[gmx-users] Error in domain decomposition

Dipankar Roy DRoy at brooklyn.cuny.edu
Tue Sep 25 18:20:13 CEST 2012


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

Estimated maximum distance required for P-LINCS: 0.761 nm

This distance will limit the DD cell size, you can override this with

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

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

Look in the log file for details on the domain decomposition

For more information and tips for troubleshooting, please check the

website at http://www.gromacs.org/Documentation/Errors






Dipankar Roy



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