Journal of Computer Science and Technology ›› 2020, Vol. 35 ›› Issue (1): 145-160.doi: 10.1007/s11390-020-9822-9

Special Issue: Computer Architecture and Systems

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

ExaHDF5: Delivering Efficient Parallel I/O on Exascale Computing Systems

Suren Byna1,*, M. Scot Breitenfeld2, Bin Dong1, Quincey Koziol1, Elena Pourmal2, Dana Robinson2, Jerome Soumagne2, Houjun Tang1, Venkatram Vishwanath3, Richard Warren2   

  1. 1 Lawrence Berkeley National Laboratory, Berkeley, CA 94597, U.S.A;
    2 The HDF Group, Champaign, IL 61820, U.S.A;
    3 Argonne National Laboratory, Lemont, IL 60439, U.S.A
  • Received:2019-07-06 Revised:2019-08-28 Online:2020-01-05 Published:2020-01-14
  • Contact: Suren Byna
  • About author:Suren Byna received his Master's degree in 2001 and Ph.D. degree in 2006, both in computer science from Illinois Institute of Technology, Chicago. He is a Staff Scientist in the Scientific Data Management (SDM) Group in CRD at Lawrence Berkeley National Laboratory (LBNL). His research interests are in scalable scientific data management. More specifically, he works on optimizing parallel I/O and on developing systems for managing scientific data. He is the PI of the ECP funded ExaHDF5 project, and ASCR funded object-centric data management systems (Proactive Data Containers-PDC) and experimental and observational data management (EOD-HDF5) projects.
  • Supported by:
    This research was supported by the Exascale Computing Project under Grant No. 17-SC-20-SC, a joint project of the U.S. Department of Energy's Office of Science and National Nuclear Security Administration, responsible for delivering a capable exascale ecosystem, including software, applications, and hardware technology, to support the nation's exascale computing imperative. This work is also supported by the Director, Office of Science, Office of Advanced Scientific Computing Research, of the U.S. Department of Energy under Contract Nos. DE-AC02-05CH11231 and DE-AC02-06CH11357. This research was funded in part by the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract No. DE-AC02-06CH11357. This research used resources of the National Energy Research Scientific Computing Center, which is DOE Office of Science User Facilities supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Scientific applications at exascale generate and analyze massive amounts of data. A critical requirement of these applications is the capability to access and manage this data efficiently on exascale systems. Parallel I/O, the key technology enables moving data between compute nodes and storage, faces monumental challenges from new applications, memory, and storage architectures considered in the designs of exascale systems. As the storage hierarchy is expanding to include node-local persistent memory, burst buffers, etc., as well as disk-based storage, data movement among these layers must be efficient. Parallel I/O libraries of the future should be capable of handling file sizes of many terabytes and beyond. In this paper, we describe new capabilities we have developed in Hierarchical Data Format version 5 (HDF5), the most popular parallel I/O library for scientific applications. HDF5 is one of the most used libraries at the leadership computing facilities for performing parallel I/O on existing HPC systems. The state-of-the-art features we describe include:Virtual Object Layer (VOL), Data Elevator, asynchronous I/O, full-featured single-writer and multiple-reader (Full SWMR), and parallel querying. In this paper, we introduce these features, their implementations, and the performance and feature benefits to applications and other libraries.

Key words: parallel I/O, Hierarchical Data Format version 5 (HDF5), I/O performance, virtual object layer, HDF5 optimizations

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