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Biowulf: Molecular Dynamics and Parallel Computation

Explore the evolution of parallel molecular dynamics on Biowulf, detailing the increased performance over the years through domain decomposition parallelization and high-performance networking. Benchmark tests include Apoa1 and STMV simulations with varying atom counts and processing times.

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Biowulf: Molecular Dynamics and Parallel Computation

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

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

  3. Parallelization by domain decomposition

  4. High-performance, low latency networking on Biowulf Myrinet 1999 32 p (Intel Pentium, 450 MHz) 2001 +128 p (AMD Athlon, 1.4 GHz) 2002 + 64 p (AMD Athlon, 1.4 GHz) 2003 +128 p (Intel Xeon, 2.8 GHz) 2004 + 96 p (AMD Opteron, 2.0 GHz) 2005 + 64 p (AMD Opteron, 2.2 GHz) Infiniband 2006 128 p (AMD Opteron, 2.8 GHz) 2007 + 96 p (AMD Opteron, 2.8 GHz) 2008 +1792 p (Intel EMT 64, 2.8 GHz)

  5. Apoa1 benchmark (NAMD)

  6. 70 ns simulation of PEVK PME water box simulation 340 Å  70 Å  53 Å 126351 atoms, 84 amino acids Gige nodes 0.821 days/ns 48 CPUs = 57.5 days Ipath nodes 0.181 days/ns 100 CPUs = 12.5 days Unpublished J.G. Forbes and K. Wang LMB/NIAMS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

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

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