19.1-nbody - CS6230 HPC Tools and Applications Parallel...

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CS6230 HPC Tools and Applications Parallel N-Body Applications Jeffrey S. Vetter Computational Science and Engineering College of Computing Georgia Institute of Technology http://ft.ornl.gov/~vetter vetter@computer.org With input from various ORNL sources and GPU GEMS 3
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N-Body Algorithms An N-body simulation numerically approximates the evolution of a system of bodies in which each body continuously interacts with every other body Galaxies Protein folding Molecular dynamics, Materials Science Fluid flow Global illumination (for CG) Algorithms All-pairs interactions Computationally intense O(N 2 ) Easily parallelized Usually use some sort of cutoff radius and an approximation for long range forces Extensively studied for decades Barnes-Hut, FMM, Particle- mesh vetter@computer.org 2
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Theory Experiment Simulation Simulations help model behaviors too small/large for us to observe/measure directly Too small… Spallation Neutron Source Used to investigate molecular level structures Too large… Galaxies Planets
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Molecular Dynamics Molecular Dynamics is a technique for simulating the atom-by-atom behavior of molecules and deriving macroscopic properties from those behaviors Classical molecular dynamics (MD) has been an important algorithm in the fields of physics, chemistry, biology [9, 11], and others for several decades Biomolecular systems Protein folding, drug docking Liquids Materials Defects Fractures Surfaces melting, friction Electronic properties and dynamics Granular flows Image from [22]
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Computing with MD Algorithms and computer architectures for MD have been studied extensively [2, 4, 6-8, 10, 13, 15, 20-27, 30] Anton [27], MD-Grape [12], and Folding@Home [17] GROMACS [18], NAMD [13, 21, 23], AMBER [20], LAMMPS [24], SPaSM, ddcMD Performance and accuracy of Molecular Dynamics (MD) simulations at both small and large scale has garnered considerable attention
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vetter@computer.org 6
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Timescales of Interest S.R. Alam, P. Agarwal, A. Geist , and J.S. Vetter, “Performance Characterization of Molecular Dynamics Techniques for Biomolecular Simulations,” Proc. ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPOPP), 2006.
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19.1-nbody - CS6230 HPC Tools and Applications Parallel...

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