Transforming Irregular Algorithms for Heterogeneous Computing - Case Studies in Bioinformatics

Transcription

1 Trasformig Irregular lgorithms for Heterogeeous omputig - ase Studies i ioiformatics Jig Zhag dvisor: Dr. Wu Feg ollaborator: Hao Wag syergy.cs.vt.edu

2 Irregular lgorithms haracterized by Operate o irregular data structures - trees, graphs, liked lists, priority queues Data are processed i variable-iteratio loops oth memory access ad cotrol flow are irregular ad upredictable Emergig data itesive applicatios have icreasig irregularity i memory access ad cotrol flow over massive data set ioiformatics applicatios Huma geome:. billio letters (. Gb) Social etwork aalysis, graph algorithms Twitter (Jue-Dec 9) - millio users, millio tweets (Gb) syergy.cs.vt.edu

3 Heterogeeous omputig Systems Heterogeeous computig systems ca offer massively parallel computatio with high power efficiecy ad throughput GPU, MD PU Itel Xeo Phi FPG, DSP, ut, desiged for regular programs, relyig o data locality ad regular computatio to tolerate access latecies Thousads of smaller (weak), more efficiet (simple) cores Limited cache size, i.e., short cache lie lifetimes syergy.cs.vt.edu

4 Heterogeeous omputig Systems Heterogeeous computig systems ca offer massively parallel computatio with high power efficiecy ad throughput GPU, MD PU Itel Xeo Phi FPG, DSP, ut, desiged for regular programs, relyig o data locality ad regular computatio to tolerate access latecies Thousads It is of very smaller challegig (weak), more to efficiet map irregular (simple) cores, which are lack of brach predictio, out-of-order executio, etc. algorithms o heterogeeous computig systems! Limited cache size, i.e., short cache lie lifetimes syergy.cs.vt.edu

5 Impacts of Irregularity o GPU Performace Irregular cotrol flow rach divergece Occurs whe threads iside warps braches to differet executio paths Waste computatioal resource rach Path Path Wilso Fug, Iva Sham, George Yua, Tor amodt, Dyamic Warp Formatio ad Schedulig for Efficiet GPU otrol Flow, micro syergy.cs.vt.edu

6 Impacts of Irregularity o GPU Perf (cot d) Irregular memory access Ucoalesced memory access Lower memory bus utilizatio Warp Warp 8 8 Oe segmets sigle 8-byte trasactio oalesced Memory ccess ross N segmets N -byte trasactio Ucoalesced Memory ccess syergy.cs.vt.edu

7 Irregular lgorithms Optimizatios o GPU Irregular cotrol flow Kerel fissio Sortig work Warp-cetric executio... Irregular memory access Memory access reorderig Exploitig memory hierarchy Data structure adaptatio... syergy.cs.vt.edu

8 ase Study: Mappig LSTp o GPU* LST - asic Local ligmet Search Tool Fid most similar sequeces from database for a query sequece Use heuristic algorithms, which have sigificat irregularities i both memory access ad cotrol flow P is for protei sequece; N is for ucleotide sequece *: J. Zhag, H. Wag, H. Li, W. Feg, culstp: Fie-Graied Parallelizatio of Protei Sequece Search o a GPU, IPDPS 8 syergy.cs.vt.edu

9 LST lgorithm Subject Sequece (database) Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio Query Sequece 9 syergy.cs.vt.edu

10 LST lgorithm Query Sequece Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio syergy.cs.vt.edu

11 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio oe oe, Lookup Table Query Sequece syergy.cs.vt.edu

12 LST lgorithm query positio, subject positio Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio oe oe, Lookup Table Query Sequece,,,, syergy.cs.vt.edu

13 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio,, Query Sequece, distace < threshold, syergy.cs.vt.edu

14 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio, Query Sequece, syergy.cs.vt.edu

15 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio, Query Sequece X, syergy.cs.vt.edu

16 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio, Query Sequece X, syergy.cs.vt.edu

17 LST lgorithm Subject Sequece Four stages i LST. Hit detectio. Ugapped extesio. Gapped extesio. Fial extesio, Query Sequece X Kowledge: seed-ad-exted the most widely used aligmet paradigm, syergy.cs.vt.edu

18 State-of-the-rt GPU LST pproaches* Use ituitive parallelizatio - coarse-graied parallelizatio, where a thread compares the query sequece to a subject sequece Thread Thread Thread Thread... Subject Seq Subject Seq Subject Seq Subject Seq... Query Sequece *: Desig ad Implemetatio of a UD-compatible GPU-based ore for Gapped LST lgorithm (IS ) GPU- LST: Usig Graphics Processors to ccelerate Protei Sequece ligmet UD-LSTP (iformatics) UD-LSTP: cceleratig LSTP o UD-eabled Graphics Hardware (T) cceleratig Protei Sequece Search i a Heterogeeous omputig System. (IPDPS ) 8 syergy.cs.vt.edu

19 hallege #: otrol Flow Irregularity With coarse-graied parallelism, differet threads may execute across differet stages Warp Subject sequece Hit detectio Thread Thread Thread Thread subject_seq subject_seq subject_seq subject_seq No hit Hit foud Hit foud & distace < No hit Ugapped extesio extesio Divergece 9 syergy.cs.vt.edu

20 Solutio: Kerel Fissio Split hit detectio ad ugapped extesio stage ito separate kerels Use itermediate kerels to bridge the two stages syergy.cs.vt.edu

