Title :
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
fDate :
Feb. 27 2013-March 1 2013
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;
Conference_Titel :
Parallel, Distributed and Network-Based Processing (PDP), 2013 21st Euromicro International Conference on
Conference_Location :
Belfast
Print_ISBN :
978-1-4673-5321-2
Electronic_ISBN :
1066-6192
DOI :
10.1109/PDP.2013.67
