Cyberinfrastructure Partnership: Benchmarks:

Benchmarks at CyberInfrastructure Partnership

Walltime	Speedup	Relative Speed*

*Speed per processor normalized to Datastar.

“NAMD … is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit Ethernet.” [NAMD]

NAMD 2.6b1 was used for the benchmarks. The test problem is simulation of apolipoprotein A1 (ApoA1), which has 92,224 atoms. The benchmark run time is the average run time per time step after initial load balancing.

[NAMD] Scalable Molecular Dynamics,
- http://www.ks.uiuc.edu/Research/namd