21 hallege #: otrol Flow Irregularity () oarse-graied extesio, where a thread is resposible for a diagoal, ca result i divergece, sice differet diagoals could be exteded to differet legths Thread Thread Thread Oe thread per diagoal syergy.cs.vt.edu

22 Solutio: Warp-cetric Extesio Map a warp of threads to oe diagoal Threads i a warp checks differet positios cocurretly Warp Warp Warp Warp-based Extesio syergy.cs.vt.edu

23 hallege #: Memory ccess Irregularity Use a global array, called lasthit rray, to record the previous hit i each diagoal Subject Sequece Query Sequece LastHit rray - syergy.cs.vt.edu

24 hallege #: Memory ccess Irregularity Read LastHit rray to get last hit positio i the diagoal Write back curret positio to lasthit rray Query Sequece Thread, - Subject Sequece WR Operatio Positio Read Write syergy.cs.vt.edu

25 hallege #: Memory ccess Irregularity Read LastHit rray to get last hit positio i the diagoal Write back curret positio to lasthit rray Query Sequece Thread,, - Subject Sequece WR Operatio Positio Read Write Read - Write - syergy.cs.vt.edu

26 hallege #: Memory ccess Irregularity Read LastHit rray to get last hit positio i the diagoal Write back curret positio to lasthit rray Query Sequece Thread,,, - Subject Sequece WR Operatio Read Positio Write Read - Write - Read Write syergy.cs.vt.edu

27 hallege #: Memory ccess Irregularity Read LastHit rray to get last hit positio i the diagoal Write back curret positio to lasthit rray Query Sequece Thread,,,, - Subject Sequece WR Operatio Read Positio Write Read - Write - Read Write Read Write syergy.cs.vt.edu

28 hallege #: Memory ccess Irregularity Irregular Read/Write Ops o LastHit array Thread Irregular Memory ccess Subject Sequece Operatio Positio Query Sequece,,,, Read Write Read - Write - Read Write Read Write 8 - syergy.cs.vt.edu

29 Solutio: Memory ccess Reorderig ollect ad group hits by diagoal umbers via biig Threads Subject Sequece Query Sequece,,,, iig is, Out-of-order,, 9 -, syergy.cs.vt.edu

30 Solutio: Memory ccess Reorderig Sort hits by positios i each bi Threads,,,, iig is,,, Sort is,,, -, -, syergy.cs.vt.edu

31 Solutio: Memory ccess Reorderig Filter out o-exteable hits by distace of adjacet hits Threads,,,, iig is,,, Sort X, X, is, Filter, is -, -, syergy.cs.vt.edu -

32 Threads Solutio: Memory ccess Reorderig Trasform a irregular algorithm (lasthit array method) ito three regular phases,, Regular read, irregular write,, iig -,,, is Regular memory access, Sort - X, X,, is, Filter, is syergy.cs.vt.edu -

33 Performace Numbers ompared to origial versio, culstp has... Less brach divergece overhead % 8% % % % % culstp - Hit Detectio culstp - Hit Filterig Origial The lower the better culstp rach Divergece Overhead* The higher the better culstp Occupacy chieved culstp - Hit Sortig culstp - Ugapped Extesio The higher the better culstp Global Load Efficiecy *: rach Divergece Overhead: the ratio of diverget executio to total executio syergy.cs.vt.edu

34 Performace Numbers ompared to origial versio, culstp has... Less brach divergece overhead etter occupacy % 8% % % % % culstp - Hit Detectio culstp - Hit Filterig Origial The lower the better culstp rach Divergece Overhead* The higher the better culstp Occupacy chieved culstp - Hit Sortig culstp - Ugapped Extesio The higher the better culstp Global Load Efficiecy *: rach Divergece Overhead: the ratio of diverget executio to total executio syergy.cs.vt.edu

35 Performace Numbers ompared to origial versio, culstp has... Less brach divergece overhead etter occupacy etter load efficiecy % 8% % % % % culstp - Hit Detectio culstp - Hit Filterig Origial The lower the better culstp rach Divergece Overhead* The higher the better culstp Occupacy chieved culstp - Hit Sortig culstp - Ugapped Extesio The higher the better culstp Global Load Efficiecy *: rach Divergece Overhead: the ratio of diverget executio to total executio syergy.cs.vt.edu

36 Speedup With swissprot database, culstp achieves Up to.-fold speedup of hit detectio ad ugapped extesio over GPU-LSTP, which is the fastest GPU-based LST Up to.-fold overall speedup over GPU-LSTP (culstp has parallelizatio of the rest of stages) query query query Speedup of Hit Detectio & Ugapped Extesio query query query Overall Speedup syergy.cs.vt.edu

37 oclusio ad Future Work oclusio Mappig irregular algorithms to heterogeeous system is o-trivial, eed couples of trasformatio ad adaptio o algorithms ad data structures ut these cocepts of trasformatios are propagable Kerel fissio, memory access reorderig, warp-cetric executio, Future Work Geeralize optimizatios from culstp for differet algorithms ad other heterogeeous systems Desig a library for irregular algorithms with optimized irregular data structure ad operatios syergy.cs.vt.edu

38 Other Research Topics Optimizig W (urrows Wheeler ligmet) o multicore PU ad Itel Xeo Phi dbblast: database idex based LST o multicore PU ad Itel Xeo Phi Dyamic parallelism o MD PU (New) Optimizig irregular applicatios for GPU/Xeo Phi clusters (Future) Other Research Iterests loud computig MapReduce with accelerators 8 syergy.cs.vt.edu