Re: parallel execution speedup

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.

- Eric

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>
> wrote:
>> 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
>> patches
>> NAMD divides your system into for independent calculation on
>> individual
>> 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
>> performance
>> 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
>> experience.
>> In practice, one should benchmark simulation speed before a full
>> production
>> run, using different numbers of processors, and choose the one with
>> the best
>> tradeoff between computation speed and cost in processor hours.
>> -Eric
>> 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
>> memory
>>
>> 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
>> memory
>>
>> 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
>>
>> ericlee_at_ks.uiuc.edu
>>
>
>
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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