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

by Alexander Heinecke, Wolfgang Eckhardt, Martin Horsch, Hans-Joachim Bungartz

Overview

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.

Product Details

ISBN-13:	9783319171470
Publisher:	Springer International Publishing
Publication date:	03/31/2015
Series:	SpringerBriefs in Computer Science
Edition description:	2015
Pages:	76
Product dimensions:	6.10(w) x 9.25(h) x (d)

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.