Methodology of Firmware Development for ARUZ-An FPGA-Based HPC System

ARUZ is a large scale, massively parallel, FPGA-based reconfigurable computational system dedicated primarily to molecular analysis. This paper presents a methodology for ARUZ firmware development that simplifies the process, offers low-level optimization, and facilitates verification. According to this methodology, firstly an expanded, generic, all-in-one VHDL description of variable Processing Elements (PEs) is developed manually. GCC preprocessing is then used to extract only the desired target functionality. A dedicated software instantiates and connects PEs in form of a scalable network, divides it into subsets for chips and generates its HDL description. As a result, individual HDL-coded specification, optimized for certain analysis, is provided for the synthesis tool. Code reuse and automated generation of up to 81% of the code economizes the workload. Using well-optimized VHDL for core description rather than High Level Synthesis eliminates unnecessary overhead. The PE network can be scaled inversely proportional to PEs complexity, in order to efficiently utilize available resources. Moreover, downscaling the problem makes verification during HDL simulations and testing the prototype systems easier.