Cellular level agent based modelling on the graphics processing unit

HiBi09 - 2009 International Workshop on High Performance Computational Systems Biology

Volumn , Issue , 2009, Pages 43-50

  Richmond, Paul ^a   Coakley, Simon ^a   Romano, Daniela ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Agent based modelling; CUDA; GPU computing; Parallel computing; Scientific visualization

Indexed keywords

AGENT ARCHITECTURES; AGENT-BASED MODELLING; C LANGUAGE; CELLULAR FORCE; CELLULAR LEVELS; COMPUTE UNIFIED DEVICE ARCHITECTURES; DATA-PARALLEL ARCHITECTURES; EMERGING TECHNOLOGIES; GPU COMPUTING; GRAPHICS PROCESSING UNIT; KERATINOCYTES; MESSAGE COMMUNICATION; MODEL SPECIFICATIONS; MODELLING TECHNIQUES; NON-LINEAR; PARALLEL COMPUTING; PC GRIDS; PERFORMANCE GAIN; REAL TIME; SCIENTIFIC VISUALIZATIONS; SEQUENTIAL PROCESSING; SIMULATION PERFORMANCE; SIMULATION TIME; STEEP LEARNING CURVE; VISUALISATION;

BIOLOGY; PARALLEL ARCHITECTURES; PROGRAM PROCESSORS; VISUALIZATION;

COMPUTER GRAPHICS EQUIPMENT;

EID: 73449086319     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HiBi.2009.12     Document Type: Conference Paper

References (22)

1. Anderson, J., Lorenz, C. and Travesset, A. 2008. General purpose molecular dynamics simulations fully implemented on graphics processing units, Journal of Computational Physics 227 (2008) 5342-5359
2. Barnard, J., Whitworth, J., and Woodeard, M. 1996. Communicating X-Machines. Journal of Information and Software Technology, Vol 38. no. 6
3. Chiara, R., Erra, U., Scarano, V. and Tatafiore, M.2004. Massive Simulation using GPU of a distributed behavioural model of a flock with obstacle avoidance. In Proceedings of 9th International Fall Workshop Vision, Modelling, And Visualization
4. Coakley, S., Smallwood, R., and Holcombe, M. 2006. Using {X}-Machines as a Formal Basis for Describing Agents in Agent-Based Modelling, Proceedings of the 2006 Spring Simulation Multiconference, April 2006, pages 33-40.
5. D'Souza, R. M., Lysenko, M., and Rahmani, K. 2007. SugarScape on steroids: simulating over a million agents at interactive rates. Proceedings of Agent2007 conference. Chicago, IL
6. Eilenberg, S. 1974. Automata, Languages and Machines. volume A. Academic Press.
7. Green, S. 2007. CUDA Particles, NVIDIA Whitepaper, November 2007.
8. Harris, M., Coobe, G., Scheuermann, T., and Lastra, A. 2002. Physically-Based Visual Simulation on Graphics Hardware. In Procedings SIGGRAPH 2002 / Eurographics Workshop on Graphics Hardware 2002.
9. Harris, M., Sengupta, S., and Owens, J. 2007. Parallel Prefix Sum (Scan) with CUDA. GPU Gems 3. Chapter 39.
10. Howes, L. 2007. Loading Structured Data Efficiently With CUDA. NVIDIA Technical Report. http://developer.download.nvidia.com/compute/cuda/sdk/website/ projects/vectorLoads/doc/vectorLoads.pdf
11. Kipfer, P., Segal, M., and Westermann, R. 2004. UberFlow: a GPU-based particle engine. In Proceedings of the ACM SIGGRAPH/EUROGRAPHICS Conference on Graphics Hardware. Grenoble, France, August 29 - 30
12. NVIDIA Corporation. 2007. CUDA Programming Guide Version 2.0, http://www.nvidia.com/object/cuda-develop.html
13. Nyland, L., Harris, M., and Prins, Jan. 2007. Fast N-Body Simulation with CUDA, GPU Gems 3, Addison Wesley Professional, Chapter 31
14. Owens, J., Luebke, D., Govindaraju, N., Harris, M., Krüger, J., Lefohn, A., and Purcell, T. 2005. A Survey of General-Purpose Computation on Graphics Hardware. In Proceedings of Eurographics 2005, State of the Art Reports, pages 21-51
15. Richmond, P., Coakley, S. And Romano, D. 2009, A High Performance Agent Based Modelling Framework on Graphics Card Hardware with CUDA, Proc. of 8th Int. Conf. on Autonomous Agents and Multiagent Systems (AAMAS 2009), May, 10-15, 2009, Budapest, Hungary, in press.
16. Richmond, P., and Romano, D. 2008. Agent Based GPU, a Real-time 3D Simulation and Interactive Visualisation Framework for Massive Agent Based Modelling on the GPU. Proceedings of International Workshop on Supervisualisation 2008. Kos Island, Greece. June 2008.
17. th International Conference on Parallel and Distributed Systems. June 2005.
18. Stone, J., Phillips, J., Freddolino, P., Hardy, D., Trabuco, L. and Schulten. K. 2007. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry. 28:2618-2640
19. Sun, T., McMinn, P., Coakley, S., Holcombe, M., Smallwood, R., and MacNeil, S. 2006. Development and validation of an agent-based computational model of normal human keratinocytes organisation in vitro. European Cells and Materials, Volume 11, Number 3. Pages 28
20. Van der Vlist, E. 2002. XML Schema. O'Riley Media ISBN:0-596-00252-1. pages 197-223
21. Van Meel, J., Arnold, A., Frenkel, D., Zwart, S. and Belleman, R. 2008. Havesting graphics power for MD simulations. Molecular Simulation, Volume 34, Issue 3, p259-266
22. Walker, D., Hill, G., Wood, S., Smallwood, R. and Southgate, J. 2004. Agent-based computational modelling of wounded epithelial cell monolayers. IEEE Trans Nanobioscience 3:153-163