David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher
Rodrigues, and Klaus Schulten.
Fast molecular electrostatics algorithms on GPUs.
In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp.
43-58. Morgan Kaufmann Publishers, 2011.
HARD2011
In this chapter, we present GPU kernels for calculating electrostatic potential maps, which is
of practical importance to modeling biomolecules. Calculations on a structured grid
containing a large amount of fine-grained data parallelism make this problem especially
well-suited to GPU computing and a worthwhile case study. We discuss in detail the effective
use of the hardware memory subsystems, kernel loop optimizations, and approaches to
regularize the computational work performed by the GPU, all of which are important
techniques for achieving high performance.
