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Title: Using FPGA Devices to Accelerate Biomolecular Simulations

Abstract

A field-programmable gate array implementation of the particle-mesh Ewald 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.

Authors:
 [1];  [1];  [1];  [1];  [1]
  1. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
931390
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Computer; Journal Volume: 40; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
97; 59 BASIC BIOLOGICAL SCIENCES; MICROELECTRONICS; MICROPROCESSORS; PERFORMANCE; COMPUTERIZED SIMULATION; MOLECULAR DYNAMICS METHOD; BIOLOGY

Citation Formats

Alam, Sadaf R, Agarwal, Pratul K, Smith, Melissa C, Vetter, Jeffrey S, and Caliga, David E. Using FPGA Devices to Accelerate Biomolecular Simulations. United States: N. p., 2007. Web. doi:10.1109/MC.2007.108.
Alam, Sadaf R, Agarwal, Pratul K, Smith, Melissa C, Vetter, Jeffrey S, & Caliga, David E. Using FPGA Devices to Accelerate Biomolecular Simulations. United States. doi:10.1109/MC.2007.108.
Alam, Sadaf R, Agarwal, Pratul K, Smith, Melissa C, Vetter, Jeffrey S, and Caliga, David E. Thu . "Using FPGA Devices to Accelerate Biomolecular Simulations". United States. doi:10.1109/MC.2007.108.
@article{osti_931390,
title = {Using FPGA Devices to Accelerate Biomolecular Simulations},
author = {Alam, Sadaf R and Agarwal, Pratul K and Smith, Melissa C and Vetter, Jeffrey S and Caliga, David E},
abstractNote = {A field-programmable gate array implementation of the particle-mesh Ewald 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.},
doi = {10.1109/MC.2007.108},
journal = {Computer},
number = 3,
volume = 40,
place = {United States},
year = {Thu Mar 01 00:00:00 EST 2007},
month = {Thu Mar 01 00:00:00 EST 2007}
}