Google Protocol Buffers, HDF5, NumPy comparison (transferring data)?

There does seem to be a slight contradiction in your question - you want to be able to store Python objects, but you also want C/C++ access. I think that regardless of which choice you go with, you will need to convert your fancy Python data structures into more static structures such as arrays.

I don't know about HDF5, but you can store Python objects in NumPy arrays, you just lose all the important functionality by disallowing C-level operations to be performed on the array.

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