[gmx-users] Running GROMACS on mini GPU cluster

Tim Moore tcmoore3 at gmail.com
Fri Jul 26 00:09:39 CEST 2013

I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying to bench mark some systems, and I am getting this message:

NOTE: The number of threads is not equal to the number of (logical) cores
      and the -pin option is set to auto: will not pin thread to cores.
      This can lead to significant performance degradation.
      Consider using -pin on (and -pinoffset in case you run multiple jobs).

Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set -nt 2. But since we have a queuing system, there is no way to know which cores will be available to set -pinoffset. Does anyone have a solution, or should I even be worrying about that at all?


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