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Can you work with an HDF5 file in memory?

Yes. You can create an HDF5 file in memory using H5Pset_fapl_core and use the backing_store parameter to write the data to disk on closing.

Can I subsequently open the file and put the data in memory ?

Yes, as of HDF5 1.8, you can bring the file into memory, read it, modify it and write it back, using the core driver. With HDF5 1.6, you could only write it back, with no open.