Petascale molecular dynamics simulation using the fast multipole method on K computer

Handle URI:
http://hdl.handle.net/10754/563774
Title:
Petascale molecular dynamics simulation using the fast multipole method on K computer
Authors:
Ohno, Yousuke; Yokota, Rio ( 0000-0001-7573-7873 ) ; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda ( 0000-0001-5208-5366 ) ; Narumi, Tetsu; Taiji, Makoto
Abstract:
In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.
KAUST Department:
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Extreme Computing Research Center; Computer Science Program
Publisher:
Elsevier
Journal:
Computer Physics Communications
Issue Date:
Oct-2014
DOI:
10.1016/j.cpc.2014.06.004
Type:
Article
ISSN:
00104655
Sponsors:
This work was partially supported by the Integrated Simulation of Living Matter Project, commissioned by the Ministry of Education, Culture, Sports, Science and Technology, Japan. This work was partially supported in part by the Japan Science and Technology Agency (JST) Core Research of Evolutional Science and Technology (CREST) research programs "Highly Productive, High Performance Application Frameworks for Post Petascale Computing". Part of the results is obtained by using the K computer at the RIKEN Advanced Institute for Computational Science (early access and HPCI systems research project: Proposal number hp120068). We thank the Next-Generation Supercomputer R&D Center, especially Kazuo Minami, Akiyoshi Kuroda and Masaaki Terai (in the Application Development Team) for their outstanding support. We appreciate Mikio Hondou and Hikaru Inoue, from Fujitsu Co. Ltd., for their optimization support. We also thank the RIKEN Integrated Cluster of Clusters (RICC) for the computer resources used for our code development and calculations. We gratefully acknowledge the exceptional support provided by the late Takayuki Shigetani at RIKEN Advanced Center for Computing and Communication (ACCC). We also thank Toru Takinaka at NEC Informatec Systems, Ltd. for the supporting code development.
Appears in Collections:
Articles; Extreme Computing Research Center; Computer Science Program; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorOhno, Yousukeen
dc.contributor.authorYokota, Rioen
dc.contributor.authorKoyama, Hiroshien
dc.contributor.authorMorimoto, Gentaroen
dc.contributor.authorHasegawa, Akien
dc.contributor.authorMasumoto, Genen
dc.contributor.authorOkimoto, Noriakien
dc.contributor.authorHirano, Yoshinorien
dc.contributor.authorIbeid, Hudaen
dc.contributor.authorNarumi, Tetsuen
dc.contributor.authorTaiji, Makotoen
dc.date.accessioned2015-08-03T12:09:40Zen
dc.date.available2015-08-03T12:09:40Zen
dc.date.issued2014-10en
dc.identifier.issn00104655en
dc.identifier.doi10.1016/j.cpc.2014.06.004en
dc.identifier.urihttp://hdl.handle.net/10754/563774en
dc.description.abstractIn this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.en
dc.description.sponsorshipThis work was partially supported by the Integrated Simulation of Living Matter Project, commissioned by the Ministry of Education, Culture, Sports, Science and Technology, Japan. This work was partially supported in part by the Japan Science and Technology Agency (JST) Core Research of Evolutional Science and Technology (CREST) research programs "Highly Productive, High Performance Application Frameworks for Post Petascale Computing". Part of the results is obtained by using the K computer at the RIKEN Advanced Institute for Computational Science (early access and HPCI systems research project: Proposal number hp120068). We thank the Next-Generation Supercomputer R&D Center, especially Kazuo Minami, Akiyoshi Kuroda and Masaaki Terai (in the Application Development Team) for their outstanding support. We appreciate Mikio Hondou and Hikaru Inoue, from Fujitsu Co. Ltd., for their optimization support. We also thank the RIKEN Integrated Cluster of Clusters (RICC) for the computer resources used for our code development and calculations. We gratefully acknowledge the exceptional support provided by the late Takayuki Shigetani at RIKEN Advanced Center for Computing and Communication (ACCC). We also thank Toru Takinaka at NEC Informatec Systems, Ltd. for the supporting code development.en
dc.publisherElsevieren
dc.subjectFast multipole methoden
dc.subjectK computeren
dc.subjectMolecular crowdingen
dc.subjectMolecular dynamicsen
dc.titlePetascale molecular dynamics simulation using the fast multipole method on K computeren
dc.typeArticleen
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentExtreme Computing Research Centeren
dc.contributor.departmentComputer Science Programen
dc.identifier.journalComputer Physics Communicationsen
dc.contributor.institutionLaboratory for Computational Molecular Design, Computational Biology Research Core, RIKEN Quantitative Biology Center, Japanen
dc.contributor.institutionHigh-performance Computing Team, RIKEN Computational Science Research Program, Japanen
dc.contributor.institutionHigh Performance Computing Development Team, RIKEN HPCI Program for Computational Life Sciences, Japanen
dc.contributor.institutionProcessor Research Team, RIKEN Advanced Institute for Computational Science, Japanen
dc.contributor.institutionDepartment of Computer Science, University of Electro-Communications, Japanen
kaust.authorYokota, Rioen
kaust.authorIbeid, Hudaen
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