Large-scale agent-based modeling with repast HPC: A case study in parallelizing an agent-based model

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 9523, Issue , 2015, Pages 454-465

  Collier, Nicholson ^a,b   Ozik, Jonathan ^a,b   Macal, Charles M ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

Author keywords

ABMS; Agent based modeling; Distributed simulation; High performance computing; Parallel simulation; Repast HPC

Indexed keywords

APPLICATION PROGRAMMING INTERFACES (API); AUTONOMOUS AGENTS; SOFTWARE AGENTS;

ABMS; AGENT-BASED MODEL; DISTRIBUTED SIMULATIONS; HIGH PERFORMANCE COMPUTING; PARALLEL SIMULATIONS; REPAST HPC;

COMPUTATIONAL METHODS;

EID: 84951914669     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-27308-2_37     Document Type: Conference Paper

References (17)

1. Thiele, J.C., Kurth, W., Grimm, V.: Facilitating parameter estimation and sensitivity analysis of agent-based models: a cookbook using NetLogo and R. J. Artif. Soc. Soc. Simul. 17(3), 11 (2014)
2. https://gist.github.com/ncollier/8030c144c902cf803584
3. Macal, C.M., North, M.J., Collier, N.T., Dukic, V.M., Wegener, D.T., David, M.Z., Daum, R.S., Schumm, P., Evans, J.A., Wilder, J.R., Miller, L.G., Eells, S.J., Lauderdale, D.S.: Modeling the transmission of community-associated methicillin-resistant Staphylococcus aureus: a dynamic agent-based simulation. J. Transl. Med. 12, 124 (2014)
4. Chambers, H.F., Deleo, F.R.: Waves of resistance: Staphylococcus aureus in the antibiotic era. Nat. Rev. Microbiol. 7(9), 629-641 (2009)
5. Dukic, V.M., Lauderdale, D.S., Wilder, J., Daum, R.S., David, M.Z.: Epidemics of community-associated methicillin-resistant Staphylococcus aureus in the United States: a meta-analysis. PLoS One. 8(1), E52722 (2013)
6. Moran, G.J., Krishnadasan, A., Gorwitz, R.J., Fosheim, G.E., McDougal, L.K., Carey, R.B., Talan, D.A.: Methicillin-resistant S. aureus infections among patients in the emergency department. N. Engl. J. Med. 355(7), 666-674 (2006)
7. Klevens, R.M., Morrison, M.A., Nadle, J., Petit, S., Gershman, K., Ray, S., Harrison, L.H., Lynfield, R., Dumyati, G., Townes, J.M., Craig, A.S., Zell, E.R., Fosheim, G.E., McDougal, L.K., Carey, R.B., Fridkin, S.K.: Invasive methicillin-resistant Staphylococcus aureus infections in the United States. JAMA 298(15), 1763-1771 (2007)
8. Wheaton, W.D., Cajka, J.C., Chasteen, B.M., Wagener, D.K., Cooley, P.C., Ganapathi, L., Roberts, D.J., Allpress, J.L.: Synthesized Population Databases: A US Geospatial Database for Agent-Based Models. RTI Press, Durham (2009). Publication No MR-0010-0905
9. Ozik, J., Collier, N.T., Murphy, J.T., North, M.J.: The ReLogo agent-based modeling language. In: Proceedings Of The WSC 2013, Washington, D.C. 2013
10. Collier, N., North, M.: Parallel agent-based simulation with repast for high performance computing. Simulation 89(10), 1215-1235 (2012)
11. Instruments User Guide. https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/InstrumentsUserGuide/Introduction/Introduction.html. Accessed 1 Jun 2015
12. OpenMP specification home page. http://openmp.org. Accessed 1 Jun 2015
13. MPI standard official website. http://www.mcs.anl.gov/research/projects/mpi/index.htm. Accessed 1 Jun 2015
14. Karypis, G., Kumar, V.: A fast and highly quality multilevel scheme for partitioning irregular graphs. SIAM J. Sci. Comput. 20(1), 359-392 (1999)
15. METIS home page. http://glaros.dtc.umn.edu/gkhome/views/metis. Accessed 1 Jun 2015
16. Shende, S., Malony, A.D.: TAU: the TAU parallel performance system. Int. J. High Perform. Comput. Appl. 20(2), 287-311 (2006)
17. TAU home page, https://www.cs.uoregon.edu/research/tau/home.php. Accessed 1 Jun 2015