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SpringerBriefs in Computer Science

Supercomputing for Molecular Dynamics Simulations

Handling Multi-Trillion Particles in Nanofluidics

Authors: Heinecke, A., Eckhardt, W., Horsch, M., Bungartz, H.-J.

  • 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
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eBook $39.99
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  • ISBN 978-3-319-17148-7
  • Digitally watermarked, DRM-free
  • Included format: EPUB, PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Softcover $54.99
price for USA
  • ISBN 978-3-319-17147-0
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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.

Table of contents (6 chapters)

  • Introduction

    Heinecke, Alexander (et al.)

    Pages 1-9

  • Molecular Dynamics Simulation

    Heinecke, Alexander (et al.)

    Pages 11-29

  • Parallelization of MD Algorithms and Load Balancing

    Heinecke, Alexander (et al.)

    Pages 31-44

  • Efficient Implementation of the Force Calculation in MD Simulations

    Heinecke, Alexander (et al.)

    Pages 45-58

  • Experiments

    Heinecke, Alexander (et al.)

    Pages 59-73

Buy this book

eBook $39.99
price for USA (gross)
  • ISBN 978-3-319-17148-7
  • Digitally watermarked, DRM-free
  • Included format: EPUB, PDF
  • ebooks can be used on all reading devices
  • Immediate eBook download after purchase
Softcover $54.99
price for USA
  • ISBN 978-3-319-17147-0
  • Free shipping for individuals worldwide
  • Usually dispatched within 3 to 5 business days.
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Bibliographic Information

Bibliographic Information
Book Title
Supercomputing for Molecular Dynamics Simulations
Book Subtitle
Handling Multi-Trillion Particles in Nanofluidics
Authors
Series Title
SpringerBriefs in Computer Science
Copyright
2015
Publisher
Springer International Publishing
Copyright Holder
The Author(s)
eBook ISBN
978-3-319-17148-7
DOI
10.1007/978-3-319-17148-7
Softcover ISBN
978-3-319-17147-0
Series ISSN
2191-5768
Edition Number
1
Number of Pages
X, 76
Number of Illustrations and Tables
22 b/w illustrations, 13 illustrations in colour
Topics