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Challenge: Computing for the Life Sciences Gaining insight into protein science and protein folding mechanisms Simulating (thousands of) macromolecules.

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Presentation on theme: "Challenge: Computing for the Life Sciences Gaining insight into protein science and protein folding mechanisms Simulating (thousands of) macromolecules."— Presentation transcript:

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 Physical time for simulation10 –4 s Typical time-step size10 –15 s Number of MD time steps10 11 Atoms in a typical protein and water simulation32000 Approximate number of interactions in force calculation 10 9 Machine instructions per force calculation1000 Total number of machine instructions One year seconds Clock cycle s Three years * 10 6 processors = 3 * * 10 6 * 10 9 = machine instructions Protein folding 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.

3 Supercomputers (10 12 floating point operations / s) “Roadrunner” 1026 Teraflop/s (10 12 floating point operations / s) DOE Los Alamos Uses advanced versions of the processor in the Sony PlayStation 3 Vgl. Huygens (Sara ) 60 Tflop peak (~rank 40) news/recent/ opening_huygens/

4 Blue Gene L/P 478 Teraflops (10 12 floating point operations / s) fastest supercomputer till june 2008 not yet fast enough … Blue Gene L: max 478 Teraflops (10 12 floating point operations / s) fastest supercomputer till june 2008 not yet fast enough … up to 262,144 Blue Gene P up to 262,144 quad processor nodes, projected 3.56 Peta (=10 15 )flops 3.56 Peta (=10 15 ) flops wordt gebruikt voor de grootste radiotelescoop:

5 Dedicated chip Voor Moleculaire Dynamica MDGrape Teraflops in 2007, 20 berekeningen parallel op chip slechts 0.3 Watt/gigaflop vergelijk 14 Watt/gigaflop Pentium 4


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