High-throughput computing provides substantial time savings for landscape and conservation planning

Landscape and Urban Planning

Volumn 125, Issue , 2014, Pages 156-165

  Leonard, Paul B ^a   Baldwin, Robert F ^a   Duffy, Edward B ^a   Lipscomb, Donald J ^a   Rose, Adam M ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

Conservation planning; GIS; Grain size; High performance computing; High throughput computing; Scaling

Indexed keywords

CONSERVATION; DECISION SUPPORT SYSTEMS; ECOLOGY; GEOGRAPHIC INFORMATION SYSTEMS; GRAIN SIZE AND SHAPE; PLANNING; SUPERCOMPUTERS;

CONSERVATION PLANNING; GRAIN SIZE; HIGH PERFORMANCE COMPUTING; HIGH-THROUGHPUT COMPUTING; SCALING;

GRID COMPUTING;

COMPUTER SIMULATION; CONSERVATION PLANNING; DATA ASSIMILATION; DATA SET; DECISION SUPPORT SYSTEM; GIS; GRAIN SIZE; LANDSCAPE; NUMERICAL MODEL; REMOTE SENSING; SOFTWARE; URBAN PLANNING;

EID: 84898844645     PISSN: 01692046     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.landurbplan.2014.02.016     Document Type: Article

References (71)

