Talk:NAMD Benchmarks: Difference between revisions

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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/
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 15:29, 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

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
NAMD benchmark img1 Days cheaha dmc biowulf.png
NAMD benchmark img2 Efficiency cheaha dmc biowulf.png


Bench mark notes

Comparison of Ethernet and IB

Comparison on different nodes on Cheaha Gen 2 and Gen 3 with IB

Actual job benchmarks (Segrest job)

Perform Your Own Benchmarks