Interactive Molecular Dynamics: Scaling up to Large Systems
Identifieur interne : 000258 ( France/Analysis ); précédent : 000257; suivant : 000259Interactive Molecular Dynamics: Scaling up to Large Systems
Auteurs : Matthieu Dreher [France] ; Marc Piuzzi [France] ; Ahmed Turki [Tunisie] ; Matthieu Chavent [France] ; Marc Baaden [France] ; Nicolas Férey [France] ; Sébastien Limet [France] ; Bruno Raffin [France] ; Sophie Robert [France]Source :
- Procedia Computer Science [ 1877-0509 ] ; 2013.
English descriptors
- mix :
Abstract
Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7 M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.
Url:
DOI: 10.1016/j.procs.2013.05.165
Affiliations:
- France, Tunisie
- Aquitaine, Auvergne-Rhône-Alpes, Centre-Val de Loire, Rhône-Alpes, Région Centre
- Bordeaux, Grenoble, Orléans
- Centre Val de Loire Université, Université Joseph Fourier, Université d'Orléans, Université de Bordeaux, Université de Grenoble
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Hal:hal-01084652Le document en format XML
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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="Limet, Sebastien" sort="Limet, Sebastien" uniqKey="Limet S" first="Sébastien" last="Limet">Sébastien Limet</name><affiliation wicri:level="1"><hal:affiliation type="laboratory" xml:id="struct-241078" status="VALID"><orgName>Laboratoire d'Informatique Fondamentale d'Orléans</orgName><orgName type="acronym">LIFO</orgName><desc><address><addrLine>Bâtiment IIIA Rue Léonard de Vinci B.P. 6759 F-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-301232" 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-301232" type="direct"><org type="institution" xml:id="struct-301232" status="VALID"><orgName>Institut National des Sciences Appliquées</orgName><orgName type="acronym">INSA</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><author><name sortKey="Raffin, Bruno" sort="Raffin, Bruno" uniqKey="Raffin B" first="Bruno" last="Raffin">Bruno Raffin</name><affiliation wicri:level="1"><hal:affiliation type="researchteam" xml:id="struct-44973" status="VALID"><idno type="RNSR">200618274S</idno><orgName>PrograMming and scheduling design fOr Applications in Interactive Simulation</orgName><orgName type="acronym">MOAIS</orgName><desc><address><addrLine>Inria Grenoble - Rhône-Alpes 655 avenue de l'Europe - Montbonnot 38334 Saint Ismier Cedex</addrLine><country key="FR"></country></address><ref type="url">http://www.inria.fr/equipes/moais</ref></desc><listRelation><relation active="#struct-2497" type="direct"></relation><relation active="#struct-300009" type="indirect"></relation><relation active="#struct-24471" type="direct"></relation><relation active="#struct-300275" type="indirect"></relation><relation 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type="IdRef">026388804</idno><orgName>Institut National Polytechnique de Grenoble </orgName><orgName type="acronym">INPG</orgName><date type="end">2006-12-31</date><desc><address><addrLine>46 avenue Félix Viallet 38031 Grenoble Cedex 1</addrLine><country key="FR"></country></address></desc></org></tutelle><tutelle active="#struct-51016" type="indirect"><org type="institution" xml:id="struct-51016" status="OLD"><idno type="IdRef">026404796</idno><orgName>Université Joseph Fourier - Grenoble 1</orgName><orgName type="acronym">UJF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 53 - 38041 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.ujf-grenoble.fr/</ref></desc></org></tutelle><tutelle active="#struct-3886" type="indirect"><org type="institution" xml:id="struct-3886" status="OLD"><idno type="IdRef">02640432X</idno><orgName>Université Pierre Mendès France - Grenoble 2</orgName><orgName type="acronym">UPMF</orgName><date type="end">2015-12-31</date><desc><address><addrLine>BP 47 - 38040 Grenoble Cedex 9</addrLine><country key="FR"></country></address><ref type="url">http://www.upmf-grenoble.fr/</ref></desc></org></tutelle><tutelle name="UMR5217" active="#struct-441569" type="indirect"><org type="institution" xml:id="struct-441569" status="VALID"><idno type="ISNI">0000000122597504</idno><idno type="IdRef">02636817X</idno><orgName>Centre National de la Recherche Scientifique</orgName><orgName type="acronym">CNRS</orgName><date type="start">1939-10-19</date><desc><address><country key="FR"></country></address><ref type="url">http://www.cnrs.fr/</ref></desc></org></tutelle></tutelles></hal:affiliation><country>France</country><placeName><settlement type="city">Grenoble</settlement><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region></placeName><orgName type="university">Université Joseph Fourier</orgName><orgName type="institution" wicri:auto="newGroup">Université de Grenoble</orgName></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-70855" status="INCOMING"><orgName>CIRSEE SUEZ ENVIRONNEMENT</orgName><desc><address><addrLine>38 Rue du President Wilson 78230 LE PECQ</addrLine><country key="FR"></country></address></desc><listRelation><relation active="#struct-311488" type="direct"></relation></listRelation><tutelles><tutelle active="#struct-311488" type="direct"><org type="institution" xml:id="struct-311488" status="INCOMING"><orgName>Suez Environnement</orgName><desc><address><country key="FR"></country></address></desc></org></tutelle></tutelles></hal:affiliation><country>France</country></affiliation></author></analytic><idno type="DOI">10.1016/j.procs.2013.05.165</idno><series><title level="j">Procedia Computer Science</title><idno type="ISSN">1877-0509</idno><imprint><date type="datePub">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="mix" xml:lang="en"><term>Computational Steering with Haptic Arm</term><term>High Performance Interactive Computing</term><term>Interactive Molecular Dynamics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7 M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.</div></front></TEI><affiliations><list><country><li>France</li><li>Tunisie</li></country><region><li>Aquitaine</li><li>Auvergne-Rhône-Alpes</li><li>Centre-Val de Loire</li><li>Rhône-Alpes</li><li>Région Centre</li></region><settlement><li>Bordeaux</li><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 Bordeaux</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="Chavent, Matthieu" sort="Chavent, Matthieu" uniqKey="Chavent M" first="Matthieu" last="Chavent">Matthieu Chavent</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="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></country><country name="Tunisie"><noRegion><name sortKey="Turki, Ahmed" sort="Turki, Ahmed" uniqKey="Turki A" first="Ahmed" last="Turki">Ahmed Turki</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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