SC is the International Conference for
 High Performnance Computing, Networking, Storage and Analysis

SCHEDULE: NOV 13-19, 2010

Scaling of Multimillion-Atom MD Simulation on a Petascale Supercomputer

SESSION: Research Poster Reception


TIME: 5:15PM - 7:00PM

AUTHOR(S):Roland Schulz, Benjamin Lindner, Loukas Petridis, Berk Hess, Erik Lindahl, Jeremy C. Smith

ROOM:Main Lobby

We present performance and scaling of all-atom molecular dynamics (MD) simulation of multimillion-atom biological systems. These simulations are limited by the parallel efficiency of the MD algorithms. Highly tuned SSE compute kernels enable node performance similar to GPU performance. The bottleneck for highly-parallel all-atom simulations is the computation of the electrostatic interactions. Shown is the scaling of MD using the reaction field method to the full Jaguar XT5 size. We present also a new highly-scalable Particle Mesh Ewald decomposition.

Chair/Author Details:

Roland Schulz - University of Tennessee, Knoxville

Benjamin Lindner - University of Tennessee, Knoxville

Loukas Petridis - Oak Ridge National Laboratory

Berk Hess - Stockholm University

Erik Lindahl - Stockholm University

Jeremy C. Smith - University of Tennessee, Knoxville

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