Monte Carlo Methods in Chemistry
IEEE Computational Science & Engineering
Reconfigurable Molecular Dynamics Simulator
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Astrophysical Hydrodynamics Simulations on a Reconfigurable System
FCCM '05 Proceedings of the 13th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Partitioning Hardware and Software for Reconfigurable Supercomputing Applications: A Case Study
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Computing in Science and Engineering
Hardware/Software Approach to Molecular Dynamics on Reconfigurable Computers
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Reconfigurable accelerator for quantum Monte Carlo simulations in N-body systems
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Systolic Architecture for Computational Fluid Dynamics on FPGAs
FCCM '07 Proceedings of the 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays
Reconfigurable Computing: Accelerating Computation with Field-Programmable Gate Arrays
Monte Carlo simulation and random number generation
IEEE Journal on Selected Areas in Communications
A HyperTransport 3 Physical Layer Interface for FPGAs
ARC '09 Proceedings of the 5th International Workshop on Reconfigurable Computing: Architectures, Tools and Applications
A pipelined and parallel architecture for quantum Monte Carlo simulations on FPGAs
VLSI Design - Special issue on selected papers from the midwest symposium on circuits and systems
PPAM'09 Proceedings of the 8th international conference on Parallel processing and applied mathematics: Part I
Hardware implementation of the orbital function for quantum chemistry calculations
ARC'10 Proceedings of the 6th international conference on Reconfigurable Computing: architectures, Tools and Applications
A mixed precision Monte Carlo methodology for reconfigurable accelerator systems
Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays
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Quantum Monte Carlo methods enable us to determine the ground-state properties of atomic or molecular clusters. Here, we present a reconfigurable computing architecture using Field Programmable Gate Arrays (FPGAs) to accelerate two computationally intensive kernels of a Quantum Monte Carlo (QMC) application applied to N-body systems. We focus on two key kernels of the QMC application: acceleration of potential energy and wave function calculations. We compare the performance of our application on two reconfigurable platforms. Firstly, we use a dual-processor 2.4GHz Intel Xeon augmented with two reconfigurable development boards consisting of Xilinx Virtex-II Pro FPGAs. Using this platform, we achieve a speedup of 3x over a software-only implementation. Following this, the chemistry application is ported to the Cray XD1 supercomputer equipped with Xilinx Virtex-II Pro and Virtex-4 FPGAs. The hardware-accelerated application on one node of the high performance system equipped with a single Virtex-4 FPGA yields a speedup of approximately 25x over the serial reference code running on one node of the dual-processor dual-core 2.2GHz AMD Opteron. This speedup is mainly attributed to the use of pipelining, the use of fixed-point arithmetic for all calculations and the fine-grained parallelism using FPGAs. We can further enhance the performance by operating multiple instances of our design in parallel.