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.
-Justin
Thanks,
Amir
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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