GPU-Accelerated Computation and Interactive Display of
John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, Klaus J. Schulten · 2011
In this chapter, we present several graphics processing unit (GPU) algorithms for evaluating molecular orbitals on three-dimensional lattices, as is commonly used for molecular visualization. For each kernel, we describe necessary design trade-offs, applicability to various problem sizes, and performance on different generations of GPU hardware. We then demonstrate the appropriate and effective use of fast on-chip GPU memory subsystems for access to key data structures, show several GPU kernel optimization principles, and explore the application of advanced techniques such as dynamic kernel generation and just-in-time (JIT) kernel compilation techniques. 1