1. 29/09/2008
Exploitation of Flexible Hardware Platforms for
Massively Parallel Bioinformatics Applications
Harald Devos, Ghent University
DSP Valley Academia-to-Business Forum – 2008-09-30 pag. 1
Zuiderpoort, Gent, Belgium
Moore’s law is slowing down
• Clock frequencies do not
increase anymore
• Computational
requirements keep
increasing
• Need to fully exploit
potential for parallel
computing
The FlexWare Project, IWT SBO 060068 pag. 2
DSP Valley Academia-to-Business Forum – 2008-09-30
Use parallel HW acceleration
• (Sequential) Software: ‘easy’ to write, easy
to adapt
• Hardware:
• Detection & exploitation of parallelism is difficult
• Hardware (re)design is expensive
• Need automatic hardware (re)generation!
The FlexWare Project, IWT SBO 060068 pag. 3
DSP Valley Academia-to-Business Forum – 2008-09-30
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2. 29/09/2008
General need for HW
acceleration
Massively parallel applications also in other
application domains:
 bioinformatics
 image and video processing
 scientific computing
 medical imaging and diagnosis
 speech processing
 visualization and rendering
 ...
The FlexWare Project, IWT SBO 060068 pag. 4
DSP Valley Academia-to-Business Forum – 2008-09-30
Parallel approaches
 General-purpose solutions:
 Coarse grain parallelism: multi-processor
(e.g., the Cell)
 Fine grain parallelism: SIMD, VLIW
 Dedicated solutions:
 custom design (ASIC, FPGA)
 Novel (research) platforms
The FlexWare Project, IWT SBO 060068 pag. 5
DSP Valley Academia-to-Business Forum – 2008-09-30
Research Questions
 Which level of parallelism for which
application?
 Communication and memory
requirements?
 Platform selection and design/mapping
support?
The FlexWare Project, IWT SBO 060068 pag. 6
DSP Valley Academia-to-Business Forum – 2008-09-30
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3. 29/09/2008
FlexWare approach
1. Analysis and extraction of fine grain (loop-
level) parallelism;
2. Analysis of strengths/weaknesses of
range of platforms
3. Automated support for platform selection
4. Design support for mapping application to
platform
The FlexWare Project, IWT SBO 060068 pag. 7
DSP Valley Academia-to-Business Forum – 2008-09-30
The FlexWare platforms
Flexible, parallel hardware platforms
FPGA: ADRES: Coarse VLIW: Ultra Wide DSP: special
Fine grain array Grain Array Register File purpose processor
Wide Scratch P rogra m Da t a
CLB CLB CLB Pad RAM RAM
Addr
In ter n al Bu s es
DMA
AGU Da t a
Regs (A 0-A 1 5)
Regs (B 0-B 1 5)
.D1 .D2 Ser. P ort
LD/ST
Ext erna l .M1 .M2 Hos t P ort
CLB CL CLB
VWR
VWR Mem ory .L1 .L2
VWR -Sync Boot Loa d
-As ync .S1 .S2 Tim ers
Cont rol Regs
P wr Down
CP U
SWP Compl Compl
Shifter x FU1 x FU2
The FlexWare Project, IWT SBO 060068 pag. 8
DSP Valley Academia-to-Business Forum – 2008-09-30
First testcase
Smith-Waterman sequence alignment
 quantify similarity between two character sequences
CGTCAGT CG——TCAGT
CGTCAGT || | | || ||
ACGAATC ACG——AATC ACGAATC
+5 Equal characters => positive score (match)
-2 Different characters => negative score (mismatch)
-3 Aligning character with gap => negative score (gap penalty)
CGTCAGT
|| | | = 5 + 5 – 3 – 3 + 5 – 2 + 5 = 12
ACG——AATC
CG——TCAGT
|| || = 5 + 5 – 3 – 3 + 5 + 5 = 14 = best!
ACGAATC
The FlexWare Project, IWT SBO 060068 pag. 9
DSP Valley Academia-to-Business Forum – 2008-09-30
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4. 29/09/2008
First results
 Comparison of Smith-Waterman
implementations
FPGA ADRES VLIW DSP
Speed ++ 0 -/+ 0
Power + + -/+ --
Design effort - 0 0 +
 Other trade-offs expected for other
applications
 Tests needed on other applications
The FlexWare Project, IWT SBO 060068 pag. 10
DSP Valley Academia-to-Business Forum – 2008-09-30
Project Consortium
Parallel Information Systems group (UGent)
• 40 people
• Techniques and methodology for (reconfigurable) HW design
Design Technology Group (IMEC)
• 150 people
• Novel processor architectures and mapping of applications onto them
Dekimo Products NV
• Ghent based engineering company
• 50 engineers
• Provides solutions for third party companies (intelligent electronics)
Bioinformatics & Evolutionary Genomics group (UGent)
• Gene and genome annotation
• Comparative and evolutionary genomics
The FlexWare Project, IWT SBO 060068 pag. 11
DSP Valley Academia-to-Business Forum – 2008-09-30
Current user group members
Design services and tools
Bioinformatics
Generic (technology development and other application)
More candidate members are welcome !
The FlexWare Project, IWT SBO 060068 pag. 12
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5. 29/09/2008
Open User Group Meeting
 Tuesday December 16th 2008
 Overview of the project
 Results until now
 Planning for the next two years
 Open to all interested companies
 More info will be available on
http://flexware.elis.ugent.be
The FlexWare Project, IWT SBO 060068 pag. 13
DSP Valley Academia-to-Business Forum – 2008-09-30
Contact Information
 Coordinator: Prof. Dirk Stroobandt
 Dirk.Stroobandt@UGent.be
Tel.: +32-9-2643401
Ghent University, ELIS/PARIS
Sint-Pietersnieuwstraat 41
B-9000 Gent, BELGIUM
 IWT SBO 060068
(Jan 2007 – Dec 2010)
 http://flexware.elis.ugent.be
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