Computer Architecture and Automated Design Lab

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Recent publications

 
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  • A.Mahram and M.C. Herbordt (2014): NCBI BLASTP on High Performance Reconfigurable Computing Systems, ACM Transactions on Reconfigurable Technology and Systems, TBD(TBD), pp. TBD.
  • B. Humphries, H. Zhang, J. Sheng, R. Landaverde, and M.C. Herbordt (2014): 3D FFT on a Single FPGA, Proceedings of the IEEE Symposium on Field Programmable Custom Computing Machines (FCCM 2014), pp. TBD.
  • B. Sukhwani and M.C. Herbordt (2014): Increasing Parallelism and Reducing Thread Contentions in Mapping Localized N-body Simulations to GPUs, in Numerical Computations with GPUs, V. Kindratenko, editor, Springer Verlag, pp. TBD.
  • M.C. Herbordt and M.A. Khan (2013): FPGA-Accelerated Molecular Dynamics, in High Performance Computing Using FPGAs, K. Benkrid and W. Vanderbauwhede, editors, Springer Verlag, pp. 105-135.
  • A. Mahram and M.C. Herbordt (2013): NCBI BLASTP on the Convey HC1-EX, Proceedings of the 4th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies. (HEART 2013)
  • M.C. Herbordt (2013): Architecture/Algorithm Codesign of Molecular Dynamics Processors, Proceedings of the Asilomar Conference on Signals, Systems, and Computers (ASSC 2013)
  • B. Humphries and M.C. Herbordt (2013): 3D FFT for FPGAs, Proceedings of the IEEE High Performance Extreme Computing Conference (HPEC 2012)
  • A. Mahram and M.C. Herbordt(2012): CAAD BLASTP 2.0: NCBI BLASTP Accelerated with Pipelined Filters, Proceedings of the IEEE Conference on Field Programmable Logic and Applications (FPL 2012), pp. 217-22.
  • M.A. Khan and M.C. Herbordt (2012): Communication Requirements for FPGA-Centric Molecular Dynamics, Proceedings of the Symposium on Application Accelerators for High Performance Computing (SAAHPC 2012)
  • A. Mahram and M.C. Herbordt (2012): FMSA: FPGA-Accelerated ClustalW-Based Multiple Sequence Alignment Through Pipelined Prefiltering, Proceedings of the IEEE Symposium on Field Programmable Custom Computing Machines (FCCM 2012), pp. 177-183.
  • M.A. Khan, C. Hankendi, A.K. Coskun, M.C. Herbordt (2011): Application Level Optimizations for Energy Efficiency and Thermal Stability, Proceedings of High Performance Embedded Computing (HPEC 2011)
  • M.A. Khan, C. Hankendi, A.K. Coskun, M.C. Herbordt (2011): Software Optimization for Performance, Energy, and Thermal Distribution: Initial Case Studies, Proceedings of Thermal Modeling and Management: Chips to Data Centers (TEMM 2011), pp. 1-6
  • M.A. Khan and M.C. Herbordt (2011): Parallel Discrete Molecular Dynamics Simulation With Speculation and In-Order Commitment, Journal of Computational Physics, (accepted) 230 (17), pp. 6563-6582.
  • M. Chiu, M.A. Khan, M.C. Herbordt (2011): Efficient Calculation of Pairwise Nonbonded Forces, Proceedings of IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2011)
  • C. Pascoe, A. Lawande, H. Lam, A. George, Y. Sun, W. Farmerie, M. Herbordt (2010): Reconfigurable Supercomputing with Scalable Systolic Arrays and In-Stream Control for Wavefront Genomics Processing, Proceedings of the Symposium on Application Accelerators for High Performance Computing (SAAHPC10)
  • M. Chiu and M.C. Herbordt (2010): Towards Production FPGA-Accelerated Molecular Dynamics: Progress and Challenges, Proceedings of High Performance Reconfigurable Computing Technology and Applications (HPRCTA10)
  • Atabak Mahram and M.C. Herbordt (2010): Fast and Accurate NCBI BLASTP: Acceleration with Multiphase FPGA-Based Prefiltering, Proceedings of the 24th International Conference on Supercomputing (ICS 2010)
  • J.H. Park, Y. Qiu and M.C. Herbordt (2010): CAAD BLASTn: Accelerated NCBI BLASTn with FPGA Prefiltering, Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS 2010)
  • B. Sukhwani and M.C. Herbordt (2010): Fast Binding Site Mapping using GPUs and CUDA, Proceedings of the Ninth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2010) (Technical report TR2010_1)
  • M. Chiu and M.C. Herbordt (2010): Molecular Dynamics Simulations on High Performance Reconfigurable Computing Systems, ACM Transactions on Reconfigurable Technology and Systems (ACM-TRETS) 3 (4), pp. 23:1-23:37.
  • B. Sukhwani and M.C. Herbordt (2010): FPGA Acceleration of Rigid-Molecule Docking Codes, IET Computers & Digital Techniques (IET-CDT) 4(3), pp. 184-195
