Please also analyse this:
no HDF5 involved...
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@rossant, a big part of this is that the fancy-indexing code in h5py uses a naive algorithm based on repeated hyperslab selection, which is quadratic in the number of indices. It was designed/tested for small numbers of indices.
The particular example you have here (0 to 10000 in steps of 10) can be mapped to slices (although of course this is not generally true). In this case the results are:
This is a great argument to improve the implementation of fancy indexing in h5py, but I would hesitate to conclude "HDF5 is slow".