Presentation of the Master thesis titled: "Cell Processor Based Sequence Alignment"

1. Miloš Bošković Cell Processor Based Sequence Alignment

2. Prof. Vassil Alexandrov Janko Straßburg University of Reading, Aristotle University, University Carlos III European Commission Acknowledgments

3. Sequence Alignment on the Playstation 3 Six SPEs Smith-Waterman Algorithm only Accelerating Multiple SequenceAlignment with the Cell BE Processor Designed to accelerate a particular sequence alignment application Modeling and SchedulingWavefront Computations on the Cell Broadband Engine Smith-Waterman Algorithm State of the art

4. Cell BroadBand Engine Cell Processor

5. SIMD approach Working with vectors Parallelisation Using multiple SPEs Cell Processor features

7. Used for aligning sequences of DNA nucleotides or amino acids (proteins)

9. Needleman-Wunsch Scoring matrix Each cell’s value is based on its upper, left, and upper-left neighbour Main issue – data dependencies Sequence Alignment

10. Traceback HEAGAWGHEE -PA--WHEAE Sequence Alignment

11. Main issue – data dependencies Parallelisation

12. Two possible approaches Use the existing code and modify it Develop the code from scratch Chose the latter one Code development

13. One SPE – one row Each SPE one cell behind the previous one Not efficient DMA overhead Potential solution

14. Grouping cells into tiles Tile size 8 X 8 up to 64 x 64 Solution

15. Tiles grouped into blocks Each block is 16 tiles high or more Algorithm first covers one block, then moves to the next one Solution

16. Wavefront algorithm also applied on the tile level One antidiagonal – one or more vectors Vectorisation

17. Always try to transfer as much as possible Maximum transfer allowed – 16 KB Integer size – 4 B If tile size is 64, the transfer size is 64 X 64 X 2 = 8192 X 4 = 32768 B Solution – short integers New transfer size - 64 X 64 X 2 = 8192 X 2 = = 16 384 B = 16 KB Technical issues

18. Double buffering

19. Each SPE – two tiles Double buffering

20. Results (8 KB sequence size)

21. It is possible to efficiently employ Cell Broadband Engine for Sequence alignment Further optimisation needed Reduction of context creations Inter-SPE communication Implementing sequence alignment across multiple pairs of sequences Using ALF – Accelerated Library Framework Conclusion

22. Thank you for your time!

23. Results (4 KB sequence size)

24. Results (2 KB sequence size)