Tuning HDF5 for Lustre File Systems

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HDF5 is a cross-platform parallel I/O library that is used by a wide variety of HPC applications for the flexibility of its hierarchical object-database representation of scientific data. We describe our recent work to optimize the performance of the HDF5 and MPI-IO libraries for the Lustre parallel file system. We selected three different HPC applications to represent the diverse range of I/O requirements, and measured their performance on three different systems to demonstrate the robustness of our optimizations across different file system configurations and to validate our optimization strategy. We demonstrate that the combined optimizations improve HDF5 parallel I/O performance ... continued below

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Howison, Mark; Koziol, Quincey; Knaak, David; Mainzer, John & Shalf, John September 24, 2010.

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HDF5 is a cross-platform parallel I/O library that is used by a wide variety of HPC applications for the flexibility of its hierarchical object-database representation of scientific data. We describe our recent work to optimize the performance of the HDF5 and MPI-IO libraries for the Lustre parallel file system. We selected three different HPC applications to represent the diverse range of I/O requirements, and measured their performance on three different systems to demonstrate the robustness of our optimizations across different file system configurations and to validate our optimization strategy. We demonstrate that the combined optimizations improve HDF5 parallel I/O performance by up to 33 times in some cases running close to the achievable peak performance of the underlying file system and demonstrate scalable performance up to 40,960-way concurrency.

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  • Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS10),, Heraklion, Crete, Greece, September 24, 2010

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  • Report No.: LBNL-4803E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 1050648
  • Archival Resource Key: ark:/67531/metadc837191

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  • September 24, 2010

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  • May 19, 2016, 9:45 a.m.

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  • Nov. 7, 2016, 8:45 p.m.

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Howison, Mark; Koziol, Quincey; Knaak, David; Mainzer, John & Shalf, John. Tuning HDF5 for Lustre File Systems, article, September 24, 2010; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc837191/: accessed November 16, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.