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International Conference on Computational Methods in Systems Biology

CMSB 2012: Computational Methods in Systems Biology pp 247–266Cite as

Population Dynamics P Systems on CUDA

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7605))

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.

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Author information

Authors and Affiliations

  1. Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, University of Seville, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain

    Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Adolfo Gastalver-Rubio & Mario J. Pérez-Jiménez

  2. HPC-Lab, Department of Computer and Information Science, Norwegian University of Science and Technology, Sem Sælands vei 9, NO-7491, Trondheim, Norway

    Anne C. Elster

Authors
  1. Miguel A. Martínez-del-Amor
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  2. Ignacio Pérez-Hurtado
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  3. Adolfo Gastalver-Rubio
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  4. Anne C. Elster
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  5. Mario J. Pérez-Jiménez
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Editor information

Editors and Affiliations

  1. School of Information Systems, Computing and Mathematics, Brunel University, UB8 3PH, Uxbridge, UK

    David Gilbert

  2. Computer Science Institute, University of Technology, 03013, Cottbus, Germany

    Monika Heiner

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© 2012 Springer-Verlag Berlin Heidelberg

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Martínez-del-Amor, M.A., Pérez-Hurtado, I., Gastalver-Rubio, A., Elster, A.C., Pérez-Jiménez, M.J. (2012). Population Dynamics P Systems on CUDA. In: Gilbert, D., Heiner, M. (eds) Computational Methods in Systems Biology. CMSB 2012. Lecture Notes in Computer Science(), vol 7605. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33636-2_15

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  • DOI: https://doi.org/10.1007/978-3-642-33636-2_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33635-5

  • Online ISBN: 978-3-642-33636-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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