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.

Information on how to submit NAMD jobs to Cheaha is avaiable here.

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.


 * ASC-DMC

Hardware Notes
Generation 3 hardware contains 576 cores. 2.66 GHz Intel Xeon Hex-core (48-2x6 core) Generation 2 hardware contains 192 cores. 3.06 GHz Intel Xeon Quad-core (24-2x4 core) More information about the hardware used on Cheaha is available here.

Actual job benchmarks (Segrest job)
Actual NAMD job courtesy of Center for Computational and Structural Biology.

STRUCTURE SUMMARY: Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps 245956 ATOMS 174192 BONDS 130742 ANGLES 84410 DIHEDRALS 1622 IMPROPERS 0 CROSSTERMS 0 EXCLUSIONS 232802 RIGID BONDS 505063 DEGREES OF FREEDOM 84698 HYDROGEN GROUPS 4 ATOMS IN LARGEST HYDROGEN GROUP 84698 MIGRATION GROUPS 4 ATOMS IN LARGEST MIGRATION GROUP TOTAL MASS = 1.48179e+06 amu TOTAL CHARGE = 2.7746e-05 e MASS DENSITY = 1.01378 g/cm^3 ATOM DENSITY = 0.101334 atoms/A^3

Comparison to IBM BG/L
NAMD comparison of job data between UAB IBM BlueGene/L and Cheaha.

Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps (same as actual user job described above)

The Cheaha outperforms the BG/L using only 32 cores on the gen 3 hardware. At equal processor count the Cheaha is roughly 8 times faster than the BG/L.