New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems

In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the per...

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Vydáno v:	Journal of computational chemistry Ročník 42; číslo 4; s. 231 - 241
Hlavní autoři:	Jung, Jaewoon, Kobayashi, Chigusa, Kasahara, Kento, Tan, Cheng, Kuroda, Akiyoshi, Minami, Kazuo, Ishiduki, Shigeru, Nishiki, Tatsuo, Inoue, Hikaru, Ishikawa, Yutaka, Feig, Michael, Sugita, Yuji
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Hoboken, USA John Wiley & Sons, Inc 05.02.2021 Wiley Subscription Services, Inc
Témata:	Algorithms ARM CPU architecture Central processing units Computational Biology - methods CPUs DNA - chemistry fast Fourier transform Fugaku supercomputer Molecular dynamics Molecular Dynamics Simulation parallel input/output setup RNA - chemistry Simulation ARM CPU architecture parallel input/output setup fast Fourier transform Fugaku supercomputer molecular dynamics simulation
ISSN:	0192-8651, 1096-987X, 1096-987X
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Abstract	In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal‐space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell. We propose a novel parallelization algorithm of nonbonded interactions such that it can perform cellular‐scale molecular dynamics (MD) with more than 100,000 CPU cores. The new algorithm implemented in GENESIS MD software shows good scalability up to 16,384 nodes for more than 1 billion atoms. Up to our understanding, it is the world best performance for a biomolecule consisting of more than 1 billion atoms.
AbstractList	In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal‐space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell. In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real‐space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal‐space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell. We propose a novel parallelization algorithm of nonbonded interactions such that it can perform cellular‐scale molecular dynamics (MD) with more than 100,000 CPU cores. The new algorithm implemented in GENESIS MD software shows good scalability up to 16,384 nodes for more than 1 billion atoms. Up to our understanding, it is the world best performance for a biomolecule consisting of more than 1 billion atoms. In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space non-bonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space non-bonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell. In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.
Author	Tan, Cheng Ishiduki, Shigeru Sugita, Yuji Kuroda, Akiyoshi Inoue, Hikaru Ishikawa, Yutaka Minami, Kazuo Nishiki, Tatsuo Jung, Jaewoon Kobayashi, Chigusa Feig, Michael Kasahara, Kento
AuthorAffiliation	2 Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 7 Biochemistry & Molecular Biology department, Michigan State University, 603 Wilson Road, Room 218 BCH, East Lansing, MI 48824 6 System Software Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan 1 Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan 4 Operations and Computer Technologies Division, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan 5 Fujitsu company, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan 3 Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
AuthorAffiliation_xml	– name: 5 Fujitsu company, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan – name: 7 Biochemistry & Molecular Biology department, Michigan State University, 603 Wilson Road, Room 218 BCH, East Lansing, MI 48824 – name: 1 Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan – name: 6 System Software Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan – name: 3 Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan – name: 2 Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan – name: 4 Operations and Computer Technologies Division, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Snippet	In this paper, we address high performance extreme‐scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular‐scale molecular dynamics... In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics...
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StartPage	231
SubjectTerms	Algorithms ARM CPU architecture Central processing units Computational Biology - methods CPUs DNA - chemistry fast Fourier transform Fugaku supercomputer Molecular dynamics Molecular Dynamics Simulation parallel input/output setup RNA - chemistry Simulation
Title	New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems
URI	https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fjcc.26450 https://www.ncbi.nlm.nih.gov/pubmed/33200457 https://www.proquest.com/docview/2473397012 https://www.proquest.com/docview/2461397881 https://pubmed.ncbi.nlm.nih.gov/PMC7975918
Volume	42
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