1. Afgan E., Bangalore P. Embarrassingly parallel jobs are not embarrassingly easy to schedule on the grid. Workshop on many-task computing on grids and supercomputers, MTAGS 2008, 1-10.
2. Anderson M.G., Clark M., Sheldon O.A. Resilient sites for terrestrial conservation in the northeast and mid-Atlantic region 2012, The Nature Conservancy, Eastern Division.
3. Anderson M.G., Ferree C.E. Conserving the stage: Climate change and the geophysical underpinnings of species diversity. PLoS One 2010, 5(7):e11554.
4. Anderson M.G., Olivero A., Feree C., Morse D., Khanna S. Conservation status of the Northeastern U.S, and Maritime Canada 2006, The Nature Conservancy, Boston, MA.
5. Arc Advisory Group Esri has 40+% of GIS Marketshare 2010, Retrieved from. http://apb.directionsmag.com/entry/esri-has-40-of-gis-marketshare/215188.
6. Armstrong M.P., Cowles M.K., Wang S.W. Using a computational grid for geographic information analysis: A reconnaissance. Professional Geographer 2005, 57(3):365-375.
7. Armstrong M.P., Pavlik C.E., Marciano R. Parallel-processing of spatial statistics. Computers & Geosciences 1994, 20(2):91-104.
8. Arponen A., Lehtomaki J., Leppanen J., Tomppo E., Moilanen A. Effects of connectivity and spatial resolution of analyses on conservation prioritization across large extents. Conservation Biology 2012, 26(2):294-304.
9. Asner G.P., Hughes R.F., Vitousek P.M., Knapp D.E., Kennedy-Bowdoin T., Boardman J., et al. Invasive plants transform the three-dimensional structure of rain forests. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(11):4519-4523.
10. Baldwin R.F., Calhoun A.J.K., deMaynadier P.G. Conservation planning for amphibian species with complex habitat requirements: A case study using movements and habitat selection of the wood frog Rana sylvatica. Journal of Herpetology 2006, 40:443-454.
11. Beier P., Brost B. Use of land facets to plan for climate change: Conserving the arenas, not the actors. Conservation Biology 2010, 24(3):701-710.
12. Biggs D., Abel N., Knight A.T., Leitch A., Langston A., Ban N.C. The implementation crisis in conservation planning: Could "mental models" help?. Conservation Letters 2011, 4(3):169-183.
13. Brown J.H., Maurer B.A. Macroecology - The division of food and space among species on continents. Science 1989, 243(4895):1145-1150.
14. Calhoun A.J.K., Walls T.E., Stockwell S.S., McCollough M. Evaluating vernal pools as a basis for conservation strategies: A maine case study. Wetlands 2003, 23(1):70-81.
15. Carroll C., McRae B.H., Brookes A. Use of linkage mapping and centrality analysis across habitat gradients to conserve connectivity of gray wolf populations in western North America. Conservation Biology 2012, 26(1):78-87.
16. Crooks K.R., Sanjayan M.A. Connectivity conservation 2006, 712. Cambridge University Press, Cambridge, UK.
17. Dungan J.L., Perry J.N., Dale M.R.T., Legendre P., Citron-Pousty S., Fortin M.J., et al. A balanced view of scale in spatial statistical analysis. Ecography 2002, 25(5):626-640.
18. Faria S., Pendelberry S., Hawker J.S. ArcGIS in a high performance computing (HPC) virtual environment. ESRI international user conference proceedings 2010, Unpublished conference proceedings.
19. Graham S.L., Snir M., Patterson C.A. Getting up to speed. The future of supercomputing 2004, Report of National Research Council of the National Academies Sciences.
20. Groves C. Drafting a conservation blueprint. The nature conservancy 2003, 457. Island Press, Washington, DC.
21. Hauge Ø., Ayala C., Conradi R. Adoption of open source software in software-intensive organizations - A systematic literature review. Information and Software Technology 2010, 52(11):1133-1154.
22. Hortal J., Lobo J.M. An ED-based protocol for optimal sampling of biodiversity. Biodiversity and Conservation 2005, 14(12):2913-2947.
23. Huang F., Liu D., Tan X., Wang J., Chen Y., He B. Explorations of the implementation of a parallel IDW interpolation algorithm in a Linux cluster-based parallel GIS. Computers & Geosciences 2011, 37(4):426-434.
24. Huang Q., Yang C. Optimizing grid computing configuration and scheduling for geospatial analysis: An example with interpolating DEM. Computers & Geosciences 2011, 37(2):165-176.
25. Immanuel A., Berry M.W., Gross L.J., Palmer M., Wang D. A parallel implementation of ALFISH: Simulating hydrological compartmentalization effects on fish dynamics in the Florida Everglades. Simulation Modelling Practice and Theory 2005, 13(1):55-76.
26. Janssen R., Van Herwijnen M., Stewart T.J., Aerts J. Multiobjective decision support for land-use planning. Environment and Planning Design 2008, 35(4):740.
27. Johnson D.H. Validating and evaluating models. Modeling in natural resources management: Development, interpretation and application 2001, 105-119. Island Press, Washington, DC. T. Shenk, A.B. Franklin (Eds.).
28. Jørgensen S.E., Chon T.S., Recknagel F. Handbook of ecological modelling and informatics 2009, 448. Wit Press, Southampton, UK.
29. Juve G., Deelman E., Berriman G.B., Berman B.P., Maechling P. An evaluation of the cost and performance of scientific workflows on Amazon EC2. Journal of Grid Computing 2012, 10(1):5-21.
30. Knight A.T., Cowling R.M., Campbell B.M. An operational model for implementing conservation action. Conservation Biology 2006, 20(2):408-419.
31. Knight A.T., Cowling R.M., Rouget M., Balmford A., Lombard A.T., Campbell B.M. Knowing but not doing: Selecting priority conservation areas and the research-implementation gap. Conservation Biology 2008, 22(3):610-617.
32. Landguth E.L., Hand B.K., Glassy J., Cushman S.A., Sawaya M.A. UNICOR: A species connectivity and corridor network simulator. Ecography 2012, 35(1):9-14.
33. Legendre P., Borcard D., Peres-Neto P.R. Analyzing beta diversity: Partitioning the spatial variation of community composition data. Ecological Monographs 2005, 75(4):435-450.
34. Leonard P.B., Baldwin R.F., Homyack J.A., Wigley T.B. Remote detection of small wetlands in the Atlantic coastal plain of North America: Local relief models, ground validation, and high-throughput computing. Forest Ecology and Management 2012, 284:107-115.