  • B. Sukhwani and M.C. Herbordt (2009): FPGA-based Acceleration of CHARMM-potential Minimization, Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA 2009)
  • B. Sukhwani, M. Chiu, Md. Ashfaquzzaman Khan and M.C. Herbordt (2009): Effective Floating Point Applications on FPGAs: Examples from Molecular Modeling, Proceedings of High Performance Embedded Computing (HPEC 2009)
  • M. Chiu and M.C. Herbordt (2009): Efficient Particle-Pair Filtering for Acceleration of Molecular Dynamics Simulation, Proceedings of International Conference on Field Programmable Logic and Applications (FPL 2009) (Winner of Best Paper award)
  • B. Sukhwani and M.C. Herbordt (2009): Accelerating Energy Minimization using Graphics Processors, Proceedings of Symposium on Application Accelerators in High Performance Computing (SAAHPC 2009)
  • M.C. Herbordt, B. Sukhwani, M. Chiu and Md. Ashfaquzzaman Khan (2009): Production Floating Point Applications on FPGAs, Proceedings of Symposium on Application Accelerators in High Performance Computing (SAAHPC 2009)
  • M.C. Herbordt, Md. Ashfaquzzaman Khan and T. Dean (2009): Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition, Proceedings of IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009)
  • J.H. Park, Y. Qiu and M.C. Herbordt (2009): CAAD BLASTP: NCBI BLASTP Accelerated with FPGA-Based Pre-Filtering, Proceedings of IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2009)
  • T. VanCourt and M.C. Herbordt (2009): Elements of High Performance Reconfigurable Computing, Advances in Computers, v75, pp. 113-157; Marvin Zelkowitz, editor; Elsevier, Inc.
  • B. Sukhwani and M.C. Herbordt (2009): GPU Acceleration of a Production Molecular Docking Code, Proceedings of the Second Workshop on General-Purpose Computation on Graphics Processing Units (GPGPU 2009), ACM International Conference Proceeding Series, v383, pp. 19-27, 2009.
  • M. Chiu, M. C. Herbordt, and M. Langhammer (2008): Performance Potential of Molecular Dynamics Simulations on High Performance Reconfigurable Computing Systems, Proceedings of International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA 2008)
  • M. C. Herbordt, Y. Gu, T. VanCourt, J. Model, B. Sukhwani, and M. Chiu (2008): Computing Models for FPGA-Based Accelerators, Computing in Science & Engineering, 10 (6), pp. 35-45.
  • T. Dean, J. Model and M.C. Herbordt (2008): Multicore versus FPGA in the Acceleration of Discrete Molecular Dynamics, Proceedings of High Performance Embedded Computing (HPEC 2008)
  • B. Sukhwani and M.C. Herbordt (2008): Acceleration of a Production Rigid Molecule Docking Code, Proceedings of International Conference on Field Programmable Logic and Applications (FPL 2008), September 2008
  • M.C. Herbordt, Y. Gu, T. VanCourt, J. Model, B. Sukhwani, M. Chiu (2008): Computing Models for FPGA-Based Accelerators with Case Studies in Molecular Modeling, Proceedings of the Reconfigurable Systems Summer Institute (RSSI 2008), July 2008
  • Y. Gu, T. VanCourt, M.C. Herbordt (2008): Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations, Parallel Computing, 34 (4-5), pp. 261-271. Special issue on Best Papers From the Reconfigurable Systems Summer Institute (RSSI)
  • M.C. Herbordt, F. Kosie and J. Model (2008): An Efficient O(1) Priority Queue for Large FPGA-Based Discrete Event Simulations of Molecular Dynamics, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2008)
  • M.C. Herbordt, J. Model, B. Sukhwani, Y. Gu, Tom VanCourt (2007): Single Pass Streaming BLAST on FPGAs, Parallel Computing, 33 (2007), pp. 741-756. Special issue on High-Performance Computing Using Accelerators
  • Y. Gu and M.C. Herbordt (2007): Amenability of Multigrid Computations to FPGA-Based Acceleration, Proceedings of High Performance Embedded Computing (HPEC 2007)
  • J. Model and M.C. Herbordt (2007): Discrete Event Simulation of Molecular Dynamics with Configurable Logic, Proceedings of Field Programmable Logic and Applications (FPL 2007) pp. 151-158, August, 2007
  • Y. Gu, T. VanCourt, M.C. Herbordt (2007): High Performance Molecular Dynamics Simulations with FPGA Coprocessors (Extended Version), Proceedings of the Reconfigurable Systems Summer Institute (RSSI 2007)
  • Y. Gu, M.C. Herbordt (2007): FPGA-based Multigrid Computation for Molecular Dynamics Simulation, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007)
