From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu Aug 21 2008 - 16:31:32 CDT
Yes, the beginning of the log file will show the benchmark speed for
how many CPUs you used for that particular run.
On Aug 21, 2008, at 4:28 PM, Roman Petrenko wrote:
> Thank you for you responses,
> so the time i see in namd.log file is the actual speed of calculations
> using multiple CPUs, right?
> or is it the calculation speed of just one CPU?
> How can i check our network connection speed limit? What other info
> should i supply?
> On Thu, Aug 21, 2008 at 5:07 PM, Eric H. Lee <ericlee_at_ks.uiuc.edu>
>> As a rule, the speedup one obtains with scaling with greater number
>> of CPUs
>> is based on a variety of factors. One of these are the number of
>> NAMD divides your system into for independent calculation on
>> nodes. Depending on the shape of your system, the number of patches
>> generate may roughly correspond to the number of atoms in the
>> system you are
>> simulating as well. Historically NAMD achieved excellent linearity
>> in speed
>> up down to a limit of 1000 atoms per processor. However, this
>> has been improved somewhat in the latest version that you can grab
>> from the
>> NAMD CVS, which scales quite well to 500 atoms per processor from my
>> In practice, one should benchmark simulation speed before a full
>> run, using different numbers of processors, and choose the one with
>> the best
>> tradeoff between computation speed and cost in processor hours.
>> On Aug 21, 2008, at 3:51 PM, Roman Petrenko wrote:
>> Dear all,
>> when i run a job on one cpu i have this speed
>> Info: Initial time: 1 CPUs 0.196443 s/step 1.13682 days/ns 17304 kB
>> but when i run it on 6 computers with ppn=4, i get this speed
>> Info: Benchmark time: 24 CPUs 0.0710909 s/step 0.411406 days/ns
>> 8328 kB
>> the question is: do i have mere 3 times speedup using 24 CPUs???
>> Roman Petrenko.
>> Physics Department
>> University of Cincinnati
>> Eric H. Lee
>> Medical Scholars Program
>> Theoretical and Computational Biophysics Group, UIUC
> Roman Petrenko.
> Physics Department
> University of Cincinnati
Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
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