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Using FPGA Devices to Accelerate Biomolecular Simulations
March 2007 (vol. 40 no. 3)
pp. 66-73
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
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
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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