Hello,
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
settings
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.
Suggestions?
Thanks
-Nisha P
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