Chapter 11

GPU-accelerated molecular dynamics clustering analysis with OpenACC

John E. Stone; Juan R. Perilla; C. Keith Cassidy; Klaus Schulten     University of Illinois at Urbana-Champaign, Urbana, IL, United States

Abstract

This chapter explores the use of OpenACC directives to accelerate the calculation of a so-called dissimilarity matrix, the most costly computation required for clustering analysis of molecular dynamics simulations.

By the end of this chapter, the reader will have an understanding of:

 Key algorithmic analysis steps that help guide decision making involved in application acceleration and parallelization and help set realistic performance targets for a successful OpenACC implementation on GPUs and other accelerators ...

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