Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor
Guochun Shi
Kindratenko, V.
Nat. Center for Supercomput. Applic., Univ. of Illinois at Urbana-Champaign, Urbana-Champaign, IL;
This paper appears in: Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on
Publication Date: 14-18 April 2008
On page(s): 1-8
Location: Miami, FL,
ISSN: 1530-2075
ISBN: 978-1-4244-1693-6
INSPEC Accession Number: 10025349
Digital Object Identifier: 10.1109/IPDPS.2008.4536470
Current Version Published: 2008-06-03
Abstract
We present results of porting an important kernel of a production molecular dynamics simulation program, NAMD, to the Cell/B.E. processor. The non-bonded force-field kernel, as implemented in the NAMD SPEC 2006 CPU benchmark, has been implemented. Both single-precision and double-precision floating-point kernel variations are considered, and performance results obtained on the Cell/B.E., as well as several other platforms, are reported. Our results obtained on a 3.2 GHz Cell/B.E. blade show linear speedups when using multiple synergistic processing elements.
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