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More bang for your buck: Improved use of GPU nodes for GROMACS 2018.

MPS-Authors
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Kutzner,  C.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Fechner,  M.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Esztermann,  A.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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de Groot,  B. L.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Grubmüller,  H.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

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Citation

Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L., & Grubmüller, H. (2019). More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry, 40(27), 2418-2431. doi:10.1002/jcc.26011.


Cite as: http://hdl.handle.net/21.11116/0000-0003-ED8C-5
Abstract
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.