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Supercomputing for Molecular Dynamics Simulations

Handling Multi-Trillion Particles in Nanofluidics

  • Book
  • © 2015

Overview

Authors:
  1. Alexander Heinecke

    1. Intel Corporation, Santa Clara, USA

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  2. Wolfgang Eckhardt

    1. Technische Universität München, Garching, Germany

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  3. Martin Horsch

    1. University of Kaiserslautern, Kaiserslautern, Germany

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  4. Hans-Joachim Bungartz

    1. Technische Universität München, Garching, Germany

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  • Describes the state-of-the-art algorithms and implementations essential for molecular simulation in chemical engineering
  • Includes high-performance implementations of MD algorithms on current HPC systems covering shared-memory, distributed-memory parallelization and vectorization
  • Presents a special focus on hybrid systems using Intel Xeon processors and Intel Xeon Phi coprocessors
  • Includes supplementary material: sn.pub/extras

Part of the book series: SpringerBriefs in Computer Science (BRIEFSCOMPUTER)

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Table of contents (6 chapters)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Introduction

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 1-9

  3. Molecular Dynamics Simulation

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 11-29

  4. Parallelization of MD Algorithms and Load Balancing

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 31-44

  5. Efficient Implementation of the Force Calculation in MD Simulations

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 45-58

  6. Experiments

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 59-73

  7. Conclusion

    • Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz
    Pages 75-76
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Keywords

About this book

This work presents modern implementations of relevant molecular dynamics algorithms using ls1 mardyn, a simulation program for engineering applications. The text focuses strictly on HPC-related aspects, covering implementation on HPC architectures, taking Intel Xeon and Intel Xeon Phi clusters as representatives of current platforms. The work describes distributed and shared-memory parallelization on these platforms, including load balancing, with a particular focus on the efficient implementation of the compute kernels. The text also discusses the software-architecture of the resulting code.

Authors and Affiliations

  • Intel Corporation, Santa Clara, USA

    Alexander Heinecke

  • Technische Universität München, Garching, Germany

    Wolfgang Eckhardt, Hans-Joachim Bungartz

  • University of Kaiserslautern, Kaiserslautern, Germany

    Martin Horsch

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