Talk:NAMD Benchmarks

The efficiency of a parallel system describes the fraction of the time that is being used by the processors for a given computation. It is defined as

        Execution time using one processor       ts
E(n)= --------------------------------------  = ----
      N * Execution time using N processors     N tn

In general, parallel jobs should scale to at least 70% efficiency. On the ASC's DMC the recommended scaling efficiency is 75% or greater. For NAMD the efficiency of a parallel job can be calculated like this (where N is processors committed to the job):

  days/ns where N = 1
 --------------------- * 100 = Efficiency
      N * days/ns

Benchmark introduction Calculation of efficiency Scaling to higher processor count- Calculation for scaling

Sample Benchmark using NAMD

Sample Benchmark comparing Days/ns for Cheaha, Biowulf, and DMC using InfiniBand

Days/ns (efficiency) on Cheaha, Biowulf, and DMC

Processors	Cheaha	Biowulf	DMC
1	15.4054 (100%)	18.0535 (100%)	19.1000 (100%)
2	7.7119 (99.87%)	9.5163 (94.86%)	9.7600 (97.84%)
4	3.8933 (98.92%)	4.9222 (91.69%)	4.7570 (100.3%)*
8	1.9653 (97.98%)	2.5763 (87.59%)	2.5360 (94.14%)
16	0.9950 (96.76%)	1.2658 (89.14%)	1.3870 (86.06%)
32	0.5101 (94.37%)	0.6463 (87.29%)	0.7438 (80.24%)
64	0.2592 (92.83%)	0.3390 (83.22%)	0.3938 (75.78%)
128	0.1360 (88.45%)	NA	NA
256	0.0770 (78.09%)	NA	NA