Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Architectures and APIs: assessing requirements for delivering FPGA performance to applications
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Examining the viability of FPGA supercomputing
EURASIP Journal on Embedded Systems
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
Application development on hybrid systems
Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Visions for application development on hybrid computing systems
Parallel Computing
FPGA acceleration of a quantum Monte Carlo application
Parallel Computing
From Silicon to Science: The Long Road to Production Reconfigurable Supercomputing
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Sorting on architecturally diverse computer systems
Proceedings of the Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications
FPGA-accelerated molecular dynamics simulations: an overview
ARC'07 Proceedings of the 3rd international conference on Reconfigurable computing: architectures, tools and applications
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
Molecular Dynamics Simulations on High-Performance Reconfigurable Computing Systems
ACM Transactions on Reconfigurable Technology and Systems (TRETS)
A coarse-grained stream architecture for cryo-electron microscopy images 3D reconstruction
Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays
Journal of Parallel and Distributed Computing
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With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applications, such as those in scientific computing. There has been a resulting development of reconfigurable computers-computers which have both general purpose processors and reconfigurable hardware, as well as memory and high-performance interconnection networks. In this paper, we study the acceleration of molecular dynamics simulations using reconfigurable computers. We describe how we partition the application between software and hardware and then model the performance of several alternatives for the task mapped to hardware. We describe an implementation of one of these alternatives on a reconfigurable computer and demonstrate that for two real-world simulations, it achieves a 2 speed-up over the software baseline. We then compare our design and results to those of prior efforts and explain the advantages of the hardware/ software approach, including flexibility.