Re: scalability problem on linux cluster

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Nov 12 2008 - 09:40:07 CST

Hi Ruchi, if you use ++local, you'll keep running only on the first
node. You actually create N processes, but they get distributed
always among two processors only.

Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
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 mail: giacomo.fiorin_<at>_gmail.com
 web: http://www.cmm.upenn.edu/
---- ----

On Wed, Nov 12, 2008 at 9:28 AM, Ruchi Sachdeva <ruchi.namd_at_gmail.com> wrote:
> Dear All,
>
> I am using NAMD2.6 (pre compiled binaries) on linux (x86_64) 288 nodes
> cluster based on HP Intel Xeon-based ProLiant systems. It has InfiniBand
> 10Gbps cluster interconnect. I ran apoA1 test job on different number of
> processors as follows:
>
> /nfshomen278/rsachdeva/NAMD_2.6_Linux-i686-TCP/charmrun
> /nfshomen278/rsachdeva/NAMD_2.6_Linux-i686-TCP/namd2 ++local +p2 apoa1.namd
>> apoa1.log &
>
> The jobs were submiited using bsub command. I got the following speed:
>
> Benchmark time: 1 CPUs 3.12916 s/step 36.2171 days/ns
>
> Benchmark time: 2 CPUs 1.62206 s/step 18.7738 days/ns
>
> Benchmark time: 4 CPUs 1.65563 s/step 19.1624 days/ns
>
> Benchmark time: 8 CPUs 1.64875 s/step 19.0828 days/ns
>
> Benchmark time: 16 CPUs 1.67945 s/step 19.4381 days/ns
>
> As we can see that CPU effiecieny is not increasing beyond 2 cpus. With 4 &
> more number of cpus, runtime is not decreasing much, rather it is increasing
> with 4 & 16-cpus. Can anybody please tell me why I am getting poor
> performance with greater number of cpus?
>
> Shall I gain better scalability if I compile namd on the cluster rather than
> using pre compiled binaries? And which version of namd would be better:
> charm based or mpi based?
>
> Thanks in advance
>
> Ruchi
>
>

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