OpenCL for HPC with FPGAs: Case Study in Molecular Electrostatics

FPGAs have emerged as a cost-effective accelerator alternative in clouds and clusters. Programmability remains a challenge, however, with OpenCL being generally recognized as a likely part of the solution. In this work we seek to advance the use of OpenCL for HPC on FPGAs in two ways. The first is by examining a core HPC application, Molecular Dynamics. The second is by examining a fundamental design pattern that we believe has not yet been described for OpenCL: passing data from a set of producer datapaths to a set of consumer datapaths, in particular, where the producers generate data non-uniformly. We evaluate several designs: single level versions in Verilog and in OpenCL, a two-level Verilog version with optimized arbiter, and several two-level OpenCL versions with different arbitration and hand-shaking mechanisms, including one with an embedded Verilog module. For the Verilog designs, we find that FPGAs retain their high-efficiency with a factor of 50x to 80x performance benefit over a single core. We also find that OpenCL may be competitive with HDLs for the straightline versions of the code, but that for designs with more complex arbitration and hand-shaking, relative performance is substantially diminished.