Using FPGA devices to accelerate biomolecular simulations

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

doi:10.1109/MC.2007.108

Using FPGA devices to accelerate biomolecular simulations

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

Computer Science and Mathematics Div

Research output: Contribution to specialist publication › Article

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 language	English
Pages	66-73
Number of pages	8
Volume	40
No	3
Specialist publication	Computer
DOIs	https://doi.org/10.1109/MC.2007.108
State	Published - 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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10.1109/MC.2007.108

Cite this

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title = "Using FPGA devices to accelerate biomolecular simulations",

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.",

keywords = "Biomolecular simulations, FPGAs, Reconfigurable computing",

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year = "2007",

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journal = "Computer",

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AU - Alam, Sadaf R.

AU - Agarwal, Pratul K.

AU - Smith, Melissa C.

AU - Vetter, Jeffrey S.

AU - Caliga, David

PY - 2007/3

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N2 - 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.

AB - 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.

KW - Biomolecular simulations

KW - FPGAs

KW - Reconfigurable computing

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U2 - 10.1109/MC.2007.108

DO - 10.1109/MC.2007.108

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AN - SCOPUS:34147177681

SN - 0018-9162

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SP - 66

EP - 73

JO - Computer

JF - Computer

ER -

Using FPGA devices to accelerate biomolecular simulations

Abstract

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Keywords

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