Data-parallel techniques for agent-based tissue modeling on graphics processing units

Proceedings of the ASME Design Engineering Technical Conference

Volumn 3, Issue PARTS A AND B, 2008, Pages 57-64

  Richards, Ryan S ^a   Lysenko, Mikola ^a   D'Souza, Roshan M ^b   An, Gary ^c  

^a Michigan Technological University   (United States)

^b Michigan Technological University   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGENT BASED; AGENT-BASED MODEL; AGENT-BASED MODELING; BIOLOGICAL CELLS; BIOLOGICAL SIMULATION; CELL SYSTEM; CURRENT GENERATION; DATA PARALLEL; EMERGENT BEHAVIORS; EXPERIMENTAL STUDIES; GRAPHICS PROCESSING UNIT; IN-SILICO; INDIVIDUAL CELLS; INFLAMMATORY RESPONSE; LARGE-SCALE MODELS; MULTI-SCALE MODELING; NETLOGO; NOVEL ALGORITHM; POPULATION SIZES; PROBLEM SIZE; PROGRAMMABLE GRAPHICS PROCESSING UNIT; SIMULATION TOOLKITS; TEST CASE; THREE ORDERS OF MAGNITUDE; TISSUE MODELING;

ALGORITHMS; CELLS; COMPUTATIONAL METHODS; COMPUTER HARDWARE; DESIGN; MULTI AGENT SYSTEMS; PARALLEL PROCESSING SYSTEMS; POPULATION STATISTICS; PROGRAM PROCESSORS; REAL TIME SYSTEMS; TISSUE; TISSUE ENGINEERING;

MATHEMATICAL MODELS;

EID: 81155127385     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1115/DETC2008-49661     Document Type: Conference Paper

References (20)

1. Axelrod, R., 2005. Agent-based modeling as a bridge between disciplines. In Kenneth L. Judd and Leigh Tesfatsion (Eds.), Handbook of Computational Economics, Vol. 2: Agent-Based Computational Economics, Handbooks in Economics Series, North-Holland.
2. Christley, S. Madey, G. 2006. Abstract process model for systems biology. In Proceedings of the 2006 Agent-Directed Simulation Symposium, Huntsville, AL.
3. Gilbert, N., Bankes, S. 2002. Platforms and methods for agent-based modeling. PNAS, 99(3),71977198.
4. Railsback, S. F, Lytinen, S. L, and Jackson, S. K. 2006. Agent-based simulation platforms: review and development recommendations. SIMULATION, in press.
5. Massaioli, F., Castiglione, F., Bernaschi, M. 2005. OpenMP parallelization of agent-based models. OpenMP, 31(10-12),1068-1081.
6. Quinn, M. J., Metoyer, R., Hunter-Zaworski, K. 2003. Parallel implementation of the social forces model. In Proceedings of the Second International Conference in Pedestrian and Evacuation Dynamics (August 2003), 63-74.
7. Scheutz, M., Schermerhorn, P. 2006. Adaptive algorithms for dynamic distribution and parallel execution of agent-based models. Journal of Parallel and Distributed Computing, 66(8),1037-1051.
8. Logan, B., Theodoropoulos, G., (2001), The distributed simulation of multi-agent systems. In Proceedings of the IEEE, 89 (2),174186.
9. Lees, M., Logan, M., Oguara, T., Theodoropoulos, G. 2003. Simulating agent-based systems with HLA: The case of SIM AGENT part ii. In Proceedings of the 2003 European Simulation Interoperability Workshop, Stockholm, Sweden.
10. Harris, M., Coombe, G., Scgeuermann, T., and Lastra, A. 2002. Physically-based visual simulation on graphics hardware. In Proceedings Eurographics/SIGGRAPH Workshop on Graphics Hardware 2002.
11. A. Kolb, L. Latta, C. Rezk-Salama, Hardware-based simulation and collision detection for large particle systems, Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware, August 29-30, 2004, Grenoble, France
12. Millan, E. and Rudomin, I. 2006. Impostors and pseudo-instancing for GPU crowd rendering. In Proceedings of the 4th international Conference on Computer Graphics and interactive Techniques in Australasia and Southeast Asia (Kuala Lumpur, Malaysia, November 29 - December 02, 2006). GRAPHITE /06. ACM, New York, NY, 49-55. (Pubitemid 47113687)
13. Kessenich, J. 2006. The OpenGL Shading Language, http://www.opengl.org/ documentation/glsl/ (Feb 1, 2008)
14. D/Souza, R. M., Lysenko, M., Rahmani, K., 2007, SugarScape on steroids: simulating over a million agents at interactive rates, Proceedings of Agent2007 conference. Chicago, IL.
15. An, G. Agent-based computer simulation and sirs: building a bridge between basic science and clinical trials. Shock 16.4 (2001):266-73. (Pubitemid 33599113)
16. Resnick, M. 1996. StarLogo: an environment for decentralized modeling and decentralized thinking. In Conference Companion on Human Factors in Computing Systems: Common Ground (Vancouver, British Columbia, Canada, April 13 - 18, 1996). M. J. Tauber, Ed. CHI /96. ACM, New York, NY, 11-12.
17. An, G. 2007. NetLogo User Community Models: Toy Infection Model, http://ccl.northwestern.edu/netlogo/models/community/Toy-Infection-Model (Feb 1, 2008)
18. Chris J. Thompson, Sahngyun Hahn, Mark Oskin, "Using Modern Graphics Architectures for General-Purpose Computing: A Framework and Analysis," micro, p. 306, 35th Annual IEEE/ACM International Symposium on Microarchitecture (MICRO-35), 2002
19. Luebke, D., Harris, M., Krger, J., Purcell, T., Govindaraju, N., Buck, I., Woolley, C., and Lefohn, A. 2004. GPGPU: general purpose computation on graphics hardware. In ACM SIGGRAPH 2004 Course Notes (Los Angeles, CA, August 08 - 12, 2004). SIGGRAPH /04. ACM, New York, NY, 33.
20. Owens, J. 2007. Data-parallel algorithms and data structures. In ACM SIGGRAPH 2007 Courses (San Diego, California, August 05 - 09, 2007). SIGGRAPH /07. ACM, New York, NY, 3.