Electrostatic force computation for bio-molecules on supercomputers with torus networks

Authors:
Peter Rissland;Yuefan Deng
Affiliations:
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook 11794-3600, United States;Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook 11794-3600, United States
Venue:
Parallel Computing
Year:
2007

Citing 5
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Abstract

We present an application of the Ewald algorithm for electrostatic force computation on a supercomputer with a torus network, like those on QCDOC and BlueGene/L. Typical bio-molecular systems have thousands, possibly millions of atoms interacting, with simulation time ranging from microseconds to milliseconds. The most dominant time consuming calculation for bio-molecules is the electrostatic interactions. The importance of an efficient all-gather method is discussed, in particular for QCDOC since it does not have a network specific for global communication like the tree network on BlueGene/L. In addition, we demonstrate the ability for QCDOC to run non QCD (Quantum Chromodynamics) applications, in particular, electrostatic force computation on bio-molecules.