Solving the Linearized Poisson-Boltzmann Equation on GPUs Using CUDA

Author

Colmenares, Juan ; Ortiz, Javier ; Decherchi, S. ; Fijany, A. ; Rocchia, W.

Author_Institution

Drug Discovery & Dev. Dept., Italian Inst. of Technol., Genoa, Italy

fYear

2013

fDate

Feb. 27 2013-March 1 2013

Firstpage

420

Lastpage

426

Abstract

In this work an implementation of a linearized Poisson-Boltzmann equation solver based on a Finite Differences scheme on the GPU architecture is presented. The algorithm exploits the checkerboard structure of the discretized Laplace operator and follows the footprints of a popular solver called DelPhi, which is widely used in the Computational Biology community. The algorithm has been implemented using CUDA. This implementation has then been integrated with the DelPhi solver and tested over a few representative cases of biological interest. Details of the implementation as well as performance test results are illustrated.

Keywords

Boltzmann equation; Poisson equation; biology computing; finite difference methods; graphics processing units; mathematics computing; parallel algorithms; parallel architectures; software performance evaluation; CUDA; DelPhi solver; GPU architecture; algorithm implementation; computational biology community; discretized Laplace operator; finite difference scheme; linearized Poisson-Boltzmann equation solver; performance test results; Convergence; Dielectrics; Electrostatics; Equations; Graphics processing units; Instruction sets; Mathematical model; CUDA; Finite Differences; Poisson-Boltzmann;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel, Distributed and Network-Based Processing (PDP), 2013 21st Euromicro International Conference on

Conference_Location

Belfast

ISSN

1066-6192

Print_ISBN

978-1-4673-5321-2

Electronic_ISBN

1066-6192

Type

conf

DOI

10.1109/PDP.2013.67

Filename

6498584