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Scalable In situ Analysis of Molecular Dynamics Simulations

Published:12 November 2017Publication History

ABSTRACT

Analysis of scientific simulation data enables scientists to glean insight from simulations. In situ analysis, which can be simultaneously executed with the simulation, mitigates I/O bottlenecks and can accelerate discovery of new phenomena. However, in typical modes of operation, this requires either stalling simulation during analysis phase or transferring data for analysis. We study the scalability challenges of time- and space-shared modes of analyzing large-scale molecular dynamics simulations. We also propose topology-aware mapping for simulation and analysis. We demonstrate the benefits of our approach using LAMMPS code on two supercomputers.

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  • Published in

    cover image ACM Conferences
    ISAV'17: Proceedings of the In Situ Infrastructures on Enabling Extreme-Scale Analysis and Visualization
    November 2017
    53 pages
    ISBN:9781450351393
    DOI:10.1145/3144769

    Copyright © 2017 ACM

    Publication rights licensed to ACM. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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    Association for Computing Machinery

    New York, NY, United States

    Publication History

    • Published: 12 November 2017

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    Acceptance Rates

    ISAV'17 Paper Acceptance Rate9of28submissions,32%Overall Acceptance Rate23of63submissions,37%

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