Accelerating a Virtual Ecology Model with FPGAs

This paper describes the acceleration of virtual ecology models using field-programmable gate arrays (FPGAs). Our approach targets models generated by the Virtual Ecology Workbench (VEW); an existing tool used by biological oceanographers to build and analyze models of the plankton ecosystem in the upper ocean. Depending on the plankton study and required level of detail, the logic, memory, and data transfer requirements of the generated models can vary significantly. Using FPGAs, hardware implementations can be customized to the specific requirements of the ecological system under study and provide significant speed-ups compared to software implementations. This paper describes a framework for maximizing the speedup of VEW generated models implemented on FPGA-based acceleration platforms and then describes the implementation of a typical VEW generated model to validate the framework and demonstrate that significant speedups are possible. Based on timing and area estimates from a commercial synthesis tool, the example model implemented on a Celoxica RCHTX acceleration board featuring a Xilinx Virtex-4 FPGA performs 39 times faster at 150 MHz than the software implementation on an AMD Opteron 2200 series CPU at 1.0 GHz.