Performance enhancements for GROMACS nonbonded interactions on BlueGene

Performance enhancements for GROMACS nonbonded interactions on BlueGene

Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded tabl...

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Veröffentlicht in:Journal of computational chemistry 2011-07, Vol.32 (9), p.2041-2046
1. Verfasser: Abraham, Mark J.
Format: Artikel
Sprache:eng
Schlagworte:
BlueGene
Computer architecture
Freeware
GROMACS
Molecular Dynamics Simulation
Molecular physics
PowerPC
rounding
SIMD optimization
Simulation
Software
table lookups
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Zusammenfassung:Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look‐ups. Some other GROMACS simulations will show a small gain. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.21766