Efficient large-scale replica-exchange simulations on production infrastructure.
Identifieur interne : 000699 ( Main/Exploration ); précédent : 000698; suivant : 000700Efficient large-scale replica-exchange simulations on production infrastructure.
Auteurs : Abhinav Thota [États-Unis] ; André Luckow ; Shantenu JhaSource :
- Philosophical transactions. Series A, Mathematical, physical, and engineering sciences [ 1364-503X ] ; 2011.
English descriptors
- KwdEn :
- MESH :
- metabolism : Hepacivirus.
- methods : Biophysics.
- virology : Hepatitis C.
- Algorithms, Humans, Models, Theoretical, Probability.
Abstract
Replica-exchange (RE) algorithms are used to understand physical phenomena--ranging from protein folding dynamics to binding affinity calculations. They represent a class of algorithms that involve a large number of loosely coupled ensembles, and are thus amenable to using distributed resources. We develop a framework for RE that supports different replica pairing (synchronous versus asynchronous) and exchange coordination mechanisms (centralized versus decentralized) and which can use a range of production cyberinfrastructures concurrently. We characterize the performance of both RE algorithms at an unprecedented number of cores employed--the number of replicas and the typical number of cores per replica--on the production distributed infrastructure. We find that the asynchronous algorithms outperform the synchronous algorithms, even though details of the specific implementations are important determinants of performance.
DOI: 10.1098/rsta.2011.0151
PubMed: 21768142
Affiliations:
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Le document en format XML
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Series A, Mathematical, physical, and engineering sciences</title><idno type="ISSN">1364-503X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Biophysics (methods)</term><term>Hepacivirus (metabolism)</term><term>Hepatitis C (virology)</term><term>Humans</term><term>Models, Theoretical</term><term>Probability</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Hepacivirus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Biophysics</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Hepatitis C</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Humans</term><term>Models, Theoretical</term><term>Probability</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Replica-exchange (RE) algorithms are used to understand physical phenomena--ranging from protein folding dynamics to binding affinity calculations. They represent a class of algorithms that involve a large number of loosely coupled ensembles, and are thus amenable to using distributed resources. We develop a framework for RE that supports different replica pairing (synchronous versus asynchronous) and exchange coordination mechanisms (centralized versus decentralized) and which can use a range of production cyberinfrastructures concurrently. We characterize the performance of both RE algorithms at an unprecedented number of cores employed--the number of replicas and the typical number of cores per replica--on the production distributed infrastructure. We find that the asynchronous algorithms outperform the synchronous algorithms, even though details of the specific implementations are important determinants of performance.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Louisiane</li></region></list><tree><noCountry><name sortKey="Jha, Shantenu" sort="Jha, Shantenu" uniqKey="Jha S" first="Shantenu" last="Jha">Shantenu Jha</name><name sortKey="Luckow, Andre" sort="Luckow, Andre" uniqKey="Luckow A" first="André" last="Luckow">André Luckow</name></noCountry><country name="États-Unis"><region name="Louisiane"><name sortKey="Thota, Abhinav" sort="Thota, Abhinav" uniqKey="Thota A" first="Abhinav" last="Thota">Abhinav Thota</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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