Using FPGA Devices to Accelerate Biomolecular Simulations

Sadaf R. Alam; Jeffrey S. Vetter; David Caliga; Pratul K. Agarwal; Melissa C. Smith

doi:10.1109/MC.2007.108

Computer
2007
Issue No. 3 - March
Abstract - Using FPGA Devices to Accelerate Biomolecular Simulations

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Using FPGA Devices to Accelerate Biomolecular Simulations

March 2007 (vol. 40 no. 3)

pp. 66-73

	ASCII Text	x
	Sadaf R. Alam, Pratul K. Agarwal, Melissa C. Smith, Jeffrey S. Vetter, David Caliga, "Using FPGA Devices to Accelerate Biomolecular Simulations," Computer, vol. 40, no. 3, pp. 66-73, March, 2007.

	BibTex	x
	@article{ 10.1109/MC.2007.108, author = {Sadaf R. Alam and Pratul K. Agarwal and Melissa C. Smith and Jeffrey S. Vetter and David Caliga}, title = {Using FPGA Devices to Accelerate Biomolecular Simulations}, journal ={Computer}, volume = {40}, number = {3}, issn = {0018-9162}, year = {2007}, pages = {66-73}, doi = {http://doi.ieeecomputersociety.org/10.1109/MC.2007.108}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - MGZN JO - Computer TI - Using FPGA Devices to Accelerate Biomolecular Simulations IS - 3 SN - 0018-9162 SP66 EP73 EPD - 66-73 A1 - Sadaf R. Alam, A1 - Pratul K. Agarwal, A1 - Melissa C. Smith, A1 - Jeffrey S. Vetter, A1 - David Caliga, PY - 2007 KW - reconfigurable computing KW - FPGAs KW - Biomolecular simulations VL - 40 JA - Computer ER -

Sadaf R. Alam, Oak Ridge National Laboratory

Pratul K. Agarwal, Oak Ridge National Laboratory

Melissa C. Smith, Oak Ridge National Laboratory

Jeffrey S. Vetter, Oak Ridge National Laboratory

David Caliga, SRC Computers

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/MC.2007.108

A field-programmable gate array implementation of a molecular dynamics simulation method reduces the microprocessor time-to-solution by a factor of three while using only high-level languages. The application speedup on FPGA devices increases with the problem size. The authors use a performance model to analyze the potential of simulating large-scale biological systems faster than many cluster-based supercomputing platforms.

Index Terms:

reconfigurable computing, FPGAs, Biomolecular simulations

Citation:

Sadaf R. Alam, Pratul K. Agarwal, Melissa C. Smith, Jeffrey S. Vetter, David Caliga, "Using FPGA Devices to Accelerate Biomolecular Simulations," Computer, vol. 40, no. 3, pp. 66-73, March 2007, doi:10.1109/MC.2007.108

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