Abstract
In this paper we present a Spiking Neural P system (SNP system) simulator based on graphics processing units (GPUs). In particular we implement the simulator using NVIDIA CUDA enabled GPUs. The massively parallel architecture of current GPUs is very suitable for the maximally parallel computations of SNP systems. We simulate a wider variety of SNP systems, after presenting a previous work on SNP system matrix representation which led to their simulation in GPUs, and the simulation algorithm included here. Finally, we compare and present the performance speedups of the CPU-GPU based simulator over the CPU only simulator.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Cabarle, F., Adorna, H., Martínez-del-Amor, M.A.: Simulating Spiking Neural P systems without delays using GPUs. In: Proceedings of the 9th Brainstorming Week on Membrane Computing, Sevilla, Spain (February 2011)
Cabarle, F., Adorna, H., Martínez-del-Amor, M.A.: An Improved GPU Simulator For Spiking Neural P Systems. In: IEEE Sixth International Conference on Bio-Inspired Computing: Theories and Applications, Penang, Malaysia (September 2011), doi:10.1109/BIC-TA.2011.37
Cecilia, J.M., García, J.M., Guerrero, G.D., Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Simulation of P systems with active membranes on CUDA. Briefings in Bioinformatics 11(3), 313–322 (2010)
Cecilia, J.M., García, J.M., Guerrero, G.D., Martínez-del-Amor, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Simulating a P system based efficient solution to SAT by using GPUs. Journal of Logic and Algebraic Programming 79(6), 317–325 (2010)
Chen, H., Ionescu, M., Ishdorj, T.-O., Păun, A., Păun, G., Pérez-Jiménez, M.: Spiking neural P systems with extended rules: universality and languages. Natural Computing: an International Journal 7(2), 147–166 (2008)
Ciobanu, G., Wenyuan, G.: P Systems Running on a Cluster of Computers. In: Martín-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2003. LNCS, vol. 2933, pp. 123–139. Springer, Heidelberg (2004)
Díaz, D., Graciani, C., Gutiérrez, M.A., Pérez-Hurtado, I., Pérez-Jiménez, M.J.: Software for P systems. In: Păun, G., Rozenberg, G., Salomaa, A. (eds.) The Oxford Handbook of Membrane Computing, ch. 17, pp. 437–454. Oxford University Press, Oxford (2009)
Fatahalian, K., Sugerman, J., Hanrahan, P.: Understanding the efficiency of GPU algorithms for matrix-matrix multiplication. In: Proceedings of the ACM SIGGRAPH/EUROGRAPHICS Conference on Graphics Hardware (HWWS 2004), pp. 133–137. ACM, NY (2004)
Garland, M., Kirk, D.B.: Understanding throughput-oriented architectures. Communications of the ACM 53(11), 58–66 (2010)
Harris, M.: Mapping computational concepts to GPUs. In: ACM SIGGRAPH 2005 Courses, NY, USA (2005)
Ionescu, M., Păun, G., Yokomori, T.: Spiking Neural P Systems. Journal Fundamenta Informaticae 71(2,3), 279–308 (2006)
Kirk, D., Hwu, W.: Programming Massively Parallel Processors: A Hands on Approach, 1st edn. Morgan Kaufmann, MA, USA (2010)
Klöckner, A., Pinto, N., Lee, Y., Catanzaro, B., Ivanov, P., Fasih, A.: PyCUDA: GPU Run-Time Code Generation for High-Performance Computing, no. 2009-40. Scientific Computing Group, Brown University, RI, USA (2009)
Păun, G., Ciobanu, G., Pérez-Jiménez, M. (eds.): Applications of Membrane Computing. Natural Computing Series. Springer, Heidelberg (2006)
Nguyen, V., Kearney, D., Gioiosa, G.: A Region-Oriented Hardware Implementation for Membrane Computing Applications. In: Păun, G., Pérez-Jiménez, M.J., Riscos-Núñez, A., Rozenberg, G., Salomaa, A. (eds.) WMC 2009. LNCS, vol. 5957, pp. 385–409. Springer, Heidelberg (2010)
Zeng, X., Adorna, H., Martínez-del-Amor, M.Á., Pan, L., Pérez-Jiménez, M.J.: Matrix Representation of Spiking Neural P Systems. In: Gheorghe, M., Hinze, T., Păun, G., Rozenberg, G., Salomaa, A. (eds.) CMC 2010. LNCS, vol. 6501, pp. 377–391. Springer, Heidelberg (2010)
NVIDIA corporation, NVIDIA CUDA C programming guide, version 3.0. NVIDIA, CA, USA (2010)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Cabarle, F.G.C., Adorna, H., Martínez, M.A. (2012). A Spiking Neural P System Simulator Based on CUDA. In: Gheorghe, M., Păun, G., Rozenberg, G., Salomaa, A., Verlan, S. (eds) Membrane Computing. CMC 2011. Lecture Notes in Computer Science, vol 7184. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28024-5_8
Download citation
DOI: https://doi.org/10.1007/978-3-642-28024-5_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28023-8
Online ISBN: 978-3-642-28024-5
eBook Packages: Computer ScienceComputer Science (R0)