In several industry and science applications, a filesystem-like storage model such as HDF5 is the more appropriate solution for manipulating large amounts of data. However, suppose that data changes over time. In that case, it's not obvious how to track those different versions, since HDF5 is a binary format and is not well suited for traditional version control systems and tools.
In a previous post, we introduced the Versioned HDF5 library, which implements a mechanism for storing binary data sets in a versioned way that feels natural to users of other version control systems, and described some of its features. In this post, we'll show some of the performance analysis we did while developing the library, hopefully making the case that reading and writing versioned HDF5 files can be done with a nice, intuitive API while being as efficient as possible. The tests presented here show that using the Versioned HDF5 library results in reduced disk space usage, and further reductions in this area can be achieved with the use of HDF5/h5py-provided compression algorithms. That only comes at a cost of <10x file writing speed.