[gmx-users] domain decomposition and load balancing

Amit Choubey kgp.amit at gmail.com
Fri Feb 19 22:50:24 CET 2010

Hi Everyone,

I am trying to run a simulation with the option "pbc=xy" turned on. I am
using 64 processors for the simulation. The mdrun_mpi evokes the following
error message before starting the md steps

There is no domain decomposition for 64 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

This has to do with the load balancing in the domain decomposition version
of mdrun. Can anyone suggest me how to set the option -rdd or -dds?

Also the simulation runs fine on one node (with domain decomposition) and
with particle decomposition but both of them extremely slow.

Thank you,
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