  • M.C. Herbordt, T. VanCourt, Y. Gu, B. Sukhwani, A. Conti, J. Model, D. DiSabello(2007): Achieving High Performance with FPGA-Based Computing, IEEE Computer, 40 (3), pp. 50-57.
  • T. VanCourt and M.C. Herbordt (2007): Families of FPGA Accelerators for Approximate String Matching, Microprocessors and Microsystems, 31 (2), pp. 135-145.
  • M.C. Herbordt, et al. (2006): Case Studies in FPGA Acceleration of Computational Biology and their Implications to Development Tools, Presented at the Reconfigurable Systems Summer Institute (RSSI 2006)
  • T. VanCourt, Y. Gu, V. Mundada, M.C. Herbordt (2006): Rigid Molecule Docking: FPGA Reconfiguration for Alternative Force Laws, Journal on Applied Signal Processing, v2006, pp. 1-10.
  • Y. Gu, M.C. Herbordt, and T. VanCourt (2006): Improved Interpolation and System Integration for FPGA-Based Molecular Dynamics Simulations, Proceedings of Field Programmable Logic and Applications (FPL 2006)
  • T. VanCourt and M.C. Herbordt (2006): Application-Specific Memory Interleaving for FPGA-Based Grid Computations: A General Design Technique, Proceedings of Field Programmable Logic and Applications (FPL 2006)
  • T. VanCourt and M.C. Herbordt (2006): Sizing of Processing Arrays for FPGA-Based Computation, Proceedings of Field Programmable Logic and Applications (FPL 2006)
  • M.C. Herbordt, J. Model, Y. Gu, B. Sukhwani and T. VanCourt (2006): Single Pass, BLAST-Like, Approximate String Matching on FPGAs, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2006) (Slides)
  • Y. Gu, M.C. Herbordt, and T. VanCourt (2006): Integrating FPGA Acceleration into the ProtoMol Molecular Dynamics Code, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2006)
  • T. VanCourt and M.C. Herbordt, and (2006): Application-Dependent Memory Interleaving Enables High Performance in FPGA-based Grid Computations, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2006) (Download software)
  • Y. Gu, T. VanCourt and M.C. Herbordt (2006): Accelerating Molecular Dynamics Simulations with Configurable Circuits, IEE Proceedings on Computers and Digital Technology. 153(3):37-195 Special issue devoted to selected papers from the 2005 Field Programmable Logic and Applications Conference, one of seven papers chosen for this special issue from over 300 submitted to the conference.
  • Tom VanCourt and Martin Herbordt (2006): Requirements for any FPGA/HPC Application Development Tool Flow (BARC 2006) (Slides)
  • Tom VanCourt and Martin Herbordt (2005): LAMP: A Tool Suite for Families of FPGA-based Computation Accelerators, Field Programmable Logic and Applications (FPL 2005)
  • Yongfeng Gu, Tom VanCourt, and Martin Herbordt : Accelerating Molecular Dynamics Simulations With Configurable Circuits, Field Programmable Logic and Applications (FPL 2005)
  • Yongfeng Gu, Tom VanCourt, Martin C. Herbordt (2005): FPGA Acceleration of Molecular Dynamics Computations, presented at the IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 05) Workshop, April 2005
  • T. VanCourt, Y. Gu, and M. C. Herbordt (2005): Three-Dimensional Template Correlation: Object Recognition in Voxel Data, Proceedings of Computer Architecture for Machine Perception (CAMP), July 2005 (Slides)
  • T. VanCourt and M. C. Herbordt (2005): Making FPGAs a Cost-Effective Computing Architecture, presented at the Third Boston Area Computer Architecture (BARC) Workshop, January 2005 (Slides)
  • T. VanCourt and M.C. Herbordt (2004): Families of FPGA-Based Algorithms for Approximate String Matching, Proceedings of Application-Specific Systems, Architectures, and Processors. (ASAP 04) (Extended version)
  • T. VanCourt, M.C. Herbordt, R.J. Barton (2004): Microarray Data Analysis Using an FPGA-Based Coprocessor, Microprocessors and Microsystems, 28(5-6), special issue on FPGAs: Applications, Algorithms and Tools, pp. 213-222.
  • A. Conti, T. VanCourt, M.C. Herbordt (2004): Processing Repetitive Structures with Mismatches at Streaming Rate, Proceedings of Field Programmable Logic and Applications (FPL 2004), Also in Lecture Notes in Computer Science, LNCS 3203, J. Becker, et al., editors, Springer Verlag (Technical report TR2004-01) (Extended version)
  • T. VanCourt, Y. Gu, M.C. Herbordt (2004): FPGA Acceleration of Rigid Molecule Interactions, Proceedings of Field Programmable Logic and Applications (FPL 2004), Also in Lecture Notes in Computer Science, LNCS 3203, J. Becker, et al., editors, Springer Verlag (Technical report TR2004-02)
