This is because of change of default path and name of hdf5
head files and libraries in Ubuntu 16.04
Append /usr/include/hdf5/serial/
to INCLUDE_DIRS
in Makefile.config
.
change it as: INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
Modify hdf5_hl
and hdf5
to hdf5_serial_hl
and hdf5_serial
in line LIBRARIES
in Makefile
LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_serial_hl hdf5_serial