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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...
While acceleration of Molecular Dynamics has received much attention, a significant part of that application, the bonded force calculation, has not. We present what we believe to be the first description and analysis of bonded force calculations outside of ASICs. We characterize the computational requirements. We find that a naive direct implementation requires FPGA resources out of proportion with...
The 3D FFT is critical in many physical simulations and image processing applications. On FPGAs, however, the 3D FFT was thought to be inefficient relative to other methods such as convolution-based implementations of multigrid. We find the opposite: a simple design, operating at a conservative frequency, takes 4Μs for 163, 21Μs for 323, and 215Μs for 643...
Molecular Dynamics is notable in High Performance Computing in that it is both sufficiently critical, and not well-enough served by off-the-shelf processors, that it has been continually targeted with domain-specific architectures. These range from the common, i.e., use of accelerators, to FPGA-centric servers describe here, to full-scale ASIC-based systems (e.g., the Anton processor). The strict...
The 3D FFT is critical in electrostatics computations such as those used in Molecular Dynamics simulations. On FPGAs, however, the 3D FFT was thought to be inefficient relative to other methods such as convolution-based implementations of multigrid. We find the opposite: a simple design using less than half the chip resources, and operating at a very conservative frequency, takes less than 50us for...
Recent work in the FPGA acceleration of molecular dynamics simulation has shown that including on-the-fly neighbor list calculation (particle filtering) in the device has the potential for an 80× per core speed-up over the CPU-based reference code and so to make the approach competitive with other computing technologies. In this paper we report on progress and challenges in advancing this work towards...
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