From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Sat Jul 28 2012 - 21:05:53 CDT
That tells a lot. A system of this size will run well on 4-8 CPU cores
within a single node.
The other issue is that you are dumping your DCD file so often that file
I/O is going to kill your performance. Try something more reasonable
like dcdFreq=20000.
Regards,
J.
On 7/28/2012 11:10 AM, amin_at_imtech.res.in wrote:
> Thanks. I have read the link. I have a PBC system with 20,000 atoms with time
> step=1, dcdFreq=500, outputEnergies=1000. I am trying to run NPT simulation
> using 24 processors on 4 nodes having 8 processors each.
>
> Regards.
> Amin.
>
>
>> Amin,
>>
>> Provide more data about the size of your system, output data, and see:
>>
>> http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning
>>
>> Branko
>>
>> On 7/28/2012 8:33 AM, amin_at_imtech.res.in wrote:
>>> Dear all,
>>> I am trying to run NAMD on a linux cluster. I am using NAMD Linux-x86_64
>>> (64-bit Intel/AMD with ethernet). While i am able to run the program on the
>>> nodes listed in the nodelist file but I find that all the processes are
>>> running at only 8-12 % CPU usage. Can someone please guide me?
>>>
>>> Regards.
>>> Amin.
>>>
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-- ====================================================================== Jeffrey J. Potoff jpotoff_at_wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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