Performance and cost effectiveness of a cluster of workstations and MD-GRAPE 2 for MD simulations

Authors:
J. V. Sumanth;David R. Swanson;Hong Jiang
Affiliations:
University of Nebraska-Lincoln, Dept. of Computer Science and Engineering, Lincoln, NE;University of Nebraska-Lincoln, Dept. of Computer Science and Engineering, Lincoln, NE;University of Nebraska-Lincoln, Dept. of Computer Science and Engineering, Lincoln, NE
Venue:
ISPDC'03 Proceedings of the Second international conference on Parallel and distributed computing
Year:
2003

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Abstract

Molecular dynamics (MD) simulations are performed on systems of various sizes up to 32 million atoms. Performance is compared between an MD-GRAPE 2 board, specialized hardware optimized for MD, and a general purpose cluster computer utilizing varied numbers of processors for both short- and long-range potentials. While it is possible to outperform a single MD-GRAPE 2 board with a sufficient number of processors, tests verses a local cluster and comparison of original purchase price show the MD-GRAPE 2 board is often cost-effective. Potential-specific considerations are discussed.