Production Floating Point Applications on FPGAs

While FPGAs have only one fifth the raw floating point capability of GPUs, other attributes allow them to be surprisingly competitive with respect to a number of critical floating point intensive applications. In the first part we review these FPGA attributes. The bulk of this extended abstract then provides an overview of efficient FPGA implementations of Molecular Dynamics, Molecular Docking, and Molecular Dynamics based on discrete event simulation.

[1]  Martin C. Herbordt,et al.  Application-Specific Memory Interleaving Enables High Performance in FPGA-based Grid Computations , 2006, 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines.

[2]  Martin C. Herbordt,et al.  GPU acceleration of a production molecular docking code , 2009, GPGPU-2.

[3]  Martin Langhammer.  Floating point datapath synthesis for FPGAs , 2008, 2008 International Conference on Field Programmable Logic and Applications.

[4]  Martin C. Herbordt,et al.  FPGA-Based Multigrid Computation for Molecular Dynamics Simulations , 2007, 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007).

[5]  Franz Franchetti,et al.  How to Write Fast Numerical Code: A Small Introduction , 2007, GTTSE.

[6]  Martin C. Herbordt,et al.  Performance potential of molecular dynamics simulations on high performance reconfigurable computing systems , 2008 .

[7]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[8]  Martin C. Herbordt,et al.  Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition , 2009, 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors.

[9]  Martin C. Herbordt,et al.  Acceleration of a production rigid molecule docking code , 2008, 2008 International Conference on Field Programmable Logic and Applications.

[10]  Martin C. Herbordt,et al.  Performance potential of molecular dynamics simulations on high performance reconfigurable computing systems , 2008, 2008 Second International Workshop on High-Performance Reconfigurable Computing Technology and Applications.