  • T. VanCourt, Y. Gu, M.C. Herbordt (2004): FPGA Acceleration of Rigid Molecule Interactions, Proceedings of Field Programmable Custom Computing Machines. (FCCM 04) (Extended version)
  • M.C. Herbordt, J.B. Cravy, H. Zhang (2004): Array Control for High-Performance SIMD Systems, Journal of Parallel and Distributed Computing, 64 (4) pp. 400-413.
  • T. VanCourt and M. C. Herbordt (2004): Processor-Memory Networks Based on Steiner Systems, presented at the Second Boston Area Computer Architecture Workshop (BARC), January 2004
  • T. VanCourt, M.C. Herbordt, R.J. Barton (2003): Case Study of a Functional Genomics Application for an FPGA-Based Coprocessor, Proceedings of Field Programmable Logic and Applications (FPL 2003), pp. 365-374. Also in Lecture Notes in Computer Science, LNCS 2778, P.Y.K. Cheung, et al., editors, Springer Verlag.
  • M.C. Herbordt and P. Swarztrauber (2003): Towards Scalable Multicomputer Communication Through Offline Routing, CAAD Lab Technical Report 2003-01.
  • M.C. Herbordt, J. Cravy, C. Lin (2003): Memory Considerations for High-Performance SIMD Systems with On-Chip Control, Proceedings of Computer Architectures for Machine Perception.
  • Tom VanCourt (2001): Reverse Engineering Design Patterns: Detecting Design Patterns in Compiled Programs, Boston University, Metropolitan College.
  • M.C. Herbordt, J.B. Cravy, R. Sam, O. Kidwai, C. Lin (2000): A System for Evaluating Performance and Cost of Massively Parallel Array Designs, Journal of Parallel and Distributed Computing, 60 (2), pp. 217-246.
  • M.C. Herbordt, J. Cravy, H. Zhang, C. Lin, H. Rao (2000): An Array Control Unit for High-Speed SIMD Arrays (preliminary version), Proceedings of Computer Architectures for Machine Perception, pp. 293-301.
  • M.C. Herbordt, J. Cravy, H. Zhang, C. Lin, H. Rao (2000): Control for High-Speed PE Arrays, Proceedings of Application-Specific Systems, Architectures, and Processors (ASAP 2000), pp. 247-257.
  • B. Obrenic, M.C. Herbordt, A.L. Rosenberg, C.C. Weems (1999): Using Emulations to Construct High-Performance Virtual Parallel Architectures, IEEE Transactions on Parallel and Distributed Systems, 10 (10), pp. 1-15.
  • M.C. Herbordt, Kurt Olin, Harry Le (1999): Design Trade-Offs of Low-Cost Multicomputer Networks, Proceedings of the 7th Symposium on the Frontiers of Massively Parallel Computation, pp. 25-34.
  • M.C. Herbordt, Kurt Olin (1999): Switch Design for Fine-Grained Multicomputers-on-a-Chip, Proceedings of the 7th Symposium on the Frontiers of Massively Parallel Computation.
  • M.C. Herbordt, Jade Cravy, Renoy Sam, Owais Kidwai, Calvin Lin (1999): A System for Evaluating Performance and Cost of SIMD Array Designs, Proceedings of the 7th Symposium on the Frontiers of Massively Parallel Computation, pp. 16-24.
  • P. Ruchhoeft, J. C. Wolfe, J. Wasson, J. Torres, H. Wu, H. Nounu, N. Liu, M.C. Herbordt, M. D. Morgan and R. C. Tiberio, (1998) Fabrication of Silicon Stencil Masks With Vitreous Carbon Ion-Absorbing Coatings, Journal of Vacuum Science and Technology B, 16, pp. 3599-3601.
  • J. Torres, J.R. Wasson, J.C. Wolfe, P. Ruchhoeft, M.C. Herbordt (1998): Automated Radiation Testing System for Ion Beam Stencil Masks, 42st International Conference on Electron, Ion, and Photon Technology and Nanofabrication; Chicago, IL; May 27, 1998.
  • M.C. Herbordt, C.C. Weems (1997): Associative, Multiassociative, and Hybrid Processing, in Readings in Associative Processing and Processors, Argy Krikelis, editor, IEEE Computer Society Press, pp 26-49.
  • M.C. Herbordt, O. Kidwai, C.C. Weems (1997): Preprototyping SIMD Coprocessors Using Virtual Machine Emulation and Trace Compilation, Proceedings of the 1997 ACM Sigmetrics International Conference on Measurement and Modeling of Computer Systems, pp. 88-99. Reprinted in Performance Evaluation Review, 25 (1).
  • J.L. Torres, J.R. Wasson, J.C. Wolfe, P. Ruchhoeft, M.C. Herbordt, H. Loschner (1997): Ion Absorbing Coatings for Enhanced Exposure Lifetime of Silicon Stencil Masks in Ion Projection Lithography, Journal of Vacuum Science and Technology, 15 (6), pp. 2214-2217.
  • M.C. Herbordt, J.H. Burrill, C.C. Weems (1997): Making a Dataparallel Language Portable for Massively Parallel Computers, Proceedings of Computer Architectures for Machine Perception, pp. 160-169.
