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GPU-accelerated computation of electron transfer

Authors

  • Siegfried Höfinger,

    Corresponding author
    1. Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
    2. Department of Physics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49331-1295
    • Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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    • These authors contributed equally to this work.

  • Angela Acocella,

    1. Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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    • These authors contributed equally to this work.

  • Sergiu C. Pop,

    1. Faculty of Physics, Babes-Bolyai University, Mihail Kogalniceanu 1, 400084 Cluj-Napoca, Romania
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  • Tetsu Narumi,

    1. Faculty of Informatics and Engineering, University of Electro-Communications, 1-5-1, Chofugaoka, Chofu, Tokyo 182-8585, Japan
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  • Kenji Yasuoka,

    1. Department of Mechanical Engineering, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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  • Titus Beu,

    1. Faculty of Physics, Babes-Bolyai University, Mihail Kogalniceanu 1, 400084 Cluj-Napoca, Romania
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  • Francesco Zerbetto

    1. Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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Abstract

Electron transfer is a fundamental process that can be studied with the help of computer simulation. The underlying quantum mechanical description renders the problem a computationally intensive application. In this study, we probe the graphics processing unit (GPU) for suitability to this type of problem. Time-critical components are identified via profiling of an existing implementation and several different variants are tested involving the GPU at increasing levels of abstraction. A publicly available library supporting basic linear algebra operations on the GPU turns out to accelerate the computation approximately 50-fold with minor dependence on actual problem size. The performance gain does not compromise numerical accuracy and is of significant value for practical purposes. © 2012 Wiley Periodicals, Inc.

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