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. 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

Bench mark notes

The above benchmarks were run using NAMD 2.8b1 and the Apoa1 benchmark suite from NAMD.

On Cheaha, only the third generation hardware was used for the above benchmarks. More information about the hardware used on Cheaha is available here.

The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.

Comparison of Ethernet and IB

Ethernet vs Infiniband interconnect on Cheaha Gen 3 hardware

Processors	Infiniband	Ethernet
1	15.4054 (100%)	15.4040 (100%)
2	7.7119 (99.87%)	7.7800 (98.99%)
4	3.8933 (98.92%)	3.9405 (97.72%)
8	1.9653 (97.98%)	2.2816 (84.39%)
16	0.9950 (96.76%)	1.2714 (75.74%)
32	0.5101 (94.37%)	0.6973 (69.03%)
64	0.2592 (92.83%)	0.6562 (36.67%)
128	0.1360 (88.45%)	0.8950 (13.44%)
256	0.0770 (78.09%)	0.8632 (6.97%)

Comparison of different Generations of Cheaha hardware on NAMD with Infinband

Cheaha Gen 2 and Gen 3 hardware using NAMD 2.8 and Inifiband

Processors	Generation 3	Generation 2
1	15.4054 (100%)	15.9300 (100%)
2	7.7119 (99.87%)	8.6620 (91.98%)
4	3.8933 (98.92%)	4.2560 (93.59%)
8	1.9653 (97.98%)	2.3450 (84.93%)
16	0.9950 (96.76%)	1.2060 (82.56%)
32	0.5101 (94.37%)	0.6420 (77.57%)
64	0.2592 (92.83%)	0.2750 (90.38%)
128	0.1360 (88.45%)	0.1620 (76.81%)
256	0.0770 (78.09%)	NA