AW: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark

From: Norman Geist (
Date: Tue Oct 20 2015 - 01:29:19 CDT

NAMD just calculates this value from the step times benchmarked at simulation start, cause it is a more human readable value than seconds per timestep. Lower is better as it is days needed per nanosecond simulated.


Norman Geist


Von: [] Im Auftrag von Puneet Singh
Gesendet: Dienstag, 20. Oktober 2015 08:01
Betreff: namd-l: Regarding significance of days per ns (days/ns) parameter in NAMD benchmark


Dear Sir,

I wish to know that what is meant by the parameter days/ns & how it relates to namd performance?

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@ ( 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 , <> 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,





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