From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat Jul 28 2012 - 10:29:03 CDT
Amin,
Try to use 2 nodes and see is there better scaling. Pay attention on
cut-offs and the number of patches that you have in the system. Also see
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node90.html
If you use PME see
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node23.html#SECTION00082400000000000000
Branko
On 7/28/2012 5:10 PM, 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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