[gmx-users] z always small for domain decomposition grid?

yunshi11 . yunshi09 at gmail.com
Thu Feb 6 03:15:20 CET 2014

Hi everyone,

For my MD simulations on different number of CPUs (sometimes with GPUs),
the domain decomposition grid that I got from automatic (not setting -dd)
domain decomposition is always like:
Domain decomposition grid 8 x 6 x 2, separate PME nodes 48
PME domain decomposition: 8 x 6 x 1

or in the case of GPUs:
Domain decomposition grid 4 x 3 x 1, separate PME nodes 0
PME domain decomposition: 4 x 3 x 1

This happens regardless of the systems (all proteins in explicit solvents)
I am modeling. So why it is never like 6 x 4 x 4 or 3 x 2 x 2? Isn't it
better that protein atoms be distributed more equally and into more grid


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