Computer Architecture and Automated Design Lab

Recent publications

Posters

Dissertations

Software

News items

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)	(PDF)
B. Sukhwani and M.C. Herbordt (2008): Acceleration of a Production Rigid Molecule Docking Code, Proceedings of Field Programmable Logic and Applications (FPL 2008), September 2008	(PDF)
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	(PDF)
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)	(Link) You can also request a copy by emailing Dr. Martin Herbordt
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)	(PDF)
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	(PDF)
Y. Gu and M.C. Herbordt (2007): Amenability of Multigrid Computations to FPGA-Based Acceleration, Proceedings of High Performance Embedded Computing (HPEC 2007)	(PDF)
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	(PDF)
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)	(PDF) (slides)
Y. Gu, M.C. Herbordt (2007): FPGA-based Multigrid Computation for Molecular Dynamics Simulation, IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007)	(PDF)
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.	(PDF)
T. VanCourt and M.C. Herbordt (2007): Families of FPGA Accelerators for Approximate String Matching, Microprocessors and Microsystems, 31 (2), pp. 135-145.	(PDF)
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)	(Slides)
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.	(PDF)
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)	(PDF)
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)	(PDF)
T. VanCourt and M.C. Herbordt (2006): Sizing of Processing Arrays for FPGA-Based Computation, Proceedings of Field Programmable Logic and Applications (FPL 2006)	(PDF)
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)	(PDF) (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)	(abstract) (poster)
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)	(abstract) (PowerPoint poster) (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..	(PDF)
Tom VanCourt and Martin Herbordt (2006): Requirements for any FPGA/HPC Application Development Tool Flow (BARC 2006)	(abstract) (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)	(PDF) (PowerPoint poster)
Yongfeng Gu, Tom VanCourt, and Martin Herbordt. Accelerating Molecular Dynamics Simulations With Configurable Circuits, Field Programmable Logic and Applications (FPL 2005)	(superceded by the extended version)
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	(PDF poster)
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	(PDF) (PowerPoint)
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	(PDF abstract) (PowerPoint)
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)	(PDF) (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.	(PDF)
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) (poster) (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)	(poster) (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.	(PDF)
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	(PowerPoint)
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.	(PDF)
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.	(Technical report BUMETCS-TR-2001-001)
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.	(PDF)
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.	(PDF)
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	(PDF)
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.	(PDF)
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.	(PDF)
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.	(PDF)
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

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

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

News and publicity

ACM and IEEE-mandated Copyright Notice