Alexander Heinecke & Wolfgang Eckhardt 
Supercomputing for Molecular Dynamics Simulations [PDF ebook] 
Handling Multi-Trillion Particles in Nanofluidics

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.

Cuprins

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