Premium
PAPER—Accelerating parallel evaluations of ROCS
Author(s) -
Haque Imran S.,
Pande Vijay S.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21307
Subject(s) - computer science , parallel computing , graphics , overlay , gaussian , throughput , implementation , computational science , general purpose computing on graphics processing units , graphics hardware , algorithm , computer graphics (images) , operating system , programming language , physics , quantum mechanics , wireless
Modern graphics processing units (GPUs) are flexibly programmable and have peak computational throughput significantly faster than conventional CPUs. Herein, we describe the design and implementation of PAPER, an open‐source implementation of Gaussian molecular shape overlay for NVIDIA GPUs. We demonstrate one to two order‐of‐magnitude speedups on high‐end commodity GPU hardware relative to a reference CPU implementation of the shape overlay algorithm and speedups of over one order of magnitude relative to the commercial OpenEye ROCS package. In addition, we describe errors incurred by approximations used in common implementations of the algorithm. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010