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Population Dynamics P Systems on CUDA


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Author: Martínez del Amor, Miguel Ángel
Pérez Hurtado de Mendoza, Ignacio
Gastalver Rubio, Adolfo
Elster, Anne C.
Pérez Jiménez, Mario de Jesús
Department: Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial
Date: 2012
Published in: CMSB 2012: 10th International Conference on Computational Methods in Systems Biology (2012), p 247-266
ISBN/ISSN: 978-3-642-33635-5
Document type: Presentation
Abstract: Population Dynamics P systems (PDP systems, in short) provide a new formal bio-inspired modeling framework, which has been successfully used by ecologists. These models are validated using software tools against actual measurements. The goal is to use P systems simulations to adopt a priori management strategies for real ecosystems. Software for PDP systems is still in an early stage. The simulation of PDP systems is both computationally and data intensive for large models. Therefore, the development of efficient simulators is needed for this field. In this paper, we introduce a novel simulator for PDP systems accelerated by the use of the computational power of GPUs. We discuss the implementation of each part of the simulator, and show how to achieve up to a 7x speedup on a NVIDA Tesla C1060 compared to an optimized multicore version on a Intel 4-core i5 Xeon for large systems. Other results and testing methodologies are also included.
Cite: Martínez del Amor, M.Á., Pérez Hurtado de Mendoza, I., Gastalver Rubio, A., Elster, A.C. y Pérez Jiménez, M.d.J. (2012). Population Dynamics P Systems on CUDA. En CMSB 2012: 10th International Conference on Computational Methods in Systems Biology (247-266), London, UK: Springer.
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DOI: 10.1007/978-3-642-33636-2_15

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