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Motivation & Related Work

Asynchronous Parallel Disk Sorting Roman Dementiev and Peter Sanders Max-Planck-Institut f ü r Informatik, Saarbr ücken, Germany Thanks to: A. Crauser, D. Hutchinson, L. Kettner, S. Mitra, A. Morton, N. Rajput, and J. Vitter. Motivation & Related Work. Sorting is important for EM problems

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Motivation & Related Work

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  1. Asynchronous Parallel Disk SortingRoman Dementiev and Peter SandersMax-Planck-Institut für Informatik,Saarbrücken, GermanyThanks to: A. Crauser, D. Hutchinson, L. Kettner, S. Mitra, A. Morton, N. Rajput, and J. Vitter R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  2. Motivation & Related Work • Sorting is important for EM problems • Disks are cheaper than computers • Prefetch buffers for load disk balancing and overlapping have been studied but no results which guarantee • overlapping during merging of runs • asymptotically optimal I/O volume • Here:algorithm & implementation • I/O cost lower bound • guarantees almost perfect overlapping between I/O and computation R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  3. Motivation & Related Work • [ChaudhryCormen’01’02] impl. of distributed memory, parallel disk • Theory: • Implementations: Differences: • Optimal prefetching algorithm • Overlapping of I/O and computation • Completely asynchronous implementation • Part of <stxxl> library, compatible with STL. Use as simple as: stxxl::vector<my_type> v; long long int i=vec_size; // ‘long long int’ is a 64-bit data type while(i--) v.push_back(f(i)); // fill vector with some values stxxl::sort(v.begin(), v.end()); // sort // check order using STL predicate assert(std::is_sorted(v.begin(), v.end())); [BarvGrovVit’97] [SandEgnKorst’00] [HutchVitt’01] [HutchSandVitt’02] [BarveVitter’99] Here [DementievSanders’03] R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  4. elements O(M) 1 D-head disk 2 input: chunk 0 chunk 1 chunk 2 chunk 3 chunk 4 chunk 5 chunk 6 chunk 7 chunk 8 … 3 D-head model k=O(M/B) k 4 D prefetch buffers D write buffers merge merge buffers ….. run 0 run 1 run 2 run 3 run 4 run 5 run 6 run 7 k D blocks merging buffers buffers B B B B B B B B k-merger k-merger B B run 0123 run 4567 … External Multi-way Merge Sort N – input size M – main memory size B – block size D – number of disks These algorithms do not guarantee overlapping R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  5. Multi-way Merge Sort with Overlapped I/Os Theorem 1: If I/O and computation can be overlapped, N elements can be sorted in time where is the time needed for run formation, is the time needed for merging k=(M/B) : # sequences, k’ = O(N/M): total # runs. R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  6. Overlapping Run Formation • Easy: Corollary 2: Input of size N => sorted runs of size ~ M/2 in time 2M in the paper run numbers time 3 1 2 4 k-1 k ... read sort write 2 3 4 k-1 k I/O bound case ... 1 1 2 3 4 k-1 k ... 1 2 3 4 k-1 k read sort write compute bound case 1 2 3 4 k-1 k 1 2 3 4 k-1 k R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  7. sort pairs <trigger,block_id> …. prediction sequence  : …. k-merger Simple External Merging • Smallest element of a block is a trigger merger k sorted runs …. R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  8. Overlapping I/O and Merging • Prediction of delay between issuing two reads is not easy: 1B-12 3B-14 5B-16 … merger 1B-12 3B-14 5B-16 … k … 1B-12 3B-14 5B-16 … R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  9. elements 1 D-head disk 2 3 4 D prefetch buffers D write buffers merge merge buffers ….. k D blocks merging elements 1 D-head disk 2 3 k+3D overlap buffers 4 D prefetch buffers 2D write buffers merge merge buffers ….. k D blocks merging Overlapping I/O and Merging • Prediction of delay between issuing two reads is not easy: • Solution: 2 3B-14 5B-16 … merger 2 3B-14 5B-16 … k … 2 3B-14 5B-16 … R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  10. Overlapping I/O and Merging [contd.] • Theorem 4:Merging k sequences with a total of N’ elements takes time • ℓ: time to produce one element of output • L: time to input or output D arbitrary blocks • Our I/O thread