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Challenge: Computing for the Life Sciences

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.

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Challenge: Computing for the Life Sciences

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  1. 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 Newton’s law F=m.a for all atoms where F depends on all atoms! Initialization with the help of random numbers

  2. The computational effort required to study protein folding is enormous. Using crude workload estimates for a petaflop/second capacity machine leads to an estimate of three years to simulate 100 microseconds. Physical time for simulation 10–4 s Typical time-step size 10–15 s Number of MD time steps 1011 Atoms in a typical protein and water simulation 32000 Approximate number of interactions in force calculation 109 Machine instructions per force calculation 1000 Total number of machine instructions 1023 Protein folding http://www.research.ibm.com/bluegene/ http://researchweb.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

  3. Supercomputers “Roadrunner”1026 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_huygens/

  4. 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 Pup to 262,144 quad processor nodes, projected 3.56 Peta (=1015)flops wordt gebruikt voor de grootste radiotelescoop: http://www.lofar.nl

  5. 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

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