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This is how we recommend citing HDF5:

  The HDF Group. Hierarchical Data Format, version 5, 1997-NNNN.

Where "NNNN" is the current year.

The LaTeX BibRef for this is:

    author = {{The HDF Group}},
    title = "{Hierarchical Data Format, version 5}",
    year = {1997-NNNN},
    note = {}