Supercomputing for Molecular Dynamics Simulations, 2015
Handling Multi-Trillion Particles in Nanofluidics
SpringerBriefs in Computer Science Series

Authors:

Language: English

52.74 €

In Print (Delivery period: 15 days).

Add to cartAdd to cart
Publication date:
76 p. · 15.5x23.5 cm · Paperback
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.

Introduction

Molecular Dynamics Simulation

Parallelization of MD Algorithms and Load Balancing

Efficient Implementation of the Force Calculation in MD Simulations

Experiments

Conclusion

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