More bang for your buck: Improved use of GPU nodes for GROMACS 2018
More bang for your buck: Improved use of GPU nodes for GROMACS 2018
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DOI：
10.1002/jcc.26011
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发表时间：
2019-07-01
影响因子：
3
通讯作者：
Grubmueller, Helmut
中科院分区：
文献类型：
--
作者：
Kutzner, Carsten;Pall, Szilard;Grubmueller, Helmut
我们使用GROMACS 2018模拟包确定了最适合在Linux计算集群上生成分子动力学(MD)轨迹的硬件。因此，我们在一组不同的计算节点上对GROMACS性能进行基准测试，并将其与节点的成本相关联，其中可能包括节点的能源和冷却的生命周期成本。与我们早些时候在2014年的硬件上使用GROMACS4.6进行的调查一致，消费类GPU节点的性价比远远高于CPU节点。然而，随着GROMACS 2018的推出，最佳CPU与GPU处理能力的平衡已更多地向GPU倾斜。因此，针对GROMACS 2018及更高版本进行优化的节点比针对较旧GROMACS版本进行优化的节点具有显著更高的性价比。此外，向GPU处理的转变允许用最新的GPU廉价地升级旧节点，产生基本上与可比的全新硬件相同的性能。(C)2019年威利期刊公司。
We identify hardware that is optimal to produce molecular dynamics (MD) trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more toward the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift toward GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware. (c) 2019 Wiley Periodicals, Inc.