[gmx-users] A confusion about domain decomposition

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 20 13:52:16 CEST 2010

Amir Marcovitz wrote:
> Hi all,
> I'm trying to run a parallel Job for a system of dummy atoms that 
> arranged as 2 surface (each is 6X6 atom surface- with bonds that i 
> defined between them)
> the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with 
> salt, minimized and equlibrated fine.
> however, when trying to execute parallel Job i get the following domain 
> decomposition error:
> *-------------------------------------------------------
> Program mdrun, VERSION 4.0.7
> Source code file: domdec.c, line: 5888*
> *Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the 
> given box and a minimum cell size of 3.37646 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------*
> ** 
> ** 
> i read the relevant paragraphs on the manual regarding domain 
> decomposition , but remained confused.
> my question is How do you think i should solve it, and what are the 
> thumb rules for the use of the -rdd and -dds flags? (i think that i did 
> not quit understood from the manual how are the 2 flags relate to the 
> parameters of my system)

There is a minimum size for a DD cell for every system, depending upon the use 
of constraints, the cutoffs, box size, etc.  It's rather complicated, as you've 
found out :)  Search the list archive for the error message - you will come up 
with lots of useful threads where others have had this problem.

If you want to try to troubleshoot further, posting the portion of the log file 
pertaining to the DD settings would be useful.  Otherwise, use mdrun -pd for 
particle decomposition or run in serial.


> Thanks,
> Amir


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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