A hybrid algorithm for parallel molecular dynamics simulations

TL;DR

This paper presents a hybrid parallelization and SIMD vectorization algorithm for molecular dynamics simulations, enabling efficient large-scale simulations on modern many-core processors and SIMD units.

Contribution

It introduces a novel hybrid parallelization method combining domain decomposition with thread-based approaches for molecular dynamics.

Findings

Efficient simulation of systems with up to 74 million atoms.

Good scalability on multi-core and many-core systems.

Demonstrated performance on Sandy Bridge, Haswell, and Xeon Phi processors.

Abstract

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.