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Simulation of P Systems with Active Membranes on CUDA

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6 Author(s)
Cecilia, J.M. ; Dipt. Ing. y Tecnol. de Comput., Univ. de Murcia, Murcia, Spain ; Guerrero, G.D. ; Garcia, J.M. ; Martinez-del-Amor, M.A.
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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.

Published in:

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

Date of Conference:

14-16 Oct. 2009