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Cache-Oblivious String Dictionaries Gerth Stlting Brodal University - PowerPoint PPT Presentation

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  1. ✩ ✥ ✖ ✚ ✑ ✠ ✌ ✛✜ ✘ ✢✣ ✣✤ ✘ ✌ ✁ ✄ ✖ ✏ ✠ ✁ ✄ ✁ ✘ ✦ ✖ ☛ ✏ ✄ ☛☞✌ ✠ ✠ ✡ ✟ ✁ ✍ ✎ ✁ ✆ ✟ ☞ ✏ ✁ ✑ ✞ ✄ ✆ ✒ ✁ Cache-Oblivious String Dictionaries Gerth Stølting Brodal University of Aarhus Joint work with Rolf Fagerberg �✂✁ ☎✝✆ ✓✕✔ ✞✕✗ ✓★✧ ✆✙✘

  2. ✙ ☎ ✒ ✓ ✔ ✗ ✘ ☞ ✓ � ✕ ✂ ✔ ☞ ✝ ✑ ✑ ✏ � ✡☛ ✠ ✟ � ☎ � Outline of Talk Cache-oblivious model Basic cache-oblivious techniques Cache-oblivious string algorithms Cache-oblivious string dictionaries – Cache-oblivious tries and blind tries ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  3. � ✒ ✓ ☎ ☞ ✘ ✗ ✔ ✔ ✓ ✑ ✕ ✏ ☞ ✝ ✡☛ ✠ ✟ ✑ ☎ ✂ Hierarchical Memory Models ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  4. ✤ ✑ ☛ ✌ ✁ ✖ ✘ ☞ ✑ ✣ ☎ ✟ ✠ ✡☛ ✏ ✒ ✕ ✓ ✔ ✗ ✘ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ ✍ ✂ ✎ ☛ ☛ ✝ ☞ ✌✍ ✎ ✏ ✠ ✆ ✔ ✑ ✍ ☛ ☎ ✂ ✞ ✌ ✎ ✎ ✒ ✄ ✂ ✁ � ✏ ✓ ✌ ✍ ✠ ✟✡✠ Hierarchical Memory ✗✛✚ ✗✙✜ ✗✛✢ ✗✙✘ ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  5. ✕ ✓ ✝ ☞ ✔ ✔ � ✂ ✔ ✕ � ☎ ✎ ☎ ☞ ✟ ✠ ✡☛ ✘ ✗ ✏ ✑ ✒ ✓ ✞ ✔ ☞ � ✁ ✂ ✑ ✝ ✞ ✟✠ ✡ ☛ ✌ ✏ ✍ ✎ ✞ ✏ ✑ ✟ ✒ ✒ ✟ ✑ ✓ I/O Model Aggarwal and Vitter 1988 ✄✆☎ = problem size = memory size = I/O block size One I/O moves consecutive records from/to disk Complexity measure = number of I/Os ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  6. ✠ ☞ � ✂ ✕ ✔ ✓ ☎ ☎ ✟ ✎ ✠ ✡☛ ✘ ✗ ✏ ✑ ✒ ✔ ☞ ✔ � � ✑ � ✝ � ✁ ✂ ✁ ✞ ✂ ✄ ☎ ☎ ✂ ☎ ✆ ✝ ✓ Ideal Cache Model — no parameters!? Frigo, Leiserson, Prokop, Ramachandran 1999 Program with only one memory Analyze in the I/O model for ✝ ✝✆ Optimal off-line cache replacement ✔ ✟✞ strategy arbitrary and ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  7. ✠ ✓ � � ✔ ☎ ✟ ✠ ✡☛ ✏ ✑ ✒ ✔ � ✗ ✘ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ � ✔ ✝ ✂ ✎ ☎ ✂ ☎ ☎ ✄ � ✁ ✞ � ✂ ✁ � � � ✔ ✆ Ideal Cache Model — no parameters!? Frigo, Leiserson, Prokop, Ramachandran 1999 Program with only one memory Analyze in the I/O model for ✝ ✝✆ Optimal off-line cache replacement ✔ ✟✞ strategy arbitrary and Advantages Optimal on arbitrary level optimal on all levels Portability, and not hard-wired into algorithm Dynamic changing (and ) ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  8. � ✒ ✓ ☎ ☞ ✘ ✗ ✔ ✔ ✓ ✑ ✕ ✏ ☞ ✝ ✡☛ ✠ ✟ ✑ ☎ ✂ Cache-Oblivious Preliminaries ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  9. ✄ ✟ ☎ ☞ ✘ ✗ ✂ ✔ ✓ ✒ ✑ ✏ ✔ ✓ ✡☛ ✠ ☞ ✕ ☛ ✔ � ✏ ✠ ☛ ✍ ✁ ☎ ✌ ✂ ✓ ✔ ✑ ✝ ✓ Cache-Oblivious Scanning I/Os ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  10. ✄ ✘ ✠ ✡☛ ✏ ✑ ✒ ✓ ✔ ✗ ☞ ✓ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ ✟ ☎ ✂ ✓ ✔ � ✏ ✠ ☛ ✍ ☛ ✁ ✌ ✂ ✔ � ✂ ✔ ✁ ✓ Cache-Oblivious Scanning I/Os Corollary Cache-oblivious selection requires I/Os Hoare 1961 / Blum et al. 1973 ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  11. ✓ ✗ ✟ ✠ ✡☛ ✏ ✑ ✒ ✓ ✔ ✘ ✁ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ � ☎ ✒ ✌✍ ✌ ✌ ✍ ☛ ✎✏ ✑ ✒ ☞ ☞ ✠✡ ✟ ☛ ✁ ✕ ✞ ✍ ✌ Cache-Aware B-trees ✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✁☎✁✂✁✄✆ ✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✁✂✁☎✁✄✝ ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  12. ✩ ✌ ✠ ☛ ✔ ☞ ✂ ☎ ✕ ✟ ✡☛ ✘ ✓ ☎ ✏ ✑ ✒ ✓ ✔ ☞ ✟ ✞ ✆ ✌ ✂ ✑ ✂ ✝ ☞ ✌ ✌ ✌ ✌ ✡ ✌ ✆ ✝ ✆ ✞ ✟ ✠ ✗ van Emde Boas layout Static Cache-Oblivious B-Tree � ✁� � ✁� Recursive layout of binary tree � ☎✄ � ☎✄ ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  13. ✩ ✓ ✔ ✓ ☎ ☞ ✘ ✗ ☞ ✔ ✒ ✂ ✑ ✏ ✝ ✑ ✡☛ ✠ ✟ ✩ ☎ ✕ Static Cache-Oblivious B-Tree ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  14. ✩ � ✩ ✑ ✝ ☞ ✔ ✂ ✕ ✓ ☎ ☞ ✘ ✗ ✔ ✓ ✟ � ✑ ✏ � ☎ ✡☛ ✒ ✠ Static Cache-Oblivious B-Tree ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  15. ✩ ✡☛ ✔ ✓ ☎ ☞ ✘ ✗ ☞ ✔ ✓ ✒ ✑ ✏ � ✝ ✠ ✂ � � � � � � � � ✟ � � � ✩ ☎ ✑ ✕ Static Cache-Oblivious B-Tree ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  16. ✩ ✒ � � � � � � ☎ ✟ ✠ ✡☛ ✏ ✑ ✓ � ✔ ✗ ✘ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ ✩ � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � Static Cache-Oblivious B-Tree ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  17. ✩ ✓ ✁ � ☎ ✓ � ✂ ✁ � ✄ � � ✂ ✁ � � ✔ ✟ � ✁ � ✂ ✓ ✁ ☞ ✩ ✑ ✝ ☞ ✔ ✂ ✕ ✓ ☎ ✘ ☎ ✗ ✔ ✓ ✒ ✑ ✏ ✡☛ ✠ ✟ ✄ ✂ ✂ � � ✔ � � � � � � � � � � � � � � � � � � � � � � � � � ✟ ✂ ✁ � � � � � � � � � � � � � � Static Cache-Oblivious B-Tree Each green tree has height between and Searches visit between and green trees, i.e. perform at most I/Os (misalignment) ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  18. ✙ ✓ ✁ ✂ ✄ ☎ ☎ ✟ ✠ ✡☛ ✏ ✑ ✒ ✔ ✔ ✗ ✘ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ ✩ � ✔ ✓ � ✂ � ✓ ✁ ✔ ✂ ✂ � � ✁ ✂ � ✓ ✂ � ✂ ✓ ✞ ✔ ✁ ✂ � ✁ Summary Cache-Oblivious Tools Scanning : B-tree searching : Sorting : requires a tall cache assumption Frigo, Leiserson, Prokop, Ramachandran 1999 Brodal and Fagerberg 2002, 2003 ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  19. � ✓ ✔ ✓ ☎ ☞ ✘ ✗ ☞ ✔ ✒ ✂ ✑ ✏ ✝ ✑ ✡☛ ✠ ✟ ✩ ☎ ✕ Cache-Oblivious String Algorithms ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

