Using FPGA Devices to Accelerate Biomolecular Simulations

Authors:
Sadaf R. Alam;Pratul K. Agarwal;Melissa C. Smith;Jeffrey S. Vetter;David Caliga
Affiliations:
Oak Ridge National Laboratory;Oak Ridge National Laboratory;Oak Ridge National Laboratory;Oak Ridge National Laboratory;SRC Computers
Venue:
Computer
Year:
2007

Citing 8
Cited 11

Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program

The Journal of Supercomputing - Special issue on supercomputing in medicine
Digital Principles and Applications

Digital Principles and Applications
FPGAs vs. CPUs: trends in peak floating-point performance

FPGA '04 Proceedings of the 2004 ACM/SIGDA 12th international symposium on Field programmable gate arrays
Reconfigurable Molecular Dynamics Simulator

FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Closing the Gap: CPU and FPGA Trends in Sustainable Floating-Point BLAS Performance

FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
An Analysis of the Double-Precision Floating-Point FFT on FPGAs

FCCM '05 Proceedings of the 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Performance characterization of molecular dynamics techniques for biomolecular simulations

Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers

FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines

Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

Parallel Computing
Finding the Next Computational Model: Experience with the UCSC Kestrel

Journal of Signal Processing Systems
Performance characteristics of biomolecular simulations on high-end systems with multi-core processors

Parallel Computing
GViM: GPU-accelerated virtual machines

Proceedings of the 3rd ACM Workshop on System-level Virtualization for High Performance Computing
Parallel backprojection: a case study in high-performance reconfigurable computing

EURASIP Journal on Embedded Systems - FPGA supercomputing platforms, architectures, and techniques for accelerating computationally complex algorithms
Function-level multitasking interface design in an embedded operating system with reconfigurable hardware

EUC'07 Proceedings of the 2007 international conference on Embedded and ubiquitous computing
Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Proceedings of the 7th ACM international conference on Computing frontiers
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems

ACM Transactions on Reconfigurable Technology and Systems (TRETS)
A Simulation Framework for Rapid Analysis of Reconfigurable Computing Systems

ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
A reconfigurable computing platform for real time embedded applications

Microprocessors & Microsystems

Quantified Score

Hi-index	4.10

Visualization

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.