Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor
Guochun Shi; Kindratenko, V.
Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on
Volume , Issue , 14-18 April 2008 Page(s):1 - 8
Digital Object Identifier   10.1109/IPDPS.2008.4536470
Summary: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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