neuroblastoma stroma classification on the sony playstation 3 tim hartley, olcay sertel, mansoor...

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Neuroblastoma Stroma Classification on the Sony Playstation 3 Tim Hartley, Olcay Sertel, Mansoor Khan, Umit Catalyurek, Joel Saltz, Metin Gurcan Department of Biomedical Informatics The Ohio State University

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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

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    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

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    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

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    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

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    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

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    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)

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    Algorithm workflowDisabled(yield)ReservedLab

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    Demo

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    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.

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