High Performance Parallelism Pearls Volume Two

Chapter 6

Amber PME Molecular Dynamics Optimization

Ashraf Bhuiyan*; Perri Needham^†; Ross C. Walker^{†,‡    *} Intel Corporation, USA^† San Diego Supercomputing Center, USA^‡ University of California San Diego, USA

Abstract

This chapter presents an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, which forms part of the Amber v14 MD software package, which makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct space summation and neighbor list build to the coprocessor. The modified algorithm provides performance improvement for large systems (~ 1 million atoms), achieving a 1.62× performance improvement from the baseline implementation ...