Efficient Implementation of a String Matching Algorithm for SRC and Cray Reconfigurable Computers

1
Efficient Implementation of a String Matching
Algorithm for SRC and Cray Reconfigurable
Computers

• Esam El-Araby1, Mohamed Taher1, Tarek
  El-Ghazawi1,
• Mohamed Abouellail1, Nandakishore Sastry2, and
  Kris Gaj2 1The George Washington
  University,2George Mason University

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Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

3
Introduction
4
Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

5
SRC Architecture(Hi-BarTM Based Systems)

• Hi-Bar sustains 1.4 GB/s per port with 180 ns
  latency per tier
• Up to 256 input and 256 output ports with two
  tiers of switch
• Common Memory (CM) has controller with DMA
  capability
• Controller can perform other functions such as
  scatter/gather
• Up to 8 GB DDR SDRAM supported per CM node

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SRC Reconfigurable Processor
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SRC Programming Environment
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SRC Programming Environment (cntd)
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SRC Programming Environment (cntd)
FPGA contents after the Function_1 call
Program in C or Fortran
Main program
Function_1
a

FPGA
Macro_1(a, b, c) Macro_2(b, d) Macro_2(c, e)
Function_1(a, d, e)
Macro_1

c
b
Function_2
Macro_2
Macro_2
Macro_3(s, t) Macro_1(n, b) Macro_4(t, k)
Function_2(d, e, f)
d
e

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Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

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Cray XD1 System Architecture(One Chassis)

• Compute
• 12 AMD Opteron 32/64 bit, x86 processors
• High Performance Linux
• RapidArray Interconnect
• 12 communications processors
• 1 Tb/s switch fabric
• Active Management
• Dedicated processor
• Application Acceleration
• 6 co-processors

FPGA and 2nd RAP are on Expansion Module
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Cray XD1 Application Acceleration Interfaces

• XC2VP30-50 running at up to 200 MHz
• 4 QDR II RAM  with over 400 HSTL-I I/O at 200 MHz
  DDR (400 MTransfers/s)
• 16 bit simplified HyperTransport I/F at 400 MHz
  DDR (800 MTransfers/s)
• QDR and HT I/F take up lt20 of XC2VP30.  The
  rest is available for user applications

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Cray XD1 Development Flow
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Cray XD1 Hardware Development Flow
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Design Methodology using Cray XD1

• Write application in C for system microprocessor
• Identify computation intense routine(s)
• Generate a bitstream using Cray Cores (RT
  QDRII) and language of choice
• Create module in HDL (Verilog, VHDL)
• Create module using High Level Language Tools
• Validate Module
• Synthesize using (XST, Leonardo, Synplify Pro)
• Create bitstream using Xilinx place route tools
• Replace routines with Cray API calls
• Run Application

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Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

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String Matching - Introduction

• String Matching detecting the occurrence of a
  particular substring, called the pattern, in
  another string, called the text
• Types of String matching
• Exact string matching
• Approximate string matching
• Exact string matching
• Involves match patterns, where they exist
  completely, that is unbroken and with no
  irrelevant data in between any letters
• Numerous Applications NIDS, text editing, etc.
• Approximate string matching
• Pattern rarely matches the text completely
• Finds application in Computational biology (DNA
  matching), image detection, handwriting
  recognitionetc.

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DNA Matching Basics

• Problem
• find the best pairwise alignment of GAATC and
  CATAC

• Why align two protein or DNA sequences?
• Determine whether they are descended from a
  common ancestor (homologous)
• Infer a common function
• Locate functional elements
• Infer protein structure, if the structure of one
  of the sequences is known

• We need a way to measure the quality of a
  candidate alignment
• Alignment scores consist of two parts
• substitution matrix
• gap penalty

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DNA Matching Basics (cntd)
Scoring aligned bases
Purine A G
Pyrimidine C T
Transversion (expensive)
GAAT-C CA-TAC
Transition (cheap)
-5 10 ? 10 ? 10 ?
Scoring gaps

• Linear gap penalty every gap receives a score of
  d

GAAT-C d-4 CA-TAC
-5 10 -4 10 -4 10 17

• Affine gap penalty opening a gap receives a
  score of d extending a gap receives a score of e

G--AATC d-4 CATA--C e-1
-5 -4 -1 10 -4 -1 10 5
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Approximate String Matching Algorithm(Smith-Water
man Algorithm)
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Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

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Implementation Schemes in SRC
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Operational Scenarios for Cray XD1
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Outline

• Introduction
• SRC Hardware Software
• Cray XD1 Hardware Software
• String Matching Algorithms
• Implementation Methodology
• Results and Comparisons
• Conclusions

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Performance Results

• Rate (FPGA freq.) X (cycles/cell) X ( SWPEs)
• Opteron Implementation (SSEARCH34)
• 100 Million Cell Updates Per Second (CUPS)
• Cray Inc. Implementation
• Current unoptimized design
• 80 MHz X 1 X 32 2.56 Billion CUPS (GCUPS)
• With optimization
• 100 MHZ x 1 x 50 5.0 GCUPS
• With future Virtex 4 FPGA
• 100 MHZ x 1 x 150 15 GCUPS
• 25x speedup vs. Opteron
• Our Implementation
• SRC-6
• Current unoptimized design
• 100 MHz X 1 X (16x16) 25.6 GCUPS
• 10x speedup vs. Cray
• 256x speedup vs. Opteron
• Cray XD1
• Current unoptimized design

CUG05, New Mexico, May 2005
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Conclusions

• Smith-Waterman sequence alignment algorithm has
  been implemented on both SRC-6 and Cray XD1
  systems
• Similarities and differences are highlighted with
  regard to
• System hardware architecture
• Ease of programming
• Programming model
• Development time
• Hardware/software libraries
• Performance
• The speed-up vs. microprocessor is reported
• Primary bottlenecks limiting the performance of
  both systems are recognized
• The capability to share and port applications
  between the SRC and Cray systems is explored