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Large-Scale Simulations with FLAME

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Intelligent Agents in Data-intensive Computing

Part of the book series: Studies in Big Data ((SBD,volume 14))

Abstract

This chapter presents the latest stage of the FLAME developmentā€”the high-performance environment FLAME-II and the parallel architecture designed for Graphics Processing Units, FLAMEGPU. The architecture and the performances of these two agent-based software environments are presented, together with illustrative large-scale simulations for systems from biology, economy, psychology and crowd behaviour applications.

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References

  1. Luke, S., Cioffi-Revilla, C., Panait, L., Sullivan, K., Balan, G.: MASON: A multi-agent simulation environment. Simul: Trans. Soc. Model. Simul. Int. 82(7), 517ā€“527 (2005)

    ArticleĀ  Google ScholarĀ 

  2. North, M., Collier, N., Vos, J.: Experiences creating three implementations of the Repast agent modeling toolkit. ACM Trans. Model. Comput. Simul. 16(1), 1ā€“25 (2006). January

    ArticleĀ  Google ScholarĀ 

  3. Minar, N., Burkhart, R., Langton, C., Askenazi, M.: The Swarm simulation system: a toolkit for building multi-agent simulations. Working Paper 96-06-042, Santa Fe Institute (1996)

    Google ScholarĀ 

  4. Center for Connected Learning and Computer-Based Modeling: Northwestern University. NetLogo, Evanston, IL (1999)

    Google ScholarĀ 

  5. FLAME Website: http://www.flame.ac.uk (2013)

  6. Heath, B., Hill, R., Ciarallo, F.: A survey of agent-based modelling practices. J. Artif. Soc. Soc. Simul. 12, 9 (2009)

    Google ScholarĀ 

  7. Allan, R.: Survey of agent-based modelling and simulation tools. Technical Report DL-TR-2010-007, Science and Technology Facilities Council (2010)

    Google ScholarĀ 

  8. Weidlich, A., Veit, D.: A critical survey of agent-based wholesale electricity. Energy Econ. 30, 1728ā€“1759 (2008)

    ArticleĀ  Google ScholarĀ 

  9. LeitƤo, P.: Agent-based distributed manufacturing control: a state-of-the-art survey. Eng. Appl. Artif. Intell. 22, 979ā€“991 (2009)

    ArticleĀ  Google ScholarĀ 

  10. Friesen, M.R., McLeod, R.D.: A survey of agent-based modelling of hospital environments. IEEE Access 2, 227ā€“233 (2014)

    ArticleĀ  Google ScholarĀ 

  11. Sun, T., McMinn, P., Coakley, S., Holcombe, M., Smallwood, R., MacNeil, S.: An integrated systems biology approach to understanding the rules of keratinocyte colony formation. J. R. Soc. Interface 4, 1077ā€“1092 (2007)

    ArticleĀ  Google ScholarĀ 

  12. Adra, S., Sun, T., MacNeil, S., Holcombe, M., Smallwood, R.: Development of a three dimensional multiscale computational model of the human epidermis. PLoS ONE 5 (2010)

    Google ScholarĀ 

  13. Li, X., Upadhyay, A.K., Bullock, A.J., Dicolandrea, T., Xu, J., Binder, R.L., Robinson, M.K., Finlay, D.R., Mills, K.J., Bascom, C.C., Kelling, C.K., Isfort, R.J., Haycock, J.W., MacNeil, S., Smallwood, R.H.: Skin stem cell hypotheses and long term clone survivalā€”explored using agent-based modelling. Sci. Rep. 3 (2013)

    Google ScholarĀ 

  14. Burkitt, M., Walker, D., Romano, D., Fazeli, A.: Modelling sperm behaviour in a 3D environment, pp. 141ā€“149 (2011)

    Google ScholarĀ 

  15. Dawid, H., Gemkow, S., Harting, P., Neugart, M.: On the effects of skill upgrading in the presence of spatial labor market frictions: an agent-based analysis of spatial policy design. J. Artif. Soc. Soc. Simul. 12, 334ā€“347 (2009)

