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arXiv 1808.04201cs.DCcs.PFphysics.comp-ph
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FPGA加速分子动力学模拟的可行性研究

On the Feasibility of FPGA Acceleration of Molecular Dynamics Simulations

Michael Schaffner, Luca Benini

摘要:

经典分子动力学(MD)模拟是生命和材料科学中的重要工具,因为它们可以详细研究化学和生物过程。然而,粒子-粒子相互作用的固有可扩展性问题和后续时间步长的顺序依赖性使得MD计算密集且难以扩展。为此,专门的基于FPGA的加速器已经被反复提出来改善这个问题。然而,到目前为止,没有一个领先的MD仿真软件包完全支持FPGA加速,并且到目前为止,GPU与FPGA加速代码的直接比较仍然难以捉摸。在这份报告中,我们的目标是通过比较GPU密集计算节点上测量的应用程序性能与基于FPGA的单节点系统的性能和成本估计来澄清这个问题。我们的研究结果表明,基于FPGA的系统确实可以优于类似配置的基于GPU的系统,但由于主机上的软件开销,整体应用程序级加速仍然保持在2倍左右。考虑到GPU和FPGA解决方案的价格,我们观察到基于GPU的解决方案提供了更好的成本/性能权衡,因此纯基于FPGA的解决方案可能不会在商业上可行。然而,我们还注意到,扩展的多节点系统可能会从混合组合中受益,其中GPU用于计算密集型部件,FPGA用于延迟和通信敏感任务。

英文摘要:

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.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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