Using FPGA devices to accelerate biomolecular simulations

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

Research output: Contribution to specialist publicationArticle

57 Scopus citations

Abstract

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.

Original languageEnglish
Pages66-73
Number of pages8
Volume40
No3
Specialist publicationComputer
DOIs
StatePublished - Mar 2007

Funding

Oak Ridge National Laboratory’s Laboratory-Directed Research and Development Program, which UT-Battelle manages for the US Department of Energy under contract no. DE-AC05-00OR22725, sponsored this research.

Keywords

  • Biomolecular simulations
  • FPGAs
  • Reconfigurable computing

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