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

8 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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