[gmx-users] Problem when running in many nodes

Tomy van Batis tomyvanbatis at gmail.com
Wed Mar 9 15:47:45 CET 2011

Dear all

The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I
experience some difficulties when running in parallel.

Initially, my simulation box has dimensions :

* 3.30507   2.67145  41.15800*

and it consists of 25 polymers chains with 50 beads/chain

When I run NVT using 8 or 16 cores, everything is working fine, but when I
compress it to dimensions:

*3.30507   2.67145  10.64441*

and try again to run NVT in 8 cores, I have the following error message:

*There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 2.5 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS

As I saw this is well known error, but I can't understand how to fix it :-)

>From what I understood, this is happening because* I use constrains in all
the bonds of my system*

In my .log file I see the following:

*Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 0.000 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.000 nm
Estimated maximum distance required for P-LINCS: 2.000 nm
This distance will limit the DD cell size, you can override this with -rcon
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 2.500 nm
The maximum allowed number of cells is: X 1 Y 1 Z 4*

, but I can't understand how to use -rcon or -dds in order to fix my problem

Any suggestions?

Thanks in advance
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