Huge-scale molecular dynamics simulation of multibubble nuclei

Hiroshi Watanabe; Masaru Suzuki; Nobuyasu Ito

doi:10.1016/j.cpc.2013.07.023

Huge-scale molecular dynamics simulation of multibubble nuclei

Hiroshi Watanabe, Masaru Suzuki, Nobuyasu Ito

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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.

Original language	English (US)
Pages (from-to)	2775-2784
Number of pages	10
Journal	Computer Physics Communications
Volume	184
Issue number	12
DOIs	https://doi.org/10.1016/j.cpc.2013.07.023
State	Published - Dec 2013

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-005-04
Acknowledgements: 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.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

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10.1016/j.cpc.2013.07.023

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title = "Huge-scale molecular dynamics simulation of multibubble nuclei",

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. {\textcopyright} 2013 Elsevier B.V. All rights reserved.",

author = "Hiroshi Watanabe and Masaru Suzuki and Nobuyasu Ito",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledged KAUST grant number(s): KUK-I1-005-04 Acknowledgements: 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. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

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N2 - 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.

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Huge-scale molecular dynamics simulation of multibubble nuclei

Abstract

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