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More bang for your buck: Improved use of GPU nodes for GROMACS 2018
Max Planck Inst Biophys Chem, Theoret & Computat Biophys, Fassberg 11, D-37077 Gottingen, Germany.ORCID iD: 0000-0002-8719-0307
KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
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2019 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 27, p. 2418-2431Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Wiley , 2019. Vol. 40, no 27, p. 2418-2431
Keywords [en]
molecular dynamics, GPU, parallel computing, energy efficiency, benchmark, GROMACS, computer simulations, CUDA, performance to price, high throughput MD
National Category
Communication Systems
Identifiers
URN: urn:nbn:se:kth:diva-255767DOI: 10.1002/jcc.26011ISI: 000477372600001PubMedID: 31260119Scopus ID: 2-s2.0-85068468606OAI: oai:DiVA.org:kth-255767DiVA, id: diva2:1341803
Note

QC 20190812

Available from: 2019-08-12 Created: 2019-08-12 Last updated: 2019-10-11Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
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  • modern-language-association-8th-edition
  • vancouver
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  • de-DE
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