Abstract
This paper presents a new approach to parallelize spatially-explicit structured ecological models. Previous investigations have mainly focused on the use of spatial decomposition for parallelization of these models. Here, we exploit the partitioning of species’ age structures (or layers) as part of an integrated ecosystem simulation on a high-end shared memory computer using OpenMP. As an example, we use a parallel spatially-explicit structured fish model (ALFISH) for regional ecosystem restoration to demonstrate the parallelization procedure and associated model performance evaluation. Identical simulation results, validated by a comparison with a sequential implementation, and impressive parallel model performance demonstrate that layer-wised partitioning offers advantages in parallelizing structured ecological models on high-end shared memory computers. The average execution time of the parallel ALFISH model, using 1 computational thread, is about 11 hours, while the execution of the parallel ALFISH model using 25 computational threads is about 39 minutes (the speedup factor being about 16).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
ATLSS: Across Trophic Level System Simulation., http://www.atlss.org
Gross, L., DeAngelis, D.: Multimodeling: New Approaches for Linking Ecological Models. In: Scott, J.M., Heglund, P.J., Morrison, M.L. (eds.) Predicting Species Occurrences: Issues of Accuracy and Scale, pp. 467–474 (2002)
Gaff, H., DeAngelis, D., Gross, L., Salinas, R., Shorrosh, M.: A Dynamic Landscape Model for Fish in the Everglades and its Application to Restoration. Ecological Modeling 127, 33–53 (2000)
Wolff, W.F.: An Individual-Oriented Model of a Wading Bird Nesting Colony. Ecological Modelling 114, 72–75 (1994)
Curnutt, J.L., Comiskey, E.J., Nott, M.P., Gross, L.J.: Landscape-based spatially explicit species index models for Everglade restoration. Ecological Applications 10, 1849–1860 (2000)
Wang, D., Gross, L., Carr, E., Berry, M.: Design and Implementation of a Parallel Fish Model for South Florida. In: Proceedings of the 37th Annual Hawaii International Conference on System Sciences (HICSS 2004) (2004), http://csdl.computer.org/comp/proceedings/hicss/2004/2056/09/205690282c.pdf
Immanuel, A., Berry, M., Gross, L., Palmer, M., Wang, D.: A parallel Implementation of ALFISH: Compartmentalization Effects on Fish Dynamics in the Florida Everglades. Simulation Practice and Theory 13(1), 55–76 (2005)
Wang, D., Berry, M., Carr, E., Gross, L.: A Parallel Fish Landscape Model for Ecosystem Modeling. Simulation: Transactions of the Society of Modeling and Simulation International 82(7), 451–465 (2006)
OpenMP: Simple, Portable, Scalable SMP Programming, http://www.openmp.org
Fennema, R., Neidrauer, C., Johnson, R., MacVicar, T., Perkins, W.: A Computer Model to Simulate Everglades Hydrology. In: Davis, S.M., Ogden, J.C. (eds.) Everglades: The Ecosystem and Its Restoration, pp. 249–289. St. Lucie Press (1994)
Gaff, H., Chick, J., Trexler, J., DeAngelis, D., Gross, L., Salinas, R.: Evaluation of and insights from ALFISH: a spatial-explicit, landscape-level simulation of fish populations in the Everglades. Hydrobiologia vol. 520, pp. 73–87 (2004)
U.S. Army Corps of Engineers, C & SF Restudy Draft Feasibility Report (accessed, November 17, 1998), http://www.restudy.org/overview.pdf
Wang, D., Carr, E., Palmer, M., Berry, M., Gross, L.: A Grid Service Module for Natural Resource Managers. IEEE Internet Computing 9(1), 35–41 (2005)
Wang, D., Carr, E., Ecomiske, J., Plamer, M., Berry, M., Gross, L.: Grid Computing for Regional Ecosystem Restoration., http://www.sc-conference.org/sc2004-/schedule/index.php?module=Default&action=ShowDetail&eventid=131
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wang, D., Berry, M.W., Gross, L.J. (2008). A Parallel Structured Ecological Model for High End Shared Memory Computers. In: Mueller, M.S., Chapman, B.M., de Supinski, B.R., Malony, A.D., Voss, M. (eds) OpenMP Shared Memory Parallel Programming. IWOMP 2005. Lecture Notes in Computer Science, vol 4315. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68555-5_9
Download citation
DOI: https://doi.org/10.1007/978-3-540-68555-5_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-68554-8
Online ISBN: 978-3-540-68555-5
eBook Packages: Computer ScienceComputer Science (R0)