Challenge: Computing for the Life Sciences

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Challenge Computing for the Life Sciences

• Gaining insight into protein science and protein
  folding mechanisms
• Simulating (thousands of) macromolecules
• Silicon cells

Interdisciplinary Mathematics, Physics,
Chemistry, Computer Science, Biology
Method molecular dynamics integrating Newtons
law Fm.a for all atoms where F depends on all
atoms! Initialization with the help of random
numbers
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Protein folding
http//www.research.ibm.com/bluegene/ http//resea
rchweb.watson.ibm.com/journal/sj/402/allen.html
One year 3 107 seconds Clock cycle 10-9 s Three
years 106 processors 3 3 107 106 109
1023 machine instructions
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Supercomputers

• Roadrunner1026 Teraflop/s (1012 floating point
  operations / s) DOE Los Alamos
• Uses advanced versions of the processor in the
  Sony PlayStation 3
• Vgl. Huygens (Sara 11.9.08) 60 Tflop peak (rank
  40)http//www.sara.nl/news/recent/opening_huygen
  s/

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Blue Gene L/P
Blue Gene L max 478 Teraflops (1012 floating
point operations / s) fastest supercomputer till
june 2008not yet fast enough Blue Gene P up to
262,144 quad processor nodes, projected 3.56
Peta (1015) flops wordt gebruikt voor de
grootste radiotelescoop http//www.lofar.nl
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Dedicated chip

• Voor Moleculaire Dynamica MDGrape-3 281
  Teraflops in 2007, 20 berekeningen parallel op
  chiphttp//mdgrape.gsc.riken.jp
• slechts 0.3 Watt/gigaflopvergelijk 14
  Watt/gigaflop Pentium 4