Using FPGA devices to accelerate biomolecular simulations

Computer

Volumn 40, Issue 3, 2007, Pages 66-73

  Alam, Sadaf R ^a   Agarwal, Pratul K ^a,d   Smith, Melissa C ^a,e   Vetter, Jeffrey S ^a,b   Caliga, David ^c  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c SRC Computers' Application Technology

^d UNIVERSITY OF TENNESSEE   (United States)

^e CLEMSON UNIVERSITY   (United States)

Author keywords

Biomolecular simulations; FPGAs; Reconfigurable computing

Indexed keywords

EID: 34147177681     PISSN: 00189162     EISSN: None     Source Type: Trade Journal    
DOI: 10.1109/MC.2007.108     Document Type: Article

References (10)

1. N. Azizi et al., "Reconfigurable Molecular Dynamics Simulator," IEEE Symp. Field-Programmable Custom Computing Machines (FCCM 04), IEEE Press, 2004, pp. 197-206.
2. Y. Gu, T. VanCourt, and M. Herbordt, "Accelerating Molecular Dynamics Simulations with Configurable Circuits," Proc. IEEE Conf. Computers and Digital Technology, IEEE Press, 2006, pp. 189-195.
3. K.S. Hemmert and K.D. Underwood, "An Analysis of the Double-Precision Floating-Point FFT on FPGAs," Proc. IEEE Symp. Field-Programmable Custom Computing Machines (FCCM 05), IEEE Press, 2005, pp. 171-180.
4. R. Scrofano et al., "A Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers," Proc. IEEE Symp. Field-Programmable Custom Computing Machines (FCCM 06), IEEE Press, 2006, pp. 23-34.
5. M.C. Smith, J.S. Vetter, and S.R. Alam, "Scientific Computing Beyond CPUs: FPGA Implementations of Common Scientific Kernels," Proc. 8th Ann. Int'l Military & Aerospace Programmable Logic Device Conf., NASA Office of Logic Design, 2005; www.ornl.gov/~webworks/cppr/y2005/pres/123499.pdf.
6. A.R. Leach, Molecular Modeling: Principles and Applications, Prentice Hall, 2001.
7. M. Crowley et al., "Adventures in Improving the Scaling and Accuracy of Parallel Molecular Dynamics Programs," J. Supercomputing, Nov. 1997, pp. 255-278.
8. S.R. Alam et al., "Performance Characterization of Molecular Dynamics Techniques for Biomolecular Simulations," Proc. ACM SIGPLAN Symp. Principles and Practice of Parallel Programming (PPoPP), ACM Press, 2006, pp. 59-68.
9. K. Underwood, "FPGAs vs. CPUs: Trends in Peak Floating-Point Performance," Proc. 12th Int'l Symp. Field-Programmable Gate Arrays (FPGA 04), ACM Press, 2004, pp. 171-180.
10. K.D. Underwood and K.S. Hemmert, "Closing the GAP: CPU and FPGA Trends in Sustainable Floating-Point BLAS Performance," Proc. IEEE Symp. Field-Programmable Custom Computing Machines (FCCM 04), IEEE Press, 2004, pp. 219-228.