[gmx-users] Mdrun_mip efficiency

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list