neuroblastoma stroma classification on the sony playstation 3 tim hartley, olcay sertel, mansoor...
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Neuroblastoma Stroma Classification on theSony Playstation 3Tim Hartley, Olcay Sertel, Mansoor Khan, Umit Catalyurek, Joel Saltz, Metin Gurcan
Department of Biomedical InformaticsThe Ohio State University
The Cell BE processorDesigned at IBM in conjunction with Toshiba and Sony (processor for the PS3)The Cell is a 9 core chip with a shared L2 cacheOne PowerPC (PPE) coreEight Synergistic Processing Elements (SPE)High performance I/O to support data-intensive applications
Cell BE parallelismLevels of parallelismInstruction-level parallelism via 128-bit vector operationsThread-level parallelism via independent SPE processorsCPU-level parallelism for extreme-scale problemsSome image analysis algorithms are appropriate to be parallelized
Image analysis on CellNeuroblastomaNerve cell cancer predominantly affecting childrenMicroscope slides can be very large (> 40 GB)One SPE equivalent to 2.13 GHz 64-bit Intel or AMD CPU for this application
Details of Cell port for analysisAlgorithm overviewImage partitioned into tilesRGB to LAB transformationLBP feature calculationComputationally expensive portionsRGB to LAB transformationLBP feature calculationTwo stages to Cell analysis pipelineRGB->LAB and color-space statisticsLBP feature calculation
More details of Cell portInstruction-level parallelismVector operations in pipeline stagesThread-level parallelismMultiple SPEs analyzing multiple tiles concurrentlyDynamic scheduling of operations on SPEsCPU-level parallelismUse DataCutter to decouple tile I/O from analysisTiles are read from storage node(s) and pushed to PS3(s)
ConclusionPerformance in analysis of Neuroblastoma slidesUp to 6 times faster than regular CPU with PS3Price/performance ratio is significantly better than regular CPUSony and IBM encourage Linux-based development with official Software Development Kits (SDK), Linux OS installation supportPlayStation is a registered trademark of Sony Computer Entertainment Inc.