Huge-scale molecular dynamics simulation of multibubble nuclei

Handle URI:
http://hdl.handle.net/10754/598521
Title:
Huge-scale molecular dynamics simulation of multibubble nuclei
Authors:
Watanabe, Hiroshi; Suzuki, Masaru; Ito, Nobuyasu
Abstract:
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.
Citation:
Watanabe H, Suzuki M, Ito N (2013) Huge-scale molecular dynamics simulation of multibubble nuclei. Computer Physics Communications 184: 2775–2784. Available: http://dx.doi.org/10.1016/j.cpc.2013.07.023.
Publisher:
Elsevier BV
Journal:
Computer Physics Communications
KAUST Grant Number:
KUK-I1-005-04
Issue Date:
Dec-2013
DOI:
10.1016/j.cpc.2013.07.023
Type:
Article
ISSN:
0010-4655
Sponsors:
The authors would like to thank K. Nitadori, Y. Kanada, N. Kawashima, and S. Todo for valuable comments. This work was partially supported by Grants-in-Aid for Scientific Research (Contract No. 23740287) and by KAUST GRP (KUK-I1-005-04). The computational resource of Fujitsu FX10 was awarded by "Large-scale HPC Challenge" Project, Information Technology Center of the University of Tokyo. The computation was also carried out using the facilities of the Institute for Solid State Physics of the University of Tokyo, and Research Institute for Information Technology at Kyushu University.
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Full metadata record

DC FieldValue Language
dc.contributor.authorWatanabe, Hiroshien
dc.contributor.authorSuzuki, Masaruen
dc.contributor.authorIto, Nobuyasuen
dc.date.accessioned2016-02-25T13:31:29Zen
dc.date.available2016-02-25T13:31:29Zen
dc.date.issued2013-12en
dc.identifier.citationWatanabe H, Suzuki M, Ito N (2013) Huge-scale molecular dynamics simulation of multibubble nuclei. Computer Physics Communications 184: 2775–2784. Available: http://dx.doi.org/10.1016/j.cpc.2013.07.023.en
dc.identifier.issn0010-4655en
dc.identifier.doi10.1016/j.cpc.2013.07.023en
dc.identifier.urihttp://hdl.handle.net/10754/598521en
dc.description.abstractWe have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.en
dc.description.sponsorshipThe authors would like to thank K. Nitadori, Y. Kanada, N. Kawashima, and S. Todo for valuable comments. This work was partially supported by Grants-in-Aid for Scientific Research (Contract No. 23740287) and by KAUST GRP (KUK-I1-005-04). The computational resource of Fujitsu FX10 was awarded by "Large-scale HPC Challenge" Project, Information Technology Center of the University of Tokyo. The computation was also carried out using the facilities of the Institute for Solid State Physics of the University of Tokyo, and Research Institute for Information Technology at Kyushu University.en
dc.publisherElsevier BVen
dc.subjectHybrid MPI + OpenMP programmingen
dc.subjectMolecular dynamics methoden
dc.titleHuge-scale molecular dynamics simulation of multibubble nucleien
dc.typeArticleen
dc.identifier.journalComputer Physics Communicationsen
dc.contributor.institutionUniversity of Tokyo, Tokyo, Japanen
dc.contributor.institutionKyushu University, Fukuoka, Japanen
kaust.grant.numberKUK-I1-005-04en
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