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									Biowulf: 10 Years of Large-scale Computing
                at the NIH



              Steven Fellini



       Scientific Computing Branch,
   Division of Computer System Services
                  CIT, NIH
                   The NIH Biowulf Cluster
                            http://biowulf.nih.gov
    • Central scientific supercomputing
      resource managed by CIT
    • Operational since 1999
    • Funded through NIH Management
      Fund
    • Available to all NIH intramural
      scientists
    • Used by 19 ICs in 2008
    • Among the largest biomedical
      clusters in the world
    • Value to the NIH:
      price/performance, economy of scale,
      unique resource



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                       NIH Biowulf Cluster Architecture

         Fileservers              Core network switch




                                                        Login node




    Network switches




    Compute nodes

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    Cluster Supercomputing




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    Biowulf 1999




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    Biowulf 2000-2002




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    Biowulf 2003-2005




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    Biowulf 2006-2008




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    Biowulf 2009




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     NIH Biowulf Monthly Usage
            1999-2008




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          Application Domains on Biowulf

Sequence Analysis                         Proteomics
     Blast, EMBOSS, Iprscan, MFOLD…          OMSSA, X!Tandem, Inspect…
Genome Assembly                           Mathematics/Statistics
     Phred/Phrap/Consed, MIRA, Velvet…        R, Matlab, Mathematica, SAS…
Linkage Analysis                          Image Analysis
     PLINK, Mach, Fastlink, Genehunter…       FSL, AFNI, Huygens, Imaris…
Phylogenetic Analysis                     Structural Biology
     PAUP, Phylip, PAML…                      Rosetta++, Xplor-NIH…
Molecular Dynamics                        Computational Chemistry
     NAMD, Charmm, GROMACS…                   Gaussian, GAMESS…


11                                                                     11
     Over 70 publications in 2008




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                 FY2009: Focus on Storage

• Add 200-400 TB.
• Re-architect storage from
  single to 3-tier.
• High performance parallel file
  servers.
• Goal: provide
  supercomputing-scale storage.




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     The Helix/Biowulf Systems Staff
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                                                      QuickTime™ and a
                                                        decompressor
                                               are needed to see this picture.
            QuickTime™ and a
              decompressor
     are needed to see this picture.




                                                                                    QuickTime™ and a                               Qu i ckTi me ™ an d a
                                                                                      decompressor                                    de co mp res so r
                                                                             are needed to see this picture.              a re ne ed ed to se e thi s p i ctu re .

                                            QuickTime™ and a
                                              decompressor
                                    are needed to see this picture.




                                                                                       Qu i ckTi me ™ an d a
                                                                                          de co mp res so r
                                                                               a re ne ed ed to se e thi s p i ctu re .




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          NIH Biowulf FY2008
  CPU Utilization by IC     Number of Jobs by IC
(total: 21,070,667 hours)   (total: 671,739 jobs)

								
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