Implementation of NAMD molecular dynamics non-bonded force-field on the cell broadband engine processor

Author

Shi, Guochun ; Kindratenko, Volodymyr

Author_Institution

Nat. Center for Supercomput. Applic., Univ. of Illinois at Urbana-Champaign, Urbana-Champaign, IL

fYear

2008

Firstpage

1

Lastpage

8

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.

Keywords

chemistry computing; floating point arithmetic; microprocessor chips; molecular dynamics method; Cell Broadband Engine processor; NAMD SPEC 2006 CPU benchmark; NAMD molecular dynamics nonbonded force-field; double-precision floating-point kernel linear speedup; molecular dynamics simulation program; multiple synergistic processing elements; single-precision floating-point kernel; Biological information theory; Biological system modeling; Bonding forces; Computational complexity; Computational modeling; Electrostatics; Engines; Equations; Kernel; Table lookup;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing, 2008. IPDPS 2008. IEEE International Symposium on

Conference_Location

Miami, FL

ISSN

1530-2075

Print_ISBN

978-1-4244-1693-6

Electronic_ISBN

1530-2075

Type

conf

DOI

10.1109/IPDPS.2008.4536470

Filename

4536470