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04SAAHPCpresentationScalableSystolicArray

04SAAHPCpresentationScalableSystolicArray - Reconfigurable...

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SAAHPC’ 10 Reconfigurable Supercomputing with  Scalable Systolic Arrays and In-Stream  Control for Wavefront Genomics Processing Tuesday, July 13, 2010 C. Pascoe (speaker), A. Lawande H. Lam, A. George NSF Center for High-Performance Reconfigurable Computing (CHREC), University of Florida Y. Sun, W. Farmerie Interdisciplinary Center for Biotechnology Research University of Florida M. Herbordt Department of Electrical and Computer Engineering, Boston University
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2 Motivation n Impending roadblock in health-sciences research q Current-generation sequencing technology capable of producing millions of sequences per day q Next-generation sequencing instruments poised to increase production more than 10-fold n Conventional sequence-analysis processing has not kept pace with raw sequence production Objective: Develop sustainable solution for increasing performance of sequence-analysis applications Approach: Develop in-stream control approach for systolic array to maximize hardware acceleration Capitalize on reconfigurable computing at scale to achieve sustainable supercomputing performance
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3 Presentation Outline q Background n Sequential Score Calculation n Backtrack to Produce String Representation n Sequence-Alignment Acceleration n Common Hardware Acceleration Techniques q Scalable Systolic Arrays with In-Stream Control q Novo-G System Architecture n GiDEL PROCStar-III Boards q NW/SW/ND Performance Evaluation on Novo-G q Conclusions q Q&A
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4 Background: Sequence-Alignment Example Sequence S1 : ACGGCTAACTG Sequence S2 : GGCCCAACTGCGGGT n Want to quantify similarity between S1 and S2 n Use NW or SW or other algorithms to align sequences Needleman-Wunsch Equations max 1 , max 1 ) 1 , ( ) 1 , ( ) , 1 ( ) , 1 ( ) , ( ) 1 , 1 ( max ) , ( j j i i for e j i V eog j i S e j i H eog j i S j i Sub j i S j i S + - + - + - + - + - - = matrix penalty j i Sub og i V i H eg i og i S i S eg j i V og j i S j i V eg j i H og j i S j i H = = = + = = + - + - = + - + - = ) , ( ) 0 , ( ) , 0 ( ) 0 , ( ) , 0 ( ) 1 , ( ) 1 , ( max ) , ( ) , 1 ( ) , 1 ( max ) , (
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5 Sequential Score Calculation Score Calculation --- match = 5, mismatch = -4, ogap = -10, egap = -0.5 -17 -16.5 -16 -15.5 -15 -14.5 -14 -13.5 -13 -12.5 -12 -11.5 -11 -10.5 -10 -15 -14.5 -14 -13.5 -13 -12.5 -12 -11.5 -11 -10.5 -10 0 2.5 -3 -8.5 -18.5 -12 -2 -16.5 -22 -27.5 -24 -20.5 T 3 -2.5 -8 -8.5 -14.5 -11 -7 -12.5 -18 -23.5 -20 G 3.5 -2 -7.5 -14.5 -4.5 -10.5 -7 -3 -17.5 -23 -19.5 G 4 -1.5 -7 -20 -10.5 -0.5 -6.5 -12 -8 -22.5 -19 G 4.5 -1 -6.5 -10.5 -16 -6.5 3.5 -11.5 -17 -13 -18.5 C 14.5 -0.5 -6 -16.5 -6.5 -12 -8.5 -1.5 -7.5 -13 -18 G -0.5 9.5 -5.5 -13 -12.5 -2.5 -8 -13.5 -6.5 -12.5 -17.5 T -7 -6.5 4.5 -9 -14.5 -11 -7.5 -13 -12.5 -2.5 -17 C -13 -12.5 -3.5 -0.5 -5 -10.5 -7 -12.5 -21 -11 -7.5 A -9.5 -9 -8.5 1.5 -5.5 -10 -6.5 -12 -14 -17 -7 A -14.5 -5.5 -6 -13.5 -3.5 -9.5 -6 -11.5 -13.5 -10 -15.5 C -20 -10.5 -1.5 -10 -9.5 0.5 -5.5 -11 -13 -9.5 -15 C -14 -16 -6.5 -6.5 -6 -5.5 4.5 -10.5 -12 -9 -14.5 C -4 -12.5 -12 -11.5 -11 -10.5 -10 -0.5 -9 -8 -14 G -9.5 -9 -8.5 -8 -7.5 -7 -6.5 -6 -5.5 -14 -4 G G T C A A T C G G C A S1 S2
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6 Backtrack to Produce String Representation _ T _ G T G _ _ _ G C G G G T T G _ T G C G G G T V V V H D D D D D D V T V V D V V D D D D D V G V V H D V V D D D D V G V V D H D V V D D D V G V V D D H D V D D D V C V V H D D V D D V D V G H V H H D V V D V D V T H H D D V V V H D D V C D D D D V V V H D D V A H H H D V V V D H D V A D D D H D V V D D V V C D D D H H V
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  • Spring '08
  • Staff
  • Systolic array, Reconfigurable computing, Scalable Systolic Arrays, Stratix-III E260 FPGAs, Software Runtime

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