  • M.C. Herbordt, A. Anand, O. Kidwai, C.C. Weems (1997): Processor/Memory/Array Size Tradeoffs in the Design of Massively Parallel Arrays for a Spatially Mapped Workload, Proceedings of Computer Architectures for Machine Perception, pp. 12-21.
  • M.C. Herbordt, C.C. Weems (1996): Evaluating SIMD Arrays for Domain Specific Applications, Proceedings of Domain Specific Systems.
  • M.C. Herbordt, C.C. Weems (1995): ENPASSANT: An Environment for Evaluating Massively Parallel Architectures for Spatially Mapped Applications, Int. Journal of Pattern Recognition and Artificial Intelligence, special issue on Parallel Computing, 9 (2), pp. 175-200. Reprinted in VLSI and Parallel Computing for Pattern Recognition and AI, N. Ranganathan, editor, World Scientific Publishing Co, pp. 3-28.
  • M.C. Herbordt, C.C. Weems (1995): An Empirical Study of Datapath, Memory Hierarchy, and Network in SIMD Array Architectures, Proceedings of the 1995 IEEE Int. Conference on Computer Design, pp. 546-551. (Winner of Outstanding Paper Award)
  • M.C. Herbordt, C.C. Weems (1995): Towards the Empirical Design of Massively Parallel Arrays for Spatially Mapped Applications, Proceedings of Computer Architectures for Machine Perception, pp. 59-66.
  • M.C. Herbordt, C.C. Weems (1995): Experimental Analysis of some SIMD Array Memory Hierarchies, Proceedings of the 1995 International Conference on Parallel Processing, V.I, pp. 210-214.
  • M.C. Herbordt, J.C. Corbett, J. Spalding, C.C. Weems (1994): Practical Algorithms for Online Routing on Fixed and Reconfigurable Meshes, Journal of Parallel and Distributed Computing, 20 (3), pp. 341-356.
  • M.C. Herbordt, C.C. Weems (1993): An Environment for Evaluating Architectures for Spatially Mapped Computation: System Architecture and Preliminary Results, Proceedings of Computer Architectures for Machine Perception '93, pp. 191-201.
  • M.C. Herbordt, C.C. Weems (1993): Associative, Multiassociative, and Hybrid Processing, Proceedings of the 2nd Associative Processing and Applications Workshop.
  • C.C. Weems, M.C. Herbordt, et al. (1993): Status and Current Research in the Image Understanding Architecture Program, Proceedings of the 22nd Image Understanding Workshop.
  • M.C. Herbordt, C.C. Weems, M.J. Scudder (1992): Non-Uniform Region Processing on SIMD Arrays Using the Coterie Network, Machine Vision and Applications, 5 (2), pp. 105-125.
  • M.C. Herbordt, C.C. Weems (1992): Computing Reduction and Parallel Prefix Using Coterie Structures, Proceedings of the 4th Symposium on the Frontiers of Massively Parallel Computation, pp. 141-149.
  • C.C. Weems, M.C. Herbordt, et al. (1992): Status and Current Research in the Image Understanding Architecture Effort, Proceedings of the 21st Image Understanding Workshop. pp. 269-283.
  • M.C. Herbordt, C.C. Weems, J.C. Corbett (1991): Message Passing Algorithms for a SIMD Torus with Coteries, Computer Architecture News, F.T. Leighton, L. Snyder, F. Preparata eds. (19) 1, pp. 69-78.
  • M.C. Herbordt, C.C. Weems (1991): Multi-Associativity: A Framework for Solving Multiple Non-uniform Problem Instances Simultaneously on SIMD Arrays, Proceedings of the 1991 International Conference on Parallel Processing, V. III, pp. 219-223.
  • M.C. Herbordt, C.C. Weems, M.J. Scudder (1991): A Computational Framework and SIMD Algorithms for Low-Level Support of Intermediate-Level Vision Processing, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition.
  • M.C. Herbordt, C.C. Weems, D.B. Shu (1990): General Routing on the Lowest Level of the Image Understanding Architecture, Proceedings of the 20th Image Understanding Workshop, pp. 797-804.
  • F. Annexstein, M. Baumslag, M.C. Herbordt, B. Obrenic, A. Rosenberg, C.C. Weems (1990): Achieving Multigauge Behavior in Bit-Serial SIMD Architectures via Emulation (preliminary version), Proceedings of the 3rd Symposium on the Frontiers of Massively Parallel Computation, pp. 186-195.
  • M.C. Herbordt, C.C. Weems, J.C. Corbett (1990): Message Passing Algorithms for a SIMD Torus with Coteries, Proceedings of the 2nd ACM Symposium on Parallel Algorithms and Architectures, pp. 11-20. (Reprinted in Computer Architecture News)
  • M.C. Herbordt, C.C. Weems, D.B. Shu (1990): Routing on the CAAPP, Proceedings of the 10th International Conference on Pattern Recognition, Vol. II, pp. 467-471.
  • Posters

