Journal of Computer Science and Technology ›› 2020, Vol. 35 ›› Issue (1): 4-26.doi: 10.1007/s11390-020-9801-1

Special Issue: Surveys; Computer Architecture and Systems

• Special Section on Selected I/O Technologies for High-Performance Computing and Data Analytics • Previous Articles     Next Articles

Ad Hoc File Systems for High-Performance Computing

André Brinkmann1,*, Member, ACM, Kathryn Mohror2,*, Member, ACM, IEEE, Weikuan Yu3,*, Senior Member, IEEE, Member, ACM, Philip Carns4, Toni Cortes5, Scott A. Klasky6, Alberto Miranda7, Franz-Josef Pfreundt8, Member, ACM, Robert B. Ross4, Marc-André Vef1        

  1. 1 Zentrum für Datenverarbeitung, Johannes Gutenberg University Mainz, Mainz 55128, Germany;
    2 Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, U.S.A;
    3 Department of Computer Science, Florida State University, Tallahassee, FL 32306, U.S.A;
    4 Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL 60439, U.S.A;
    5 Department of Computer Architecture, Universitat Politecnica de Catalunya, Barcelona 08034, Spain;
    6 Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, U.S.A;
    7 Computer Science Department, Barcelona Supercomputing Center, Barcelona 08034, Spain;
    8 Fraunhofer Institute for Industrial Mathematics ITWM, Fraunhofer-Platz 1, Kaiserslautern 67663, Germany
  • Received:2019-06-30 Revised:2019-08-30 Online:2020-01-05 Published:2020-01-14
  • Contact: AndréBrinkmann, Kathryn Mohror, Weikuan Yu;;
  • About author:André Brinkmann is a full professor at the Computer Science Department of Johannes Gutenberg University Mainz (JGU) and head of the university's Data Center ZDV (Zentrum für Datenverarbeitung) (since 2011). He received his Ph.D. degree in electrical engineering in 2004 from the Paderborn University, Paderborn, and has been an assistant professor in the Computer Science Department of the Paderborn University from 2008 to 2011. Furthermore, he has been the managing director of the Paderborn Centre for Parallel Computing PC2 during this time frame. His research interests focus on the application of algorithm engineering techniques in the area of data centre management, cloud computing, and storage systems.
  • Supported by:
    This work has also been partially funded by the German Research Foundation (DFG) through the German Priority Programme 1648 "Software for Exascale Computing" (SPPEXA) and the ADA-FS project, and by the European Union's Horizon 2020 Research and Innovation Program under the NEXTGenIO Project under Grant No. 671591, the Spanish Ministry of Science and Innovation under Contract No. TIN2015-65316, and the Generalitat de Catalunya under Contract No. 2014-SGR-1051. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344 (LLNL-JRNL-779789) and also supported by the U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research, under Contract No. DE-AC02-06CH11357. This work is also supported in part by the National Science Foundation of USA under Grant Nos. 1561041, 1564647, 1744336, 1763547, and 1822737.

Storage backends of parallel compute clusters are still based mostly on magnetic disks, while newer and faster storage technologies such as flash-based SSDs or non-volatile random access memory (NVRAM) are deployed within compute nodes. Including these new storage technologies into scientific workflows is unfortunately today a mostly manual task, and most scientists therefore do not take advantage of the faster storage media. One approach to systematically include nodelocal SSDs or NVRAMs into scientific workflows is to deploy ad hoc file systems over a set of compute nodes, which serve as temporary storage systems for single applications or longer-running campaigns. This paper presents results from the Dagstuhl Seminar 17202 "Challenges and Opportunities of User-Level File Systems for HPC" and discusses application scenarios as well as design strategies for ad hoc file systems using node-local storage media. The discussion includes open research questions, such as how to couple ad hoc file systems with the batch scheduling environment and how to schedule stage-in and stage-out processes of data between the storage backend and the ad hoc file systems. Also presented are strategies to build ad hoc file systems by using reusable components for networking and how to improve storage device compatibility. Various interfaces and semantics are presented, for example those used by the three ad hoc file systems BeeOND, GekkoFS, and BurstFS. Their presentation covers a range from file systems running in production to cutting-edge research focusing on reaching the performance limits of the underlying devices.

Key words: parallel architectures; distributed file system; high-performance computing; burst buffer; POSIX (portable operating system interface);

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