Abstract
We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5× overall speedup and good scaling to large problem sizes and processor counts.
•We present the projection sorting algorithm for molecular dynamics simulations.•We provide optimised implementations for Intel Broadwell and Knights Landing.•We extend our implementations to multi-node environments using MPI.•We investigate the performance of our algorithm in a biophysical MD simulation.•We observe serial speedups up to 5×, and good MPI scaling behaviour.