PAPER - Accelerating parallel evaluations of ROCS Export

@article{Haque09, abstract = {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. {\copyright} 2009 Wiley Periodicals, Inc. J Comput Chem 2009}, address = {Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Chemistry, Stanford University, Stanford, CA, USA}, author = {Haque, Imran S. and Pande, Vijay S.}, citeulike-article-id = {4486393}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21307}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122374445/ABSTRACT}, doi = {10.1002/jcc.21307}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {gpu, rocs}, number = {1}, pages = {117--132}, posted-at = {2009-09-12 05:03:57}, priority = {2}, title = {PAPER - Accelerating parallel evaluations of ROCS}, url = {http://dx.doi.org/10.1002/jcc.21307}, volume = {31}, year = {2010} }

TY - JOUR ID - Haque09 L3 - citeulike-article-id:4486393 N2 - 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 2009 IS - 1 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Chemistry, Stanford University, Stanford, CA, USA EP - 132 TI - PAPER - Accelerating parallel evaluations of ROCS VL - 31 SP - 117 KW - gpu KW - rocs AU - Haque, Imran AU - Pande, Vijay PY - 2010/// UR - http://dx.doi.org/10.1002/jcc.21307 ER -