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Computation 2015, 3(1), 58-71;

Visual Simulation of Soil-Microbial System Using GPGPU Technology

SIMBIOS. School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
These authors contributed equally to this work.
Author to whom correspondence should be addressed.
Academic Editor: James Dyke
Received: 13 August 2014 / Accepted: 21 January 2015 / Published: 27 February 2015
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General Purpose (use of) Graphics Processing Units (GPGPU) is a promising technology for simulation upscaling; in particular for bottom–up modelling approaches seeking to translate micro-scale system processes to macro-scale properties. Many existing simulations of soil ecosystems do not recover the emergent system scale properties and this may be a consequence of “missing” information at finer scales. Interpretation of model output can be challenging and we advocate the “built-in” visual simulation afforded by GPGPU implementations. We apply this GPGPU approach to a reaction–diffusion soil ecosystem model with the intent of linking micro (micron) and core (cm) spatial scales to investigate how microbes respond to changing environments and the consequences on soil respiration. The performance is evaluated in terms of computational speed up, spatial upscaling and visual feedback. We conclude that a GPGPU approach can significantly improve computational efficiency and offers the potential added benefit of visual immediacy. For massive spatial domains distribution over GPU devices may still be required. View Full-Text
Keywords: General Purpose (use of) Graphics Processing Units (GPGPU); mathematical model; soil–microbe complex; X-Ray CT; reaction–diffusion General Purpose (use of) Graphics Processing Units (GPGPU); mathematical model; soil–microbe complex; X-Ray CT; reaction–diffusion

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Falconer, R.E.; Houston, A.N. Visual Simulation of Soil-Microbial System Using GPGPU Technology. Computation 2015, 3, 58-71.

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