strategy: •  DB elements in write buffer => output step • < DB elements in write buffer AND D overlap buffers avail. => input step • To prove Theorem 4 we distinguish two cases • I/O bound case: 2L  DBℓ • Compute bound case: 2L< DBℓ R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  11. Compute Bound Case r kB+3DB • Lemma 6:In compute bound case after k/D+1 steps, the merging thread never blocks until all elements are merged. • Notation: •  # elem. in write buffer • r # of elem. in the overlap and merge buffers • Our I/O thread strategy: •  DB elements in write buffer => output step • < DB elements in write buffer AND D overlap buffers avail. => input step I/O blocking kB+2DB output fetch kB+DB kB+2 L/ℓ kB+y L/ℓ merge thread blocked kB  0 DB 2DB- L/ℓ 2DB R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  12. I/O Bound Case • Lemma 7:In I/O bound case the I/O thread never blocks until all input blocks are fetched. • Our I/O thread strategy (the same): •  DB elements in write buffer => output step • < DB elements in write buffer AND D overlap buffers avail. => input step • Proof: similar to compute bound case r kB+3DB kB+2DB+ L/ℓ blocking kB+2DB output kB+DB+ L/ℓ fetch kB+DB  kB+ L/ℓ 0 DB- L/ℓ DB 2DB- L/ℓ 2DB R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  13. elements … 1 … read buffers 2 … 3 k+O(D) overlap buffers … 4 O(D) prefetch buffers 2D write buffers merge ….. … merge buffers k D blocks merging -ping disk scheduling overlap- Multi-head Model  Multi-disk Model • Randomized Cyclic Allocation [VitHut’01] makes accesses in  balanced • Optimal prefetching from [HutchSanVitt’01,SanEgnKor’00] • Corollary 8:For any  > 0, prefetch buffer of size m=(D/) merging k sequences with a total N’ elements can be implemented to run in time R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  14. Applications Sorting, Priority queues, Search trees STL + more Caching, Mem. management Disk scheduling POSIX threads, File system OS Implementation Issues • Implementation (part of <stxxl> library) • Forming runs: Key sorting, efficient two passes MSD radix sort • Multi-way merging: [Sanders’00] • prefetch buffer + overlap buffer = read buffer • Asynchronous I/O (POSIX threads) • No superfluous copying • User blocks are transferred by DMA (O_DIRECT flag) • Buffers are passed by pointer between pools <stxxl> structure R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  15. Hardware 3000 Euro, 375 MByte/s, July 2002 R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  16. Single Disk Performance • LEDA-SM, TPIE • 2 GB volume, 32-bit keys, runs of size 256 MB, g++ 3.2 –O6 • I/O bandwidth 45.4 Mbyte/s = 95% of peak bandwidth of the disk R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  17. Multiple Disk Performance • 2 GB volume, 32-bit keys, runs of size 256 MB, g++ 3.2 –O6 • TPIE, LEDA-SM • Linux Soft-RAID 8X128KByte stripes • Bandwidth of 315 MByte/s R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  18. Element Size • 16GB volume, 32-bit keys, runs of size 256 MB, g++ 3.2 –O6 •  64  merging is I/O bound •  128  run formation is I/O bound • Small elements require special treatment R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  19. Optimal Prefetching 1 read buffers 2 3 k+O(D) overlap buffers 4 2D write buffers merge ….. … merge buffers k D blocks merging 1 read buffers 2 3 k+O(D) overlap buffers 4 O(D) prefetch buffers 2D write buffers merge ….. … merge buffers k D blocks merging R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  20. Block Size • Block sizes of several MB => good performance • Leave room for read and write buffers • Naive striping implies factor 8 block size reduction  Dramatic run time increase R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  21. Large Inputs • One-pass, curves go up because of • Slower zones • Seek times R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  22. Summary • Parallel disk sorting with high performance on state of art hardware with theoretical performance guarantees • Bandwidth is no longer a limiting factor for external memory algorithms • Price performance ratio can improve by adding disks R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

  23. ? R. Dementiev and P. Sanders: Asynchronous Parallel Disk Sorting

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