Simulation of P Systems with Active Membranes on CUDA

Author

Cecilia, Jose M. ; Guerrero, Gines D. ; Garcia, Juan Manuel ; Del Amor, Miguel A Martínez ; Perez-Hurtado, I. ; Jiménez, Mario J Pérez

Author_Institution

Dipt. Ing. y Tecnol. de Comput., Univ. de Murcia, Murcia, Spain

fYear

2009

fDate

14-16 Oct. 2009

Firstpage

61

Lastpage

70

Abstract

P systems or membrane systems provide a high level computational modeling framework that combines the structural and dynamic aspects of biological systems in a relevant and understandable way. P systems are massively parallel distributed, and non-deterministic systems. In this paper, we describe the implementation of a simulator for the class of recognizer P systems with active membranes by using the GPU (graphics processing unit). We compare the high performance parallel simulator for the GPU to the simulator developed on a single CPU (central processing unit), and we show that the GPU is better suited than the CPU to simulate P systems due to its highly parallel nature.

Keywords

biocomputing; digital simulation; membranes; parallel algorithms; CPU; CUDA; GPU; P system simulation; active membrane system; biological dynamic system; biological structural system; central processing unit; computational modeling framework; compute unified device architecture; graphics processing unit; membrane computing; nondeterministic system; parallel distributed algorithm; Analytical models; Biological processes; Biological system modeling; Biology computing; Biomembranes; Central Processing Unit; Computational modeling; Computational systems biology; Graphics; Power system modeling; CUDA; GPU; Membrane Computing; P systems; Parallel Computing;

fLanguage

English

Publisher

ieee

Conference_Titel

High Performance Computational Systems Biology, 2009. HIBI '09. International Workshop on

Conference_Location

Trento

Print_ISBN

978-0-7695-3809-9

Type

conf

DOI

10.1109/HiBi.2009.13

Filename

5298701