[gmx-users] PME nodes
Ignacio Fernández Galván
jellby at yahoo.com
Thu May 31 13:11:15 CEST 2012
There must be something I don't fully understand, by running grompp on a system, I get this:
Estimate for the relative computational load of the PME mesh part: 0.32
Good, that's approximately 1/3, or a 2:1 PP:PME ratio, which is the recommended value for a dodecahedral box. But then I run the dynamics with "mdrun_mpi -np 8" (different cores in a single physical machine) and I get:
Initializing Domain Decomposition on 8 nodes
Using 0 separate PME nodes
I would have expected at least 2 nodes (3:1, 0.25) to be used for PME, so there's obviously something wrong in my assumption.
Should I be looking somewhere in the output to find out why? Would it be better to try to get some dedicated PME node(s) (even in a single machine)?
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