NAMD How to calculate ns/day

From: Jan Fredin (
Date: Wed Dec 07 2016 - 16:02:16 CST

I am running the ApoA1 benchmark using 10,000 time steps and outputtiming=100 with all the other input from the standard benchmark apoa1.namd file. I'm running on a single node of Xeon Haswell with P100 GPUs. I am interested in the ns/day and thought 10,000 time steps would be enough to have the WallClock time be usable in the ns/day calculation. I found that taking the reciprocal of the average of the 6 Benchmark time lines day/ns gave 26.3 ns/day but the straight calculation of ns simulated (0.01 ns) and WallClock time (XX sec / 86400 sec/day) gave only 14.3 ns/day.

What work contributing to the WallClock time is not being included in the Benchmark time lines?
Under what circumstances do the 2 methods of calculating ns/day converge to the same value?


Dr. Jan Fredin
SGI, Sr. Applications Engineer - Lead
Austin, TX

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