[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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



-- 
Andrew Gonchar
Андрей Гончар



More information about the gromacs.org_gmx-users mailing list