    Google ScholarĀ 

  16. van der Hoog, S., Deissenberg, C.: Energy shocks and macroeconomic stabilization policies in an agent-based macro model. In: Dawid, H., Semmler, W. (eds.) Computational Methods of Economics Dynamic. Dynamic Modeling and Econometrics in Economics and Finance, vol. 13, pp. 159ā€“181. Springer, Berlin Heidelberg (2010)

    ChapterĀ  Google ScholarĀ 

  17. Deissenberg, C., van der Hoog, S., Dawid, H.: EURACE: a massively parallel agent-based model of the European economy. Appl. Math. Comput. 204(2), 541ā€“552 (2008)

    ArticleĀ  MATHĀ  MathSciNetĀ  Google ScholarĀ 

  18. Richmond, P., Walker, D., Coakley, S., Romano, D.: High performance cellular level agent-based simulation with FLAME for the GPU. Briefing Bioinf. 11, 334ā€“347 (2010)

    ArticleĀ  Google ScholarĀ 

  19. Holcombe, M., Adra, S., Bicak, M., Chin, S., Coakley, S., Graham, A., Green, J., Greenough, C., Jackson, D., Kiran, M., MacNeil, S., Maleki-Dizaji, A., McMinn, P., Pogson, M., Poole, R., Qwarnstrom, E., Ratnieks, F., Rolfe, M., Smallwood, R., Sun, T., Worth, D.: Modelling complex biological systems using an agent-based approach. Integr. Biol. 4, 53ā€“64 (2012)

    ArticleĀ  Google ScholarĀ 

  20. Eilenberg, S.: Automata, Languages and Machines, vol. A. Academic Press, London (1974)

    MATHĀ  Google ScholarĀ 

  21. Holcombe, M.: Towards a formal description of intracellular biochemical organisation. Technical Report CS-86-1, Department of Computer Science, University of Sheffield, Sheffield, UK (1986)

    Google ScholarĀ 

  22. Laycock, G.: The theory and practice of specification based software testing. PhD thesis, Department of Computer Science, University of Sheffield, Sheffield, UK (1993)

    Google ScholarĀ 

  23. Holcombe, M., Ipate, F.: Correct Systemsā€”Building a Business Process Solution. Springer, Berlin (1998)

    Google ScholarĀ 

  24. Barnard, J., Whitworth, J., Woodward, M.: Communicating X-machines. Inf. Softw. Technol. 38(6), 401ā€“407 (1996)

    ArticleĀ  Google ScholarĀ 

  25. Balanescu, T., Cowling, A., Georgescu, H., Gheorghe, M., Holcombe, M., Vertan, C.: Communicating stream X-machines are no more than X-machines. J. Univ. Comput. Sci. 5(9), 494ā€“507 (1999)

    MATHĀ  MathSciNetĀ  Google ScholarĀ 

  26. Kefalas, P., Eleftherakis, G., Kehris, E.: Communicating X-machines: a practical approach for formal and modular specification of large systems. Inf. Softw. Technol. 45(5), 15ā€“30 (2003)

    ArticleĀ  Google ScholarĀ 

  27. Gheorghe, M., Holcombe, M., Kefalas, P.: Computational models of collective foraging. BioSyst. 61, 133ā€“141 (2001)

    ArticleĀ  Google ScholarĀ 

  28. Jackson, D., Gheorghe, M., Holcombe, M., Bernardini, F.: An agent-based behavioural model of monomorium pharaonis colonies. In: Proceedings of the 4th International Workshop on Membrane Computing. Lecture Notes in Computer Science, vol. 2933, pp. 232ā€“239 (2004)

    Google ScholarĀ 

  29. Holcombe, M., Holcombe, L., Gheorghe, M., Talbot, N.: A hybrid machine model of rice blast fungus, manaporthe grisea. BioSyst. 68, 223ā€“228 (2003)

