Publications by authors named "Tom Vancourt"

4 Publications

  • Page 1 of 1

Explicit Design of FPGA-Based Coprocessors for Short-Range Force Computations in Molecular Dynamics Simulations.

Parallel Comput 2008 May;34(4-5):261-277

Computer Architecture and Automated Design Lab, Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215.

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.parco.2008.01.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2440579PMC
May 2008

Single Pass Streaming BLAST on FPGAs.

Parallel Comput 2007 Nov;33(10-11):741-756

Department of Electrical and Computer Engineering, Boston University; Boston, MA 02215, Web: http://www.bu.edu/caadlab .

Approximate string matching is fundamental to bioinformatics and has been the subject of numerous FPGA acceleration studies. We address issues with respect to FPGA implementations of both BLAST- and dynamic-programming- (DP) based methods. Our primary contribution is a new algorithm for emulating the seeding and extension phases of BLAST. This operates in a single pass through a database at streaming rate, and with no preprocessing other than loading the query string. Moreover, it emulates parameters turned to maximum possible sensitivity with no slowdown. While current DP-based methods also operate at streaming rate, generating results can be cumbersome. We address this with a new structure for data extraction. We present results from several implementations showing order of magnitude acceleration over serial reference code. A simple extension assures compatibility with NCBI BLAST.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.parco.2007.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2598392PMC
November 2007

Computing Models for FPGA-Based Accelerators.

Comput Sci Eng 2008 Oct;10(6):35-45

Boston University.

Field-programmable gate arrays are widely considered as accelerators for compute-intensive applications. A critical phase of FPGA application development is finding and mapping to the appropriate computing model. FPGA computing enables models with highly flexible fine-grained parallelism and associative operations such as broadcast and collective response. Several case studies demonstrate the effectiveness of using these computing models in developing FPGA applications for molecular modeling.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/MCSE.2008.143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3096930PMC
October 2008

Achieving High Performance with FPGA-Based Computing.

Computer (Long Beach Calif) 2007 Mar;40(3):50-57

Boston University.

Numerous application areas, including bioinformatics and computational biology, demand increasing amounts of processing capability. In many cases, the computation cores and data types are suited to field-programmable gate arrays. The challenge is identifying the design techniques that can extract high performance potential from the FPGA fabric.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/MC.2007.79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098506PMC
March 2007
-->