ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations
Identifieur interne : 000C25 ( Main/Exploration ); précédent : 000C24; suivant : 000C26ExaViz: a Flexible Framework to Analyse, Steer and Interact with Molecular Dynamics Simulations
Auteurs : Matthieu Dreher [France] ; Jessica Prevoteau-Jonquet [France] ; Mikael Trellet [France] ; Marc Piuzzi [France] ; Marc Baaden [France] ; Bruno Raffin [France] ; Nicolas Férey [France] ; Sophie Robert [France] ; Sébastien Limet [France]Source :
- Faraday Discussions of the Chemical Society [ 0301-7249 ] ; 2014-05-07.
Abstract
The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system.
Url:
DOI: 10.1039/C3FD00142C
Affiliations:
- France
- Auvergne-Rhône-Alpes, Centre-Val de Loire, Rhône-Alpes, Région Centre
- Grenoble, Orléans
- Centre Val de Loire Université, Université Joseph Fourier, Université d'Orléans, Université de Grenoble
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Le document en format XML
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Paris 11</orgName><orgName type="acronym">UP11</orgName><desc><address><addrLine>Bâtiment 300 - 91405 Orsay cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.u-psud.fr/</ref></desc></org></tutelle><tutelle active="#struct-93591" type="direct"><org type="institution" xml:id="struct-93591" status="VALID"><orgName>Université Pierre et Marie Curie - Paris 6</orgName><orgName type="acronym">UPMC</orgName><desc><address><addrLine>4 place Jussieu - 75005 Paris</addrLine><country key="FR"></country></address><ref type="url">http://www.upmc.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country></affiliation></author><author><name sortKey="Robert, Sophie" sort="Robert, Sophie" uniqKey="Robert S" first="Sophie" last="Robert">Sophie Robert</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-1625" status="OLD"><orgName>Laboratoire d'Informatique Fondamentale d'Orléans</orgName><orgName type="acronym">LIFO</orgName><desc><address><addrLine>Batiment IIIA 6 Rue Léonard de Vinci - 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BP 6759 45067 ORLEANS CEDEX 2</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-orleans.fr/lifo/</ref></desc><listRelation><relation name="EA4022" active="#struct-300297" type="direct"></relation><relation active="#struct-300379" type="direct"></relation></listRelation><tutelles><tutelle name="EA4022" active="#struct-300297" type="direct"><org type="institution" xml:id="struct-300297" status="VALID"><idno type="ISNI">0000000121581666 </idno><idno type="IdRef">026402971</idno><orgName>Université d'Orléans</orgName><orgName type="acronym">UO</orgName><desc><address><addrLine>Château de la Source - Avenue du Parc Floral - BP 6749 - 45067 Orléans cedex 2</addrLine><country key="FR"></country></address><ref type="url">http://www.univ-orleans.fr/</ref></desc></org></tutelle><tutelle active="#struct-300379" type="direct"><org type="institution" xml:id="struct-300379" status="VALID"><orgName>Ecole Nationale Supérieure d'Ingénieurs de Bourges</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Orléans</settlement><region type="old region" nuts="2">Région Centre</region><region type="region" nuts="2">Centre-Val de Loire</region></placeName><orgName type="university">Université d'Orléans</orgName><orgName type="institution" wicri:auto="newGroup">Centre Val de Loire Université</orgName></affiliation></author></analytic><idno type="DOI">10.1039/C3FD00142C</idno><series><title level="j">Faraday Discussions of the Chemical Society</title><idno type="ISSN">0301-7249</idno><imprint><date type="datePub">2014-05-07</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long time batch executions). During interactive sessions, at run time, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a Cave-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system.</div></front></TEI><affiliations><list><country><li>France</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Centre-Val de Loire</li><li>Rhône-Alpes</li><li>Région Centre</li></region><settlement><li>Grenoble</li><li>Orléans</li></settlement><orgName><li>Centre Val de Loire Université</li><li>Université Joseph Fourier</li><li>Université d'Orléans</li><li>Université de Grenoble</li></orgName></list><tree><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Dreher, Matthieu" sort="Dreher, Matthieu" uniqKey="Dreher M" first="Matthieu" last="Dreher">Matthieu Dreher</name></region><name sortKey="Baaden, Marc" sort="Baaden, Marc" uniqKey="Baaden M" first="Marc" last="Baaden">Marc Baaden</name><name sortKey="Ferey, Nicolas" sort="Ferey, Nicolas" uniqKey="Ferey N" first="Nicolas" last="Férey">Nicolas Férey</name><name sortKey="Limet, Sebastien" sort="Limet, Sebastien" uniqKey="Limet S" first="Sébastien" last="Limet">Sébastien Limet</name><name sortKey="Piuzzi, Marc" sort="Piuzzi, Marc" uniqKey="Piuzzi M" first="Marc" last="Piuzzi">Marc Piuzzi</name><name sortKey="Prevoteau Jonquet, Jessica" sort="Prevoteau Jonquet, Jessica" uniqKey="Prevoteau Jonquet J" first="Jessica" last="Prevoteau-Jonquet">Jessica Prevoteau-Jonquet</name><name sortKey="Raffin, Bruno" sort="Raffin, Bruno" uniqKey="Raffin B" first="Bruno" last="Raffin">Bruno Raffin</name><name sortKey="Robert, Sophie" sort="Robert, Sophie" uniqKey="Robert S" first="Sophie" last="Robert">Sophie Robert</name><name sortKey="Trellet, Mikael" sort="Trellet, Mikael" uniqKey="Trellet M" first="Mikael" last="Trellet">Mikael Trellet</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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