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Parallel simulation of Population Dynamics P systems: updates and roadmap

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Abstract

Population Dynamics P systems are a type of multienvironment P systems that serve as a formal modeling framework for real ecosystems. The accurate simulation of these probabilistic models, e.g. with Direct distribution based on Consistent Blocks Algorithm, entails large run times. Hence, parallel platforms such as GPUs have been employed to speedup the simulation. In 2012, the first GPU simulator of PDP systems was presented. However, it was able to run only randomly generated PDP systems. In this paper, we present current updates made on this simulator, involving an input modu le for binary files and an output module for CSV files. Finally, the simulator has been experimentally validated with a real ecosystem model, and its performance has been tested with two high-end GPUs: Tesla C1060 and K40.

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Acknowledgments

The authors acknowledge the support of the project TIN2012-37434 of the “Ministerio de Economía y Competitividad” of Spain, co-financed by FEDER funds. They also acknowledge the CUDA Research Center program, granted by NVIDIA to the University of Seville in 2014, 2015 and 2016, and their donation of a Tesla K40 GPU. Finally, Martínez-del-Amor also acknowledges the support of the 3rd postdoctoral phase of the PIF program associated with the project of excellence from “Junta de Andalucía” under grant P08–TIC04200, co-financed by FEDER funds.

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Authors and Affiliations

  1. Research Group on Natural Computing, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012, Seville, Spain

    Miguel A. Martínez-del-Amor, Luis F. Macías-Ramos, Luis Valencia-Cabrera & Mario J. Pérez-Jiménez

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  1. Miguel A. Martínez-del-Amor
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  2. Luis F. Macías-Ramos
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  3. Luis Valencia-Cabrera
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  4. Mario J. Pérez-Jiménez
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Correspondence to Miguel A. Martínez-del-Amor.

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Martínez-del-Amor, M.A., Macías-Ramos, L.F., Valencia-Cabrera, L. et al. Parallel simulation of Population Dynamics P systems: updates and roadmap. Nat Comput 15, 565–573 (2016). https://doi.org/10.1007/s11047-016-9566-1

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