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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Bibliographic Details
Published in:Journal of computational chemistry Vol. 42; no. 4; pp. 231 - 241
Main Authors: Jung, Jaewoon, Kobayashi, Chigusa, Kasahara, Kento, Tan, Cheng, Kuroda, Akiyoshi, Minami, Kazuo, Ishiduki, Shigeru, Nishiki, Tatsuo, Inoue, Hikaru, Ishikawa, Yutaka, Feig, Michael, Sugita, Yuji
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 05.02.2021
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Subjects:
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
Online Access:Get full text
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Summary: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.
Bibliography:Funding information
United States National Institutes of Health, Grant/Award Number: R35 GM126948; MEXT/KAKENHI, Grant/Award Number: 19H05645
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.26450