A hybrid algorithm for parallel molecular dynamics simulations
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.
Cite
@article{arxiv.1611.00075,
title = {A hybrid algorithm for parallel molecular dynamics simulations},
author = {Chris M. Mangiardi and Ralf Meyer},
journal= {arXiv preprint arXiv:1611.00075},
year = {2017}
}
Comments
16 pages, 7 figures, 5 tables; Accepted for publication in Computer Physics Communications