Add flag to specify number of frames per-chunk in intermediate hdf5 data

[yousefmoazzam]

Built on top of work done in #271

This adds the --frames-per-chunk flag which enables the ability to:

• write the intermediate hdf5 data as chunked
• specify the number of frames (projections or sinograms) per-chunk

A value of 0 will turn chunking off (ie, write the hdf5 data as contiguous), and values > 0 will be the number of frames per-chunk.

Acceptance criteria checklist:

• [x] Intermediate data is chunked as expected
• [x] Nicely handle the case when the frames per-chunk value provided exceeds the number of frames (h5py throws an error if this is the case, should be handled nicely in some way)
• [x] Add tests
• [x] All tests pass

[yousefmoazzam]

To address the problem of if the value given to the --frames-per-chunk flag exceeds the length of the slicing dim (ie, the chunk shape exceeds the boundaries of the data to be written), when this happens, the frames per-chunk value used is 1 instead of the flag value.

If other behaviour is preferred, feel free to mention, I'll open this for review now.

[dkazanc]

Actually by enabling export OMPI_MCA_fcoll=dynamic fixed the PMIX related issue and I can confirm that I can run with more than one frame per chunk.