Neuroblastoma Stroma Classification on the Sony Playstation 3

1
Neuroblastoma Stroma Classification on theSony
Playstation 3

• Tim Hartley, Olcay Sertel, Mansoor Khan,
• Umit Catalyurek, Joel Saltz, Metin Gurcan
• Department of Biomedical Informatics
• The Ohio State University

2
The Cell BE processor

• Designed at IBM in conjunction with Toshiba and
  Sony (processor for the PS3)
• The Cell is a 9 core chip with a shared L2 cache
• One PowerPC (PPE) core
• Eight Synergistic Processing Elements (SPE)
• High performance I/O to support data-intensive
  applications

3
Cell BE parallelism

• Some image analysis algorithms are appropriate to
  be parallelized

• Levels of parallelism
• Instruction-level parallelism via 128-bit vector
  operations
• Thread-level parallelism via independent SPE
  processors
• CPU-level parallelism for extreme-scale problems

4
Image analysis on Cell

• Neuroblastoma
• Nerve cell cancer predominantly affecting
  children
• Microscope slides can be very large ( 40 GB)?
• One SPE equivalent to 2.13 GHz 64-bit Intel or
  AMD CPU for this application

5
Details of Cell port for analysis

• Algorithm overview
• Image partitioned into tiles
• RGB to LAB transformation
• LBP feature calculation
• Computationally expensive portions
• RGB to LAB transformation
• LBP feature calculation
• Two stages to Cell analysis pipeline
• RGB-LAB and color-space statistics
• LBP feature calculation

6
More details of Cell port

• Instruction-level parallelism
• Vector operations in pipeline stages
• Thread-level parallelism
• Multiple SPEs analyzing multiple tiles
  concurrently
• Dynamic scheduling of operations on SPEs
• CPU-level parallelism
• Use DataCutter to decouple tile I/O from analysis
• Tiles are read from storage node(s) and pushed to
  PS3(s)?

7
Algorithm workflow
Lab
Disabled (yield)
Reserved
8
Demo
9
Conclusion

• Performance in analysis of Neuroblastoma slides
• Up to 6 times faster than regular CPU with PS3
• Price/performance ratio is significantly better
  than regular CPU
• Sony and IBM encourage Linux-based development
  with official Software Development Kits (SDK),
  Linux OS installation support

PlayStation is a registered trademark of Sony
Computer Entertainment Inc.