We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5) and demonstrate that meso-scale molecular dynamics with more than 108 particles is now possible on massively parallel MIMD computers. Typical runs show single particle update-times of 0.15μs in 2 dimensions (2D) and approximately 1μs in 3 dimensions (3D) on a 1024 node CM-5 without vector units, corresponding to more than 1.8 GFlops overall performance. We also present a scaling equation which agrees well with actually observed timings.
@article{arxiv.comp-gas/9303002,
title = {Message-Passing Multi-Cell Molecular Dynamics on the Connection Machine 5},
author = {D. M. Beazley and P. S. Lomdahl},
journal= {arXiv preprint arXiv:comp-gas/9303002},
year = {2008}
}