[gmx-users] Mdrun_mip efficiency
jalemkul at vt.edu
Tue May 21 19:20:58 CEST 2013
On 5/21/13 1:15 PM, Андрей Гончар wrote:
> Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled
> mdrun with MPI.
> Now when I try to run a MD on this cluster, it takes near 20 hours to
> complete. But when I try the same simulation on a PC with 8 cores, it takes
> near 10 hours to complete. I thought that it will take less on cluster but
> I see the opposite. What I'm doing wrong?
Are you trying to use all available cores on the cluster? No system is
infinitely parallelizable, so if you're exceeding the limit of scaling
efficiency, you're going to see degradation in performance. Do you get similar
performance using 8 cores of the cluster? What type of network do you have
between the nodes?
Note that the end of the .log file will have a breakdown of where your run spent
time doing what. That information can be informative in determining where
performance is being lost.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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