[gmx-users] Mdrun_mip efficiency
jalemkul at vt.edu
Tue May 21 21:14:00 CEST 2013
On 5/21/13 2:58 PM, Андрей Гончар wrote:
> 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.
You will never get good performance with Ethernet connectivity; it is far too
low-latency for high-speed codes like Gromacs. Most high-performance clusters
> 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
>>> 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
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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