -rcon or -dds or your LINCS
> settings
>
> 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
>
> -------------------------------------------------------
>

Did you follow the link and read the following information?

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 


Depending on the size of your system it may not be practical (or even possible) 
to decompose it into more than one or two cells.

-Justin

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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