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Journal of Biomedical Optics • Open Access

Monte Carlo simulation of photon migration in a cloud computing environment with MapReduce
Author(s): Guillem Pratx; Lei Xing

Paper Abstract

Monte Carlo simulation is considered the most reliable method for modeling photon migration in heterogeneous media. However, its widespread use is hindered by the high computational cost. The purpose of this work is to report on our implementation of a simple MapReduce method for performing fault-tolerant Monte Carlo computations in a massively-parallel cloud computing environment. We ported the MC321 Monte Carlo package to Hadoop, an open-source MapReduce framework. In this implementation, Map tasks compute photon histories in parallel while a Reduce task scores photon absorption. The distributed implementation was evaluated on a commercial compute cloud. The simulation time was found to be linearly dependent on the number of photons and inversely proportional to the number of nodes. For a cluster size of 240 nodes, the simulation of 100 billion photon histories took 22 min, a 1258 × speed-up compared to the single-threaded Monte Carlo program. The overall computational throughput was 85,178 photon histories per node per second, with a latency of 100 s. The distributed simulation produced the same output as the original implementation and was resilient to hardware failure: the correctness of the simulation was unaffected by the shutdown of 50% of the nodes.

Paper Details

Date Published: 1 December 2011
PDF: 10 pages
J. Biomed. Opt. 16(12) 125003 doi: 10.1117/1.3656964
Published in: Journal of Biomedical Optics Volume 16, Issue 12
Show Author Affiliations
Guillem Pratx, Stanford Univ. School of Medicine (United States)
Lei Xing, Stanford Univ. School of Medicine (United States)

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