NetCDF4 is a layer on top of HDF5. NetCDF4 reads/writes specially structured HDF5 files. Performance of HDF5 and NetCDF4 is highly similar including on supercomputers. The main idea behind NetCDF4 is a simpler API than HDF5, while maintaining the same performance.
h5py makes HDF5 read/write very easy. NetCDF4 is also easy to use from Python. All things being nearly equal, perhaps the choice between NetCDF4 and HDF5 will be dictated by team consensus.
C / C++ / Fortran