Re: Low CPU usage with NAMD running on linux cluster

From: amin_at_imtech.res.in
Date: Sat Jul 28 2012 - 10:10:02 CDT

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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______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202

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