What is the version of your Ubuntu install? Try this. In your Makefile.config try to append /usr/include/hdf5/serial/ to INCLUDE_DIRS:
--- INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include
+++ INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/
and rename hdf5_hl and hdf5 to hdf5_serial_hl and hdf5_serial in the Makefile:
--- LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_hl hdf5
+++ LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_serial_hl hdf5_serial
More about the bug fix here.