Supercomputing for Molecular Dynamics Simulations

Handling Multi-Trillion Particles in Nanofluidics
2015
ISBN: 978-3-319-17147-0
Verlag: Springer International Publishing

Buch, Englisch, 76 Seiten, Paperback, Format (B × H): 155 mm x 235 mm, Gewicht: 1635 g

Reihe: SpringerBriefs in Computer Science

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.

Zielgruppe

Research

Autoren/Hrsg.

Heinecke, Alexander

Bungartz, Hans-Joachim

Eckhardt, Wolfgang

Horsch, Martin

Fachgebiete

• Technische Wissenschaften Technik Allgemein Modellierung & Simulation
• Mathematik | Informatik EDV | Informatik Technische Informatik Hochleistungsrechnen, Supercomputer
• Technische Wissenschaften Verfahrenstechnik | Chemieingenieurwesen | Biotechnologie Chemische Verfahrenstechnik

Inhaltsverzeichnis

Introduction.- Molecular Dynamics Simulation.- Parallelization of MD Algorithms and Load Balancing.- Efficient Implementation of the Force Calculation in MD Simulations.- Experiments.- Conclusion.