Supercomputing for Molecular Dynamics Simulations : Handling Multi-Trillion Particles in Nanofluidics

著者名：Heinecke, Alexander/Eckhardt, Wolfgang/Horsch, Martin/Bungartz, Hans-Joachim

Springer（2015/03/30発売）

• 言語：ENG
• ISBN：9783319171470
• eISBN：9783319171487

Description

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

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