Talk:NAMD Benchmarks: Difference between revisions
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Information on NAMD performance Scaling is available at: http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning | Information on NAMD performance Scaling is available at: http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning | ||
Benchmark used for performance evaluation on the [[Cheaha]], | Benchmark used for performance evaluation on the [[Cheaha]], [http://biowulf.nih.gov Biowulf], and [http://www.asc.edu/supercomputing/index.shtml DMC] is Apoa1 from the NAMD suite and is available at: http://www.ks.uiuc.edu/Research/namd/utilities/ | ||
The parameters for the benchmark used through out are:500 steps, 92K atoms, 12A cutoff + PME every 4 steps. | The parameters for the benchmark used through out are:500 steps, 92K atoms, 12A cutoff + PME every 4 steps. | ||
Revision as of 15:28, 26 May 2011
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. The ASC's DMC recommends a scaling efficiency of 75% or greater. For NAMD the efficiency of a parallel job can be calculated as follows (where N is processors committed to the job):
days/ns where N = 1
--------------------- * 100 = Efficiency
N * days/ns
Information on NAMD performance Scaling is available at: http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning
Benchmark used for performance evaluation on the Cheaha, Biowulf, and DMC is Apoa1 from the NAMD suite and is available at: http://www.ks.uiuc.edu/Research/namd/utilities/ The parameters for the benchmark used through out are:500 steps, 92K atoms, 12A cutoff + PME every 4 steps.
Sample Benchmark using NAMD
Sample Benchmark comparing Days/ns for Cheaha, Biowulf, and DMC using InfiniBand
| 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 |
