Abstract
As high-performance computing systems now rely on hardware parallelism for continuous improvements in performance, the timescales accessible to direct molecular dynamics (MD) remain limited by the relatively stagnant performance of a single processor. While spatial decomposition allows extremely large systems to be simulated for short periods of time, alternative methods are needed to extend these simulations to significantly longer timescales. Although parallel means to produce long-timescale trajectories have been known since the late nineteen-nineties, several newer methodologies falling under the umbrella of accelerated molecular dynamics (AMD) have recently been developed with parallelism in mind. In this chapter, we review the current state-of-the-art in replica-based AMD and review several additional means of parallel scaling. Following a brief introduction to the serial AMD procedures, the chapter is organized into three general categories of parallel extensions: replication, speculation, and localization.
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Acknowledgements
This work was supported in part by the Department of Energy (DOE), Office of Basic Energy Sciences, Materials Sciences and Engineering Division. This work was also supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of two US Department of Energy organizations (Office of Science and the National Nuclear Security Administration), responsible for the planning and preparation of a capable exascale ecosystem, including software, applications, hardware, advanced system engineering, and early testbed platforms, in support of the nation’s exascale computing imperative. Los Alamos National Laboratory is operated by Los Alamos National Security, LLC, for the National Nuclear Security Administration of the DOE, under contract DE-AC52-O6NA25396.
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Zamora, R.J., Perez, D., Martinez, E., Uberuaga, B.P., Voter, A.F. (2018). Accelerated Molecular Dynamics Methods in a Massively Parallel World. In: Andreoni, W., Yip, S. (eds) Handbook of Materials Modeling . Springer, Cham. https://doi.org/10.1007/978-3-319-42913-7_25-1
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DOI: https://doi.org/10.1007/978-3-319-42913-7_25-1
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Accelerated Molecular Dynamics Methods in a Massively Parallel World- Published:
- 10 October 2019
DOI: https://doi.org/10.1007/978-3-319-42913-7_25-2
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Accelerated Molecular Dynamics Methods in a Massively Parallel World- Published:
- 05 July 2018
DOI: https://doi.org/10.1007/978-3-319-42913-7_25-1