please use anaconda to install the HDF5
please check your conda package
conda list
uninstall hdf5 if your version is 1.8.16 (default version in conda)
sudo conda uninstall hdf5
using anaconda search and checkout available packages
anaconda search -t conda hdf5
we perfer you install the 1.8.15 version (or 1.8.15.1 patchy version)
sudo conda install hdf5=1.8.15.1
first check the default h5py version (2.6.0 default)
sudo conda uninstall h5py
version 2.5.0 is recommended
sudo conda install h5py=2.5.0
now check your packages
conda list
more details >> h5py
import h5py
f = h5py.File('test.h5', 'r')