Ecological models on GPUs

With the help of Rohit Gupta and Quan-Xing Liu, I have in the past years been implementing my models on the graphics processors (GPUs) that sit in many computers. These processors are much better suited to run spatially-explicit models then is the computer’s main processor (CPU). I have been using NVidia’s CUDA in the past, I explained in the paper:

Johan van de Koppel, Rohit Gupta, and Cornelis Vuik. “Scaling-up spatially-explicit ecological models using graphics processors.” Ecological Modelling 222.17 (2011): 3011-3019.

In the past year, I have been switching from CUDA to OpenCL. The reason is that OpenCL can more generally be used on many graphics cards, while CUDA is proprietary and works only on (expensive) NVidia cards.

Below I provide OpenCL codes for the models that I or my students have published in the past years. These codes are presented on my Github page: http://johanvandekoppel.github.io

Self-organization of mussel beds into banded patterns


If you use the model or code, please cite:
Van de Koppel, J., Rietkerk, M., Dankers, M. & Herman, P.M.J. 2005 Scale-dependent feedback and regular spatial patterns in young mussel beds. The American Naturalist 165:E66-E77.

Self-organized pattern formation in arid vegetation


If you use the model or code, please cite:
Rietkerk, M., Boerlijst, M.C., Van Langevelde, F., HilleRisLambers, R., Van de Koppel, J., Kumar, L., Klausmeier, C.A., Prins, H.H.T., De Roos, A. 2002. Self-organisation of vegetation in arid ecosystems. The American Naturalist, 160:524-530.

Mussel aggregation leads to phase separation


If you use the model or code, please cite:
Liu, Q-X, Doelman, A., Rottschäfer, V., De Jager, M., Herman, P.M.J., Rietkerk, M., and Van de Koppel, J. 2013. Phase separation explains a new class of self-organized patterns in ecological systems. Proc. Natl. Acad. Sci. USA, 110 (29): 11905-11910.

Spiral wave formation in a spatial predator-prey model