[gmx-users] Mdrun_mip efficiency

Андрей Гончар gontchar at gmail.com
Tue May 21 20:58:22 CEST 2013

Yes, I'm using all cores. All nodes are connected by Ethernet. Now I see
that when I change number of processes or number of threads per node I can
change mdrun performance. But I think it is still too slow. Is there a way
to speed up mdrun on cluster? Some specific settongs or so? Sorry for my
questions, but I'm quite novice in running gromacs on cluster.

2013/5/21 Justin Lemkul <jalemkul at vt.edu>

> 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
> --
> ==============================**==========
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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Andrew Gonchar
Андрей Гончар

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