[gmx-users] Domain decomposition error

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Mon May 17 01:38:40 CEST 2010


    I got this following error when I was trying to run a simulation  
of ethanol-water box size 4*4*4 nm (~6530 atoms).

Fatal error:
There is no domain decomposition for 14 nodes that is compatible with  
the given box and a minimum cell size of 0.62175 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.

I looked into my log file and this is what I got:

Initializing Domain Decomposition on 16 nodes
Dynamic load balancing: yes
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
     two-body bonded interactions: 0.234 nm, LJ-14, atoms 1 9
   multi-body bonded interactions: 0.234 nm, Angle, atoms 2 5
Minimum cell size due to bonded interactions: 0.257 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm
Estimated maximum distance required for P-LINCS: 0.497 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.13
Will use 14 particle-particle and 2 PME only nodes
This is a guess, check the performance at the end of the log file
Using 2 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 14 cells with a minimum initial size of 0.622 nm
The maximum allowed number of cells is: X 6 Y 6 Z 6

I am using the same .mdp file that I used for methanol, and it is  
working fine, I don't understand why it's giving me problem for  
ethanol. I am running my simulation on 2 nodes.


-Nisha P

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