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.
Highlights
Computational simulations are widely used across many scientific disciplines, spanning a variety of domains of investigation from crystalline atomic structures to cell pathways, with numerous software packages available
An algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations
We investigate the performance of our algorithm in a modern biophysical molecular dynamics (MD) simulation designed to investigate chromosome condensation on two platforms, one an Intel Xeon based platform, one based on Intel’s Xeon Phi Knights Landing many-core architecture
Summary
Computational simulations are widely used across many scientific disciplines, spanning a variety of domains of investigation from crystalline atomic structures to cell pathways, with numerous software packages available. Prominent examples are LAMMPS [19], developed by Sandia National Laboratories to simulate materials under the influence of various physical potentials, and NAMD [18], which is more focused on biological applications and has been used to solve important recent medical problems, such as resolving the structure of the HIV-1 virus responsible for AIDS [26]. Simulations on this scale require enormous computational resources and the time is long since past where a single machine could provide the necessary power.
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