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GekkoFS — A Temporary Burst Buffer File System for HPC Applications

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Abstract

Many scientific fields increasingly use high-performance computing (HPC) to process and analyze massive amounts of experimental data while storage systems in today’s HPC environments have to cope with new access patterns. These patterns include many metadata operations, small I/O requests, or randomized file I/O, while general-purpose parallel file systems have been optimized for sequential shared access to large files. Burst buffer file systems create a separate file system that applications can use to store temporary data. They aggregate node-local storage available within the compute nodes or use dedicated SSD clusters and offer a peak bandwidth higher than that of the backend parallel file system without interfering with it. However, burst buffer file systems typically offer many features that a scientific application, running in isolation for a limited amount of time, does not require. We present GekkoFS, a temporary, highly-scalable file system which has been specifically optimized for the aforementioned use cases. GekkoFS provides relaxed POSIX semantics which only offers features which are actually required by most (not all) applications. GekkoFS is, therefore, able to provide scalable I/O performance and reaches millions of metadata operations already for a small number of nodes, significantly outperforming the capabilities of common parallel file systems.

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Authors and Affiliations

  1. Zentrum für Datenverarbeitung, Johannes Gutenberg University Mainz, 55128, Mainz, Germany

    Marc-André Vef, Nafiseh Moti, Tim Süß, Markus Tacke & André Brinkmann

  2. Barcelona Supercomputing Center, 08034, Barcelona, Spain

    Tommaso Tocci, Ramon Nou, Alberto Miranda & Toni Cortes

  3. Computer Architecture Department, Universitat Politècnica de Catalunya, 08034, Barcelona, Spain

    Toni Cortes

Authors
  1. Marc-André Vef
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  2. Nafiseh Moti
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  3. Tim Süß
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  4. Markus Tacke
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  5. Tommaso Tocci
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  7. Alberto Miranda
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  9. André Brinkmann
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Correspondence to Marc-André Vef.

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Vef, MA., Moti, N., Süß, T. et al. GekkoFS — A Temporary Burst Buffer File System for HPC Applications. J. Comput. Sci. Technol. 35, 72–91 (2020). https://doi.org/10.1007/s11390-020-9797-6

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  • DOI: https://doi.org/10.1007/s11390-020-9797-6

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