1 / 9

Biowulf: Molecular Dynamics and Parallel Computation

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.

johnna
Télécharger la présentation

Biowulf: Molecular Dynamics and Parallel Computation

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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atoms, 84 amino acids Gige nodes 0.821 days/ns 48 CPUs = 57.5 days Ipath nodes 0.181 days/ns 100 CPUs = 12.5 days Unpublished J.G. Forbes and K. Wang LMB/NIAMS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

More Related