Date: Sun Jul 29 2012 - 00:09:49 CDT
What I meant was that I am distributing 24 processes over 4 nodes having 8
processors each.Therefore each node will have 2 processors free. I have not
completed any run till now so I cant give the "TIMING INFORMATION" because the
simulation is running extremely slow. My 2 ns simulation is running for more
than 2 days now.I will post that information as soon as the run is completed.
> Do you really mean that you have requested 4 nodes x 8 processors each
> = 32 processors? I'm wondering because you said you have only 24
> processors. Also, Branko is not asking about output frequencies, but
> rather the details of the output that your simulation is giving. For
> example, the "TIMING" information from the log file is indicative of the
> seconds/step that your simulation is running at.
> On Sat, 2012-07-28 at 20:40 +0530, 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.
>> > 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
>> >> (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.
>> >> ______________________________________________________________________
>> >> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> >> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
>> >> स%u09
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