     

    FCCM 2006: Application-Specific Memory Interleaving Enables High Performance in FPGA-based Grid Computations

     

    FCCM 2006: Integrating FPGA Acceleration into the ProtoMol Molecular Dynamics Codes

     

    FPL 2006: Sizing of Processing Arrays for FPGA-Based Computation

     

     

    Thumbnail of memory interleaving poster

     

    Thumbnail of molecular dynamics poster

     

    Thumbnail of molecular dynamics poster

     

     

    FPL 2005: LAMP: A Tool Suite for Families of FPGA-based Computation Accelerators

     

    FCCM 2005: FPGA Acceleration of Molecular Dynamics Computations

     

    FPL 2004: Processing Repetitive Sequence Structures at Streaming Rate

     

    FCCM 2004: FPGA Acceleration of Rigid Molecule Interactions
    Thumbnail of LAMP poster

     

    Thumbnail of molecular dynamics poster

     

    Thumbnail of repetitive sequence poster

     

    Thumbnail of rigid molecule interaction poster

    Software

    These programs are freely available to the research community, with no warranty regarding the correctness of their results or suitability for any purpose whatsoever. In order to make software useful as quickly and widely as possible, it is distributed under the GNU GPL. If you come up with any interesting modifications, please let us know.

    Commercial users should contact Prof. Herbordt for licensing terms.

