On the performance of molecular dynamics applications on current high-end systems
Focusing primarily on the
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Veröffentlicht in: | Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences physical, and engineering sciences, 2005-08, Vol.363 (1833), p.1987-1998 |
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container_end_page | 1998 |
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container_issue | 1833 |
container_start_page | 1987 |
container_title | Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences |
container_volume | 363 |
creator | Hein, Joachim Reid, Fiona Smith, Lorna Bush, Ian Guest, Martyn Sherwood, Paul |
description | Focusing primarily on the |
doi_str_mv | 10.1098/rsta.2005.1624 |
format | Article |
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of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components,
including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics
codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700.</description><subject>Algorithms</subject><subject>Atoms</subject><subject>Capability Computing</subject><subject>Computer memory</subject><subject>Computer Simulation</subject><subject>Computer systems</subject><subject>Dynamic range</subject><subject>Fast Fourier transformations</subject><subject>Forest management</subject><subject>Fortran</subject><subject>High Performance Computing</subject><subject>Internet</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular Dynamics</subject><subject>Scalability</subject><subject>Science</subject><subject>Software</subject><subject>Software Validation</subject><issn>1364-503X</issn><issn>1471-2962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kktv1DAUhSMEog_YsgNlxS6Dr5_JjmrEFKSKCiiIneU4DuNpEqd2Ag2_HqcZFY0QXdnW_c7xvcdOkheAVoCK_I0Pg1phhNgKOKaPkmOgAjJccPw47gmnGUPk-1FyEsIOIQDO8NPkCDgqCsHxcfLpskuHrUl742vnW9Vpk7o6bV1j9Ngon1ZTp1qrQ6r6vrFaDdZ1IXVdqkfvTTekW_tjm5muSsMUBtOGZ8mTWjXBPN-vp8nXzbur9fvs4vL8w_rsItOs4EMGjFChdAUatCGiqikTitASdK4RokXNciOAEqwMKiOAFaIlroGUnBKoCnKavF58e-9uRhMG2dqgTdOozrgxSJ5TwXjOI7haQO1dCN7Usve2VX6SgOQcopxDlHOIcg4xCl7tnceyNdVffJ9aBMgCeDfFEZ22Zpjkzo2-i8f_214_pPr85ersJ-HEQk6IRDkBRBmjWP62_WIVi9KGMBp5hxza_3vby-W2XRicv5-BIEQKgeZ6ttRtfLXb-7ry15ILIpj8llO5_ig2YgO5PI88LPz83r-sN_JgjHjo9y3eNQdFLqLm7YOauWPtuiF-o0OlrMemkX1Vkz9DeuOL</recordid><startdate>20050815</startdate><enddate>20050815</enddate><creator>Hein, Joachim</creator><creator>Reid, Fiona</creator><creator>Smith, Lorna</creator><creator>Bush, Ian</creator><creator>Guest, Martyn</creator><creator>Sherwood, Paul</creator><general>The Royal Society</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20050815</creationdate><title>On the performance of molecular dynamics applications on current high-end systems</title><author>Hein, Joachim ; Reid, Fiona ; Smith, Lorna ; Bush, Ian ; Guest, Martyn ; Sherwood, Paul</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c596t-15347acd1c1ce37df457a34b1c8c0049f58e71432ae0be372a04b2f13b6431d93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Algorithms</topic><topic>Atoms</topic><topic>Capability Computing</topic><topic>Computer memory</topic><topic>Computer Simulation</topic><topic>Computer systems</topic><topic>Dynamic range</topic><topic>Fast Fourier transformations</topic><topic>Forest management</topic><topic>Fortran</topic><topic>High Performance Computing</topic><topic>Internet</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular Dynamics</topic><topic>Scalability</topic><topic>Science</topic><topic>Software</topic><topic>Software Validation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hein, Joachim</creatorcontrib><creatorcontrib>Reid, Fiona</creatorcontrib><creatorcontrib>Smith, Lorna</creatorcontrib><creatorcontrib>Bush, Ian</creatorcontrib><creatorcontrib>Guest, Martyn</creatorcontrib><creatorcontrib>Sherwood, Paul</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hein, Joachim</au><au>Reid, Fiona</au><au>Smith, Lorna</au><au>Bush, Ian</au><au>Guest, Martyn</au><au>Sherwood, Paul</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>On the performance of molecular dynamics applications on current high-end systems</atitle><jtitle>Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences</jtitle><addtitle>PHIL TRANS R SOC A</addtitle><date>2005-08-15</date><risdate>2005</risdate><volume>363</volume><issue>1833</issue><spage>1987</spage><epage>1998</epage><pages>1987-1998</pages><issn>1364-503X</issn><eissn>1471-2962</eissn><abstract>Focusing primarily on the</abstract><abstract>simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather
than a replicated data approach.</abstract><abstract>and</abstract><abstract>The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability
of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components,
including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics
codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700.</abstract><cop>London</cop><pub>The Royal Society</pub><pmid>16099762</pmid><doi>10.1098/rsta.2005.1624</doi><tpages>12</tpages></addata></record> |
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ispartof | Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 2005-08, Vol.363 (1833), p.1987-1998 |
issn | 1364-503X 1471-2962 |
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source | MEDLINE; JSTOR Mathematics & Statistics; Free Full-Text Journals in Chemistry |
subjects | Algorithms Atoms Capability Computing Computer memory Computer Simulation Computer systems Dynamic range Fast Fourier transformations Forest management Fortran High Performance Computing Internet Models, Chemical Models, Molecular Molecular Dynamics Scalability Science Software Software Validation |
title | On the performance of molecular dynamics applications on current high-end systems |
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