    ArticleĀ  Google ScholarĀ 

  30. Coakley, S.: Formal software architecture for agent-based modelling in biology. PhD thesis, Department of Computer Science, University of Sheffield, Sheffield, UK (2007)

    Google ScholarĀ 

  31. Sakellariou, I.: Agent based modelling and simulation using state machines. In: 2nd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2012), pp. 270ā€“279 (2012)

    Google ScholarĀ 

  32. Sakellariou, I.: Turtles as state machinesā€”agent programming in NetLogo using state machines. In: 4th International Conference on Agents and Artificial Intelligence (ICAART 2012), pp. 235ā€“378 (2012)

    Google ScholarĀ 

  33. Sakellariou, I., Kefalas, P., Stamatopoulou, I.: Evacuation simulation through formal emotional agent based modelling. In: Proceedings of the 6th International Conference on Agents and Artificial Intelligence (ICAART 2014), SciTePress, pp. 193ā€“200 (2014)

    Google ScholarĀ 

  34. Hoops, S., Sahle, S., Gauges, R., Lee, C., Nimus, M., Singhal, M., Xu, L., Mendes, P., Kummer, U.: Copasiā€”a complex pathway simulator. Bioinformatics 22, 3067ā€“3074 (2006)

    ArticleĀ  Google ScholarĀ 

  35. Raymond, G.M., Butterworth, E.A., Bassingthwaighthe, J.B.: JSim: Mathematical modelling for organ systems, tissues, and cells. FASEB J 21, 736.5 (2007)

    Google ScholarĀ 

  36. Chin, S.: libmboard Reference Manual. 0.2.1 edn (2009) http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/107/222/libmboard-0.2.1-UserManual.pdf

  37. Richmond, P., Romano, D.: Template driven agent based modelling and simulation with CUDA. In: Hwu W.M (ed.) GPU Computing Gems Emerald Edition, pp. 313ā€“324, Morgan Kaufmann (2011)

    Google ScholarĀ 

  38. Richmond, P., Coakley, S., Romano, D.: A high performance agent based modelling framework on graphics card hardware with CUDA (extended abstract), pp. 1125ā€“1126 (2009)

    Google ScholarĀ 

  39. Coakley, S., Gheorghe, M., Holcombe, M., Chin, S., Worth, D., Greenough, C.: Exploitation of high performance computing in the FLAME agent-based simulation framework. In: Proceedings of the 14th International Conference on High Performance Computing and Communications, pp. 538ā€“545 (2012)

    Google ScholarĀ 

  40. Karmakharm, T., Richmond, P., Romano, D.: Agent-based large scale simulation of pedestrians with adaptive realistic navigation vector fields, pp. 67ā€“74 (2010)

    Google ScholarĀ 

  41. Coakley, S., Smallwood, R., Holcombe, M.: From molecules to insect communities ā€” how formal agent-based computational modelling is uncovering new biological facts. Mathematicae Japonicae Online e-2006: 765ā€“778 (2006)

    Google ScholarĀ 

  42. Pogson, M., Smallwood, R., Qwarnstrom, E., Holcombe, M.: Formal agent-based modelling of intracellular chemical interactions. BioSyst. 85, 37ā€“45 (2006)

    ArticleĀ  Google ScholarĀ 

  43. Pogson, M., Holcombe, M., Smallwood, R., Qwarnstrom, E.: Introducing spatial information into predictive NF-kB modellingā€”an agent-based approach. PLoS ONE 3, e2367 (2008)

    ArticleĀ  Google ScholarĀ 

  44. Maleki-Dizaji, S., Rolfe, M., Fisher, P., Holcombe, M.: A systematic approach to understanding bacterial responses to oxygen using Taverna and Webservices. In: Proceedings of 13th International Conference on Biomedical Engineering, pp. 77ā€“80 (2009)

    Google ScholarĀ 

  45. Walker, D., Wood, S., Southgate, J., Holcombe, M., Smallwood, R.: An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation. J. Theor. Biol. 242, 774ā€“789 (2006)