35. Lipscomb D.J., Baldwin R.F. Geoprocessing solutions developed while calculating the mean Human Footprint™ for federal and state protected areas at the continent scale. Mathematical and Computational Forestry & Natural-Resource Sciences (MCFNS) 2010, 2(2):138-144.
36. Liu C., White M., Newell G., Griffioen P. Species distribution modelling for conservation planning in Victoria, Australia. Ecological Modelling 2012, 249(24):68-74.
37. Maeno T. PanDA: Distributed production and distributed analysis system for ATLAS. Journal of Physics: Conference Series 2008, 119:062036.
38. Margules C.R., Pressey R.L. Systematic conservation planning. Nature 2000, 405:243-253.
39. McRae B.H., Beier P. Circuit theory predicts gene flow in plant and animal populations. Proceedings of The National Academy of Sciences of the United States of America 2007, 104(50):19885-19890.
40. Mcrae B.H., Dickson B.G., Keitt T.H., Shah V.B. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 2008, 89(10):2712-2724.
41. Mellott L.E., Berry M.W., Comiskey E.J., Gross L.J. The design and implementation of an individual-based predator-prey model for a distributed computing environment. Simulation Practice and Theory 1999, 7(1):47-70.
42. Minor E.S., Lookingbill T.R. A multiscale network analysis of protected-area connectivity for mammals in the United States. Conservation Biology 2010, 24(6):1549-1558.
43. Mitsch W.J., Gosselink J.G. The value of wetlands: Importance of scale and landscape setting. Ecological Economics 2000, 35(1):25-33.
44. Moilanen A., Wilson K.A., Possingham H.P. Spatial conservation prioritization: Quantitative methods and computational tools 2009, Oxford University Press, New York.
45. Moilanen A.K., Ball I.R. Heuristic and approximate optimization methods for spatial conservation prioritization. Spatial conservation prioritization: Quantitative methods and computational tools 2009, 58-69. Oxford University Press, Oxford. A.K. Moilanen, K.A. Wilson, H.P. Possingham (Eds.).
46. Naughton-Treves L., Holland M.B., Brandon K. The role of protected areas in conserving biodiversity and sustaining local livelihoods. Annual Review of Environment and Resources 2005, 30(1):219-252.
47. Palmer M.W., White P.S. Scale dependence and the species-area relationship. American Naturalist 1994, 144(5):717-740.
48. Pierce S.M., Cowling R.M., Knight A.T., Lombard A.T., Rouget M., Wolf T. Systematic conservation planning products for land-use planning: Interpretation for implementation. Biological Conservation 2005, 125(4):441-458.
49. Porta J., Parapar J., Doallo R., Rivera F.F., Santé I., Crecente R. High performance genetic algorithm for land use planning. Computers, Environment and Urban Systems 2012, 38:45-58.
50. Reed M.S. Stakeholder participation for environmental management: A literature review. Biological Conservation 2008, 141(10):2417-2431.
51. Roberts J.J., Best B.D., Dunn D.C., Treml E.A., Halpin P.N. Marine geospatial ecology tools: An integrated framework for ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. Environmental Modelling & Software 2010, 25(10):1197-1207.
52. Rodrigues A.S., Andelman S.J., Bakarr M.I., Boitani L., Brooks T.M., Cowling R.M., et al. Effectiveness of the global protected area network in representing species diversity. Nature 2004, 428(6983):640-643.
53. Sanderson E.W., Jaiteh M., Levy M.A., Redford K.H., Wannebo A.V., Woolmer G. The human footprint and the last of the wild. Bioscience 2002, 52(10):891-904.
54. Scott J.M. Gap analysis: A geographic approach to protection of biological diversity. Wildlife Monographs 1993, 57(123):5-41.
55. Semlitsch R.D., Bodie J.R. Are small, isolated wetlands expendable?. Conservation Biology 1998, 12(5):1129-1133.
56. Seo C., Thorne J.H., Hannah L., Thuiller W. Scale effects in species distribution models: Implications for conservation planning under climate change. Biology Letters 2009, 5:39-43.
57. Sfiligoi I. glideinWMS - A generic pilot-based workload management system. Journal of Physics: Conference Series 2008, 119:062044.
58. Shah V.B., McRae B.H. Circuitscape: A tool for landscape ecology 2008, 62-66. G. Varoquaux, T. Vaught, J. Millman (Eds.).
59. Stewart T.J., Janssen R., van Herwijnen M. A genetic algorithm approach to multiobjective land use planning. Computers & Operations Research 2004, 31(14):2293-2313.
60. Theobald D.M. Estimating natural landscape changes from 1992 to 2030 in the conterminous US. Landscape Ecology 2010, 25(7):999-1011.
61. Theobald D.M., Reed S.E., Fields K., Soulé M. Connecting natural landscapes using a landscape permeability model to prioritize conservation activities in the United States. Conservation Letters 2012, 5(2):123-133.
62. Top 500 Supercomputer Sites. (2014). Retrieved from. http://www.top500.org/.
63. Tress B., Tress G. Scenario visualisation for participatory landscape planning - A study from Denmark. Landscape and Urban Planning 2003, 64(3):161-178.
64. Trombulak S.C. Assessing irreplaceability for systematic conservation planning. Landscape-scale conservation planning 2010, 303-324. Springer, Dordrecht. S.C. Trombulak, R.F. Baldwin (Eds.).
65. Trombulak S.C., Baldwin R.F. Creating a context for landscape-scale conservation planning. Landscape-scale conservation planning 2010, 1-16. Springer, Dordrecht. S.C. Trombulak, R.F. Baldwin (Eds.).
66. Urban D.L. Modeling ecological processes across scales. Ecology 2005, 86(8):1996-2006.
67. Wang S., Armstrong M.P. A quadtree approach to domain decomposition for spatial interpolation in Grid computing environments. Parallel Computing 2003, 29(10):1481-1504.
68. Wang S., Armstrong M.P. A theoretical approach to the use of cyberinfrastructure in geographical analysis. International Journal of Geographical Information Science 2009, 23(2):169-193.
69. Wang S., Cowles M.K., Armstrong M.P. Grid computing of spatial statistics: Using the TeraGrid for Gi*(d) analysis. Concurrency and Computation: Practice and Experience 2008, 20(14):1697-1720.
70. Woolmer G., Trombulak S.C., Ray J.C., Doran P.J., Anderson M.G., Baldwin R.F., et al. Rescaling the Human Footprint: A tool for conservation planning at an ecoregional scale. Landscape and Urban Planning 2008, 87(1):42-53.
71. Zedler P.H. Vernal pools and the concept of "isolated wetlands". Wetlands 2003, 23:597-607.