    Interleaved memory generator (download)

    This addresses grid-based FPGA applications where memory references are made in generally unpredictable order, but where each reference fetches a cluster of values. The cluster consists of a set of memory words from nearby points on the grid, with fixed offsets relative to each other.

    As an example, consider a molecular dynamics application where a force field is computed on some 3D grid. Atoms nearly never occur on actual grid points, however, so the force on one atom is computed by trilinear interpolation between the eight grid points at the corners of the cubical cell in which the atom is placed. Some implementations would benefit from the ability to fetch all eight of those grid values in one memory cycle, so that partial results within the trilinear interpolation can be computed in parallel. Those eight grid points constitute the access cluster in this application.

    This program is written in Java. It is released as a .jar file that includes execuatable class files, source code, and documentation.

    Theses and dissertations

  • Atabak Mahram (2013) FPGA Acceleration of Sequence Analysis Tools in Bioinformatics, Doctoral Dissertation
  • Ben Humphries (2013) Using Offline Routing to Implement the 3D FFT in a Multinode FPGA System , Master's Thesis
  • Ashfaq Khan (2012) Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors, Doctoral Dissertation
  • Vyas Venkataraman (2011) A High Level Modeling and Synthesis Methodology for Concurrent Systems Using Rendezvous, Doctoral Dissertation
  • Matt Chiu (2011) Accelerating Molecular Dynamics Simulations with High Performance Reconfigurable Systems, Doctoral Dissertation
  • Huaxin Dai (2010) Energy Minimization Accelerated with FPGAs, Master's Thesis
  • Bharat Sukhwani (2010) Accelerating Molecular Docking and Binding Site Mapping using FPGAs and GPUs, Doctoral Dissertation
  • Yongfeng Gu (2008) FPGA Acceleration of Molecular Dynamics Simulations, Doctoral Dissertation
  • Josh Model (2007) FPGA Acceleration of Discrete Molecular Dynamics Simulation, Master's Thesis
  • Douglas DiSabello (2006) Fault Tolerant FPGA Co-processing Toolkit, Master's Thesis (Slides)
  • Tom VanCourt (2006) LAMP: Tools for Creating Application-specific FPGA Coprocessors, Doctoral Dissertation
  • J. Ge: (2002) Evaluating the Effectiveness of Dynamically-Balanced Adaptive Wormhole Routers, Doctoral Dissertation
  • A. Mande: (2002) Performance Prediction of Message Passing Communication in Distributed Memory Systems, Master's Thesis
  • T. VanCourt: (2001) Reverse Engineering Design Patterns: Detecting Design Patterns in Compiled Programs, Master's Thesis,
    published as technical report BU Metropolitan College Technical Report BUMETCS-TR-2001-001
  • C. Adapa: (2001) Implementation Issues of Building a Multicomputer on a Chip, Master's Thesis
  • M. DeFord: (2001) Test and Integration Environment for PCI Coprocessor Cards, Master's Thesis
  • A. Svensson: (2001) Computer Simulation of a Web Cache Server with SES/Workbench, Master's Thesis
  • K. Olin: (1999) Design Tradeoffs of Embedded Networks for Systems on a Chip, Master's Thesis
  • Martin C. Herbordt: (1994) The Evaluation of Massively Parallel Array Architectures, Doctoral Dissertation
  • News and Publicity Archive