    ArticleĀ  MathSciNetĀ  Google ScholarĀ 

  46. Sun, T., McMinn, P., Holcombe, M., Smallwood, R., MacNeil, S.: Agent based modelling helps in understanding the rules by which fibroblasts support keratinocyte colony formation. PLoS ONE 3, e2129 (2008)

    ArticleĀ  Google ScholarĀ 

  47. Sun, T., Adra, S., MacNeil, S., Holcombe, M., Smallwood, R.: Exploring hypotheses of the actions of TGF-\(\beta \)1 in epidermal wound healing using a 3d computational multiscale model of the human epidermis. PLoS ONE 4, e8515 (2009)

    ArticleĀ  Google ScholarĀ 

  48. Jackson, D.E., Holcombe, M., Ratnieks, F.L.W.: Trail geometry gives polarity to ant foraging networks. Nature 432, 907ā€“909 (2004)

    ArticleĀ  Google ScholarĀ 

  49. Jackson, D.E., Martin, S.J., Ratnieks, F.L.W., Holcombe, M.: Spatial and temporal variation in pheromone composition of ant foraging trails. Behav. Ecol. 18, 444ā€“450 (2007)

    ArticleĀ  Google ScholarĀ 

  50. Holcombe, M., Coakley, S., Kiran, M., Chin, S., Greenough, C., Worth, D., Cincotti, S., Raberto, M., Teglio, A., Deissenberg, C., van der Hog, S., Dawid, H., Gemkow, S., Harting, P., Neugart, M.: Large-scale modelling of economic systems. Complex Syst. 22, 175ā€“191 (2013)

    Google ScholarĀ 

  51. Raberto, M., Teglio, A., Cincotti, S.: Credit money and macroeconomic instability in the agent-based model and simulator EURACE. Economics (2010).http://www.economics-ejournal.org/economics/discussionpapers/2010-4

  52. Corbett, A.: Agent-based modelling of transactive memory systems and knowledge processes in agile versus traditional software development teams. Ph.D. thesis, Department of Computer Science, University of Sheffield, Sheffield, UK (2012)

    Google ScholarĀ 

  53. Corbett, A., Wood, S., Holcombe, M.: Itā€™s the people stupid!ā€”Formal models for social interaction in agile software development teams. J. Adv. Soc. Sci. Res. 2(2):70ā€“85 (2015)

    Google ScholarĀ 

  54. Bakir, M.E., Ipate, F., Konur, S., Mierla, L., Niculescu, I.: Extended simulation and verification platform for kernel P systems, pp. 135ā€“152 (2014)

    Google ScholarĀ 

  55. Å¢urcanu, A., Mierlă, L., Ipate, F., Ştefănescu, A., Bai, H., Holcombe, M., Coakley, S.: Modelling and analysis of E. coli respiratory chain. In: Frisco, P., Gheorghe, M., PĆ©rez-JimĆ©nez, M.J. (eds.) Applications of Membrane Computing in Systems and Synthetic Biology. Emergence, vol. 7, pp. 247ā€“267. Complexity and Computation. Springer, Berlin Heidelberg (2014)

    Google ScholarĀ 

  56. Baqueiro, O., Wang, Y.J., McBurney, P., Coenen, F.: Integrating data mining and agent based modeling and simulation. In: Advances in Data Mining. Applications and Theoretical Aspects. Springer, pp. 220ā€“231 (2009)

    Google ScholarĀ 

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Acknowledgments

This work has been funded by EPSRC Grants EP/I030654/1 and EP/I030301/1 and the University of Sheffield Vice Chancellors Fellowship Scheme.

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Correspondence to Paul Richmond .

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Coakley, S. et al. (2016). Large-Scale Simulations with FLAME. In: Kołodziej, J., Correia, L., Manuel Molina, J. (eds) Intelligent Agents in Data-intensive Computing. Studies in Big Data, vol 14. Springer, Cham. https://doi.org/10.1007/978-3-319-23742-8_6

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  • DOI: https://doi.org/10.1007/978-3-319-23742-8_6

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