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Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 1, Iss. 2 — Sep. 1, 2010
  • pp: 658–675

Next-generation acceleration and code optimization for light transport in turbid media using GPUs

Erik Alerstam, William Chun Yip Lo, Tianyi David Han, Jonathan Rose, Stefan Andersson-Engels, and Lothar Lilge  »View Author Affiliations


Biomedical Optics Express, Vol. 1, Issue 2, pp. 658-675 (2010)
http://dx.doi.org/10.1364/BOE.1.000658


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Abstract

A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml).

© 2010 Optical Society of America

OCIS Codes
(170.3660) Medical optics and biotechnology : Light propagation in tissues
(170.5280) Medical optics and biotechnology : Photon migration
(170.7050) Medical optics and biotechnology : Turbid media
(290.4210) Scattering : Multiple scattering

ToC Category:
Image Reconstruction and Inverse Problems

History
Original Manuscript: July 9, 2010
Revised Manuscript: August 10, 2010
Manuscript Accepted: August 11, 2010
Published: August 23, 2010

Citation
Erik Alerstam, William Chun Yip Lo, Tianyi David Han, Jonathan Rose, Stefan Andersson-Engels, and Lothar Lilge, "Next-generation acceleration and code optimization for light transport in turbid media using GPUs," Biomed. Opt. Express 1, 658-675 (2010)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-1-2-658


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