Biowulf: Molecular Dynamics and Parallel Computation Susan Chacko Scientific Computing Branch, Division of Computer System Services CIT, NIH.

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Presentation transcript:

Biowulf: Molecular Dynamics and Parallel Computation Susan Chacko Scientific Computing Branch, Division of Computer System Services CIT, NIH

Apolipoprotein A1 92,000 atoms 26.4 days/ns on one cpu 71,000 years / ms

Parallelization by domain decomposition

High-performance, low latency networking on Biowulf Myrinet p (Intel Pentium, 450 MHz) p (AMD Athlon, 1.4 GHz) p (AMD Athlon, 1.4 GHz) p (Intel Xeon, 2.8 GHz) p (AMD Opteron, 2.0 GHz) p (AMD Opteron, 2.2 GHz) Infiniband p (AMD Opteron, 2.8 GHz) p (AMD Opteron, 2.8 GHz) p (Intel EMT 64, 2.8 GHz)

Apoa1 benchmark (NAMD)

70 ns simulation of PEVK PME water box simulation 340 Å  70 Å  53 Å atoms, 84 amino acids Gige nodes days/ns 48 CPUs = 57.5 days Ipath nodes days/ns 100 CPUs = 12.5 days Unpublished J.G. Forbes and K. Wang LMB/NIAMS

7 Satellite Tobacco Mosaic Virus (STMV) 1.06 Million atoms 200 days/ns on 1 cpu

9 Satellite Tobacco Mosaic Virus (STMV) 1.06 Million atoms 200 days/ns on 1 cpu 1 day/ns on 256 IB processors