Reconfigurable Molecular Dynamics Simulator

Authors:
Navid Azizi;Ian Kuon;Aaron Egier;Ahmad Darabiha;Paul Chow
Affiliations:
University of Toronto, Ontario, Canada;University of Toronto, Ontario, Canada;University of Toronto, Ontario, Canada;University of Toronto, Ontario, Canada;University of Toronto, Ontario, Canada
Venue:
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Year:
2004

Citing 0
Cited 15

Preliminary investigation of advanced electrostatics in molecular dynamics on reconfigurable computers

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Optimized high-order finite difference wave equations modeling on reconfigurable computing platform

Microprocessors & Microsystems
Using FPGA Devices to Accelerate Biomolecular Simulations

Computer
RAT: a methodology for predicting performance in application design migration to FPGAs

HPRCTA '07 Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications: held in conjunction with SC07
C is for circuits: capturing FPGA circuits as sequential code for portability

Proceedings of the 16th international ACM/SIGDA symposium on Field programmable gate arrays
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

Parallel Computing
FPGA acceleration of a quantum Monte Carlo application

Parallel Computing
Particle graphics on reconfigurable hardware

ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Examining the Feasibility of Reconfigurable Models for Molecular Dynamics Simulation

ICA3PP '08 Proceedings of the 8th international conference on Algorithms and Architectures for Parallel Processing
Don't forget memories: a case study redesigning a pattern counting ASIC circuit for FPGAs

CODES+ISSS '08 Proceedings of the 6th IEEE/ACM/IFIP international conference on Hardware/Software codesign and system synthesis
FPGA-accelerated molecular dynamics simulations: an overview

ARC'07 Proceedings of the 3rd international conference on Reconfigurable computing: architectures, tools and applications
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems

ACM Transactions on Reconfigurable Technology and Systems (TRETS)
A design scheme for a reconfigurable accelerator implemented by single-flux quantum circuits

Journal of Systems Architecture: the EUROMICRO Journal
Enhancing the area efficiency of FPGAs with hard circuits using shadow clusters

IEEE Transactions on Very Large Scale Integration (VLSI) Systems
An FPGA design to achieve fast and accurate results for molecular dynamics simulations

ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications

Quantified Score

Hi-index	0.00

Visualization

Abstract

Current high-performance applications are typically implemented on large-scale general-purpose distributed or multi-processing systems often based on commodity microprocessors. Field-Programmable Gate Arrays (FPGAs) have now reached a level of sophistication that they too could be used for such applications. In this paper we explore the feasibility of using FPGAs to implement large-scale application-specific computations by way of a case study that implements a novel Molecular Dynamics system. The system has been designed such that it is scalable and parallelizable. On the Transmogrifier 3 (TM3), the system performs calculations on an 8,192 particle system in 37 seconds at 26MHz. This implementation shows that by scaling to more modern parts running at 100MHz, a speedup of over 20x can be achieved compared to a state-of-the-art microprocessor. This can also be achieved at less cost, using less power and taking less space than a standard microprocessor-based system, while maintaining the computational precision required.