Multibillion-atom molecular dynamics simulation: Design considerations for vector-parallel processing

Progress in adapting molecular dynamics algorithms for systems with short-range interactions to utilize the features of modern supercomputers is described. Efficient utilization of the latest generation of processor architectures requires algorithms that can be both vectorized and parallelized. The approach adopted for vectorization involves combining the layer and neighbor-list methods, while parallelization employs spatial subdivision with explicit communication. The techniques presented here have been used in performance tests on the Cray X1 vector-parallel supercomputer with systems containing over 12 billion atoms. 2005 Elsevier B.V. All rights reserved. PACS: 02.70.Ns

• Type: Journal
• Year: 2006
• Where: CPHYSICS
• Authors: D. C. Rapaport
• Keywords: CPHYSICS 2006, Modern Supercomputers, Molecular Dynamics, Short-range Interactions