Download presentation

Presentation is loading. Please wait.

Published byCoby Cornett Modified over 2 years ago

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

Similar presentations

© 2016 SlidePlayer.com Inc.

All rights reserved.

Ads by Google