From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Oct 20 2015 - 09:46:32 CDT
day/ns is just the inverse of the more conventional ns/day. It is just a
measure of how long it would take to run a ns of MD; a lower number is
better. I'd expect that reporting it as days/ns makes the computation
purely an addition operation, which is less costly than division.
It should be noted that a trivial way to decrease days/ns is to increase
the timestep. This of course has its own issues in terms of accuracy. I
only bring this up bc hydrogen mass re-partitioning has quickly risen in
popularity (and apparently rightly so!). Nonetheless, inter-program
comparisons may or may not make use of this feature in all cases, so
some programs can spuriously look like they have lower performance than
others.
Regards,
Brian
On 10/20/2015 01:01 AM, Puneet Singh wrote:
> Dear Sir,
> I wish to know that what is meant by the parameter days/ns & how it
> relates to namd performance?
> i.e.
> my benchmark on Intel(R) Xeon(R) E5-2660 v2 ( NAMD V2.10 ApoA1
> example - only cpu - no MIC/GPU):
> 16 CPUs 0.078224 *s/step* 905.37 *days/ns* 380.207 *MB memory* (42.40
> seconds)
> 19 CPUs 0.0665057 *s/step* 769.742 *days/ns* 411.355 *MB memory* (36
> seconds)
> 114 CPUs 0.203145* s/step* 2351.21 *days/ns* 1976.23 *MB memory*
> (91.94 seconds)
>
>
>
> Benchmark@https://wiki.anl.gov/cnm/HPC/Applications/namd ( ApoA1 example):
> 16 CPUs 0.105658 *s/step* 1.2229 *days/ns* 50.3477 *MB memory* (NAMD V2.7)
> 16 CPUs 0.103924 *s/step* 1.20282 *days/ns* 225.961 *MB memory*(NAMD V2.9)
>
> comparing these i get a sense that with increasing version of NAMD ,
> memory requirement grows, & maybe s/step (500 nsteps in my case ,
> anl.gov <http://anl.gov> nsteps =? ) are better on my benchmark,
>
> but i am confused with days/ns , so if anyone can explain the
> significance of days/ns it would be very kind of you. Further please
> mention that the higher value is better or lower value is better wrt
> performance ?
>
> Eagerly awaiting your replies,
>
> Regards,
> Puneet
>
-- Brian Radak Postdoctoral Scholar Gordon Center for Integrative Science, W323A Department of Biochemistry & Molecular Biology University of Chicago 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 email: radak_at_uchicago.edu
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