A2 Bforum P1 09 Ugent Harald Devos Flexware

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A2 Bforum P1 09 Ugent Harald Devos Flexware

  1. 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 1
  2. 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 2
  3. 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 3
  4. 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 DSP Valley Academia-to-Business Forum – 2008-09-30 4
  5. 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 The FlexWare Project, IWT SBO 060068 pag. 14 DSP Valley Academia-to-Business Forum – 2008-09-30 5

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