  20. ✤ � � � ✂ ✄ ✁ � ✄ ✂ � ✟ ☛ � ✍ ☛ � ✍ ☛ � ☎ ✠ ☛ ✓ ✩ ✑ ✝ ☞ ✔ ✂ ✕ ☎ ✡☛ ☞ ✘ ✗ ✔ ✓ ✒ ✑ ✏ ✍ � � ☛ ✍ ✍ ✍ ✍ ☛ ☛ � ☛ ✍ ☛ � � � ✍ � ✍ ☛ ☛ � ✍ � ☛ ✍ � ✍ ☛ � ✂ ✁ � ☛ � � ✍ ☛ � ✍ ☛ Knuth-Morris-Pratt String Matching Knuth, Morris, Pratt 1977 Time Scans text left-to-right Accesses the pattern (and failure function) like a stack ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  21. ✤ ✂ ✁ ✄ ✁ � ✄ ✂ � � � ✄ ✂ ✁ � ✄ ✂ � � ☛ ✍ ☛ � ✔ ☎ � ☎ ✩ ✑ ✝ ☞ ✔ ✂ ✕ ✓ ☞ ✟ ✘ ✗ ✔ ✓ ✒ ✑ ✏ ✡☛ ✠ ✍ � ☛ ☛ ✍ ✁ ✍ � � ✍ ☛ ✍ ☛ ☛ ✍ � ☛ ☛ � � � ☛ � ✍ ✍ � ✍ ☛ � ✍ ✍ � ☛ � ✍ � ☛ � ✍ ✂ ☛ � ☛ ☛ ✍ � Knuth-Morris-Pratt String Matching Knuth, Morris, Pratt 1977 Time Scans text left-to-right Accesses the pattern (and failure function) like a stack KMP is cache-oblivious and uses I/Os ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  22. ✕ ✔ � ✂ ☎ ✟ ✠ ✡☛ ✏ ✑ ✒ ✓ ✗ ✁ ✘ ☞ ☎ ✓ ✕ ✂ ✔ ☞ ✝ ✑ ✩ ✂ ✓ ✁ � � Suffix Tree/Suffix Array Construction Farach et al. 2000 a b c dacabab$ $ abacdacabab$ b c a $ abab$ dacabab$ a $ abab$ dacabab$ b$ cdacabab$ b$ cdacabab$ aabacdacabab$ Reduces to sorting, i.e. I/Os ✁✄✂ ✆✞✝ ☞✍✌ ☞✞✎ ☞✖✕ ☞✞✎

  23. ✠ ☎ ✩ ✑ ✝ ☞ ✔ ✂ ✕ ✓ ☎ ☞ ✘ ✗ ✔ ✓ ✒ ✑ ✏ ✡☛ ✠ ✟ ☞✞✎ ☞✖✕ ☞✞✎ ☞✍✌ ✆✞✝ ✁✄✂

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