On the Feasibility of FPGA Acceleration of Molecular Dynamics Simulations
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Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle interactions and the sequential dependency of subsequent time steps render MD computationally intensive and difficult to scale. To this end, specialized FPGA-based accelerators have been repeatedly proposed to ameliorate this problem. However, to date none of the leading MD simulation packages fully support FPGA acceleration and a direct comparison of GPU versus FPGA accelerated codes has remained elusive so far. With this report, we aim at clarifying this issue by comparing measured application performance on GPU-dense compute nodes with performance and cost estimates of a FPGA-based single- node system. Our results show that an FPGA-based system can indeed outperform a similarly configured GPU-based system, but the overall application-level speedup remains in the order of 2x due to software overheads on the host. Considering the price for GPU and FPGA solutions, we observe that GPU-based solutions provide the better cost/performance tradeoff, and hence pure FPGA-based solutions are likely not going to be commercially viable. However, we also note that scaled multi-node systems could potentially benefit from a hybrid composition, where GPUs are used for compute intensive parts and FPGAs for latency and communication sensitive tasks.
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