Performance enhancements for GROMACS nonbonded interactions on BlueGene

Mark J. Abraham

doi:10.1002/jcc.21766

Performance enhancements for GROMACS nonbonded interactions on BlueGene

Mark J. Abraham

Research output: Contribution to journal › Article › peer-review

10 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	2041-2046
Number of pages	6
Journal	Journal of Computational Chemistry
Volume	32
Issue number	9
DOIs	https://doi.org/10.1002/jcc.21766
Publication status	Published - 15 Jul 2011

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title = "Performance enhancements for GROMACS nonbonded interactions on BlueGene",

abstract = "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.",

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AU - Abraham, Mark J.

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AB - 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.

KW - BlueGene

KW - GROMACS

KW - PowerPC

KW - SIMD optimization

KW - rounding

KW - table lookups

UR - http://www.scopus.com/inward/record.url?scp=79955473704&partnerID=8YFLogxK

U2 - 10.1002/jcc.21766

DO - 10.1002/jcc.21766

M3 - Article

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VL - 32

SP - 2041

EP - 2046

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

IS - 9

ER -

Performance enhancements for GROMACS nonbonded interactions on BlueGene

Abstract

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