  • March, 2010: Our two new quad-FPGA Gidel PROCStar III boards (each with 4 Altera Stratix III SE260 FPGAs and 16GB memory) arrived!
  • March, 2010: Ashfaq Khan and his wife had a baby girl Sora (Congratulations to them).
  • January, 2010: CAAD lab joined the Novo-G Forum to enable high performance bioinformatics and computational biology on the Novo-G reconfigurable computing cluster
  • December, 2009: Yunfei Qiu accepted a position at Cavium Networks
  • December, 2009: Yongfeng Gu got married (Congratulations to him).
  • September, 2009: Matt Chiu and Martin Herbordt's paper titled "Efficient Particle-Pair Filtering for Acceleration of Molecular Dynamics Simulation" received best paper award at FPL 2009.
  • July, 2009: CAAD lab received research grant to explore Acceleration of Free Energy Minimization using FPGAs and GPUs.
  • July, 2009: Martin Herbordt and Miriam Leeser co-chaired the ASAP 2009 conference, held in Boston.
  • September, 2009: Bharat Sukhwani successfully completed an internship with the IBM T. J. Watson Research Center, Yorktown Heights, NY.
  • May, 2009: Yunfei Qiu received Master of Science degree in Computer Systems Engineering.
  • March, 2009: Martin Herbordt gave the keynote talk at Many-Core and Reconfigurable Supercomputing Conference in Berlin, Germany.
  • September, 2008: Matt Chiu passed his PhD prospectus defense titled "Accelerating Molecular Dynamics Simulations with High Performance Reconfigurable Systems".
  • September, 2008: Ashfaq Khan joined the lab as a PhD student.
  • May, 2008: Yongfeng Gu hooded at the Boston University College of Engineering commencement ceremony.
  • May, 2008: Bharat Sukhwani passed his PhD prospectus defense titled "FPGA Acceleration of Molecular Docking".
  • April 16, 2008: Martin Herbordt gave an invited talk at Altera Corporation, San Jose, CA.
  • April 4, 2008: Martin Herbordt gave an invited talk at Massachusetts Institute of Technology, Cambridge, MA.
  • April 3, 2008: Martin Herbordt gave an invited talk at Brown University, Providence, RI.
  • February 2008: Martin Herbordt gave an invited talk at IBM - T. J. Watson Research Center, Yorktown Heights, NY.
  • January 2008: CAAD lab received a four-processor Altix 450 system with RASC blade from SGI.
  • January 2008: Yongfeng Gu received his Ph.D. degree and joined The MathWorks.
  • January 2008: Jin Park joined the CAAD lab as a postdoctoral researcher.
  • December 2007: George Bishop joined Lockheed Martin.
  • November 2007: Yongfeng Gu defended his Ph.D. dissertation titled "FPGA Acceleration of Molecular Dynamics Simulations".
  • November 2007: Martin Herbordt gave an invited talk at Washington University at St. Louis.
  • September 2007: Tom VanCourt served as a Distinguished Panelist at HPEC 2007 held at MIT Lincoln Labs.
  • August 2007: Martin Herbordt gave an invited talk at Imperial College, London.
  • Summer 2007: Bharat Sukhwani successfully completed an internship with the Embedded Systems group at Microsoft Research, Redmond Lab. He worked on dynamic I/O peripherals for the eMIPS extensible processor.
  • Summer 2007: Yongfeng Gu was a visiting scientist at NASA Langley Research Center, researching FPGA solutions for Lidar signal processing and data mining.
  • June 2007: The CAAD lab received research funding from National Institute of Health (NIH) to perform research on FPGA based acceleration of computational biology and bioinformatics.
  • May 2007: The CAAD lab received an XtremeData development system, under the Altera-AMD-Sun-XtremeData University program, to perform research in high-performance computing.
  • May 2007: Josh Model received his MSEE and returned to MIT Lincoln Labs.
  • January 2007: Boston University organized and hosted the Fifth Boston Area Architecture Workshop (BARC 2007).
  • 21 Oct 2005: The CAAD lab and Silicon Graphics, Inc. formed an academic/industrial partnership to explore computing applications for the Altix RASC reconfigurable accelerator.
  • The article Practical 3D template matching with FPGAs by Tom VanCourt and Prof. Herbordt published on the SPIE Newsroom website. It talks about the potential application of FPGA co-processors in performing 3D correlation
  • The 05/01/05 issue of Genome Technology includes the article "New Apps for FPGAs: Once Confined to Genome Sequence, FPGAs Break Out into Biological Modeling". The article quotes Prof. Herbordt:
  •      ... what's good about FPGAs, says Martin Herbordt, a computer architect and associate professor in the department of electrical and computer engineering at Boston University, is that they're commodity parts. Furthermore, because of their widespread use in signal processing, the cost of an average FPGA is steadily decreasing.
    The article goes on to report that
    It just so happens that Herbordt at Boston University is working with members of his group to develop such a compiler. Taking full advantage of the opportunities FPGAs provide for hardware acceleration means combining their low cost with a relatively easy programming interface, Herbordt says. To this end, Herbordt and his group member Tom VanCourt are developing a system for compiling the behaviors and parameters specific to any individual system under investigation,
  • The 03/14/05 issue of bio1nf0rm newsletter (vol. 9 no. 10) recognized the CAAD Lab's research, noting our work
  •      … to extend FPGA-based methods beyond sequence analysis," especially in "… developing FPGA-based systems for analyzing microarray data, modeling rigid molecule interactions, and processing repetitive structures in sequences."

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