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BioMed Research International
Volume 2014 (2014), Article ID 560987, 12 pages
http://dx.doi.org/10.1155/2014/560987
Research Article

A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation

1Drug Discovery and Development, Italian Institute of Technology, 16163 Genova, Italy
2Department of Geosciences, University of Padova, 35131 Padova, Italy
3IMATI, CNR, 16149 Genova, Italy
4Department of Advanced Robotics, Italian Institute of Technology, 16163 Genova, Italy

Received 21 February 2014; Revised 16 May 2014; Accepted 18 May 2014; Published 12 June 2014

Academic Editor: Horacio Pérez-Sánchez

Copyright © 2014 José Colmenares et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.