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Porting Tissue-Scale Cardiac Simulations to the Knights Landing Platform

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High Performance Computing (ISC High Performance 2017)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10524))

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Abstract

To study the performance difference between the two generations of Xeon Phi, as well as the respective programming techniques, we port and optimize a simulation code for 3D tissues of the human cardiac ventricle to the new Knights Landing (KNL) platform. The amount of computation arises from a large number of cardiac cells and a physiologically realistic model adopted for each cell, which is resolved as having \(10^4\) calcium release units and controlled by \(10^6\) stochastically changing ryanodine receptors and \(1.5 \times 10^5\) L-type calcium channels. The programming challenge arises from the fact that the involved computational tasks have various levels of arithmetic intensity and control complexity, requiring in some cases hardware-specific manual optimizations. We also study how the new memory system of KNL can be properly used to allow larger simulations beyond the capacity of the 16 GB MCDRAM. The combined advancements in hardware and software result in an almost ninefold increase in performance on the KNL over the previous generation.

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Notes

  1. 1.

    The exact values vary for the different models. See [8] for the technical specifications.

  2. 2.

    Our code generally runs at 1.5 GHz due to the built-in turbo functionality.

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Authors and Affiliations

  1. Simula Research Laboratory, 1364, Fornebu, Norway

    Johannes Langguth, Chad Jarvis & Xing Cai

  2. Department of Informatics, University of Oslo, 0316, Oslo, Norway

    Xing Cai

Authors
  1. Johannes Langguth
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  2. Chad Jarvis
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  3. Xing Cai
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Corresponding author

Correspondence to Johannes Langguth .

Editor information

Editors and Affiliations

  1. Deutsches Klimarechenzentrum (DKRZ), Hamburg, Hamburg, Germany

    Julian M. Kunkel

  2. TITECH, Tokyo, Japan

    Rio Yokota

  3. Department of Computer Science, University of Delaware, Newark, Delaware, USA

    Michela Taufer

  4. Lawrence Berkeley National Laboratory, Berkeley, California, USA

    John Shalf

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Langguth, J., Jarvis, C., Cai, X. (2017). Porting Tissue-Scale Cardiac Simulations to the Knights Landing Platform. In: Kunkel, J., Yokota, R., Taufer, M., Shalf, J. (eds) High Performance Computing. ISC High Performance 2017. Lecture Notes in Computer Science(), vol 10524. Springer, Cham. https://doi.org/10.1007/978-3-319-67630-2_28

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  • DOI: https://doi.org/10.1007/978-3-319-67630-2_28

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-67629-6

  • Online ISBN: 978-3-319-67630-2

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