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I had the same issue (twice). You don't need to install "libhdf5-dev" from source, sudo apt-get install libhdf5-dev works. In CMakeLists, add:

target_link_libraries(your_executable ${CATKIN_LIBRARIES} hdf5 hdf5_cpp hdf5_hl_cpp)

And in your cpp file:

#include "H5Cpp.h"