Here are some weaknesses of HDF5 according to NASA who was going to use it. Matlab mentioned as well
Weaknesses: HDF5 is undeniably complex, and requires a significant learning curve. However, users also applaud the quality of documentation and help-desk support available. Third-party tools with HDF5 support, such as IDL and Matlab, also help hide complexity from users. Users have expressed concern about the availability of long-term support for HDF5 and related tools, but this concern is somewhat alleviated by the availability of the source code.
Applicability: HDF5 is used for data archive and distribution. The strengths cited above, together with the availability of analysis tools, make the format suitable for data analysis as well. The new netCDF 4.0 will include the capability to use HDF5 as the data storage layer for the netCDF API, with the addition of many new features available in HDF5 such as user defined types, multiple unlimited dimensions, and per-variable data compression. This merger of the two formats will further extend the HDF5 user community.
Limitations: A major limitation for HDF5 is the loss of backward compatibility with HDF4 and earlier versions. Also, unlike less complex formats, users cannot read the HDF5 files directly without using the HDF5 software library. Of greater concern are recent postings on a mailing list discussing use of netCDF and HDF5 in high performance computing applications with thousands of processors using parallel I/O, which warn of the danger of file corruption during parallel I/O if a client dies at a particular time. The HDF Group is aware of this problem and is addressing it.
Overall, HDF5 is a widely used data format with a well-defined specification that provides a standard way of storing and working with science data. The ESDS-RFC-007 TWG thus recommends its endorsement by the SPG as an Earth Science Data Systems Standard.
Sadly, I would therefore not consider this an option for my infrastructure!!
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