Caffe didn't see hdf5.h when compiling

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.

This solution worked for me on the Ubuntu16.04LTS

sudo apt-get install libhdf5-10sudo apt-get install libhdf5-serial-devsudo apt-get install libhdf5-devsudo apt-get install libhdf5-cpp-11find /usr -iname "*hdf5.h*"/usr/include/hdf5/serial/hdf5.hexport CPATH="/usr/include/hdf5/serial/"

Another case I've experienced with:

I was using Ubuntu 14.04 and installing hdf5-1.10.0.

I found hdf5.h was located in /usr/local/hdf5/include. Thus, I modified Makefile.config file by adding that location to INCLUDE_DIRS.

# Whatever else you find you need goes here.INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include \                    /usr/local/hdf5/include

I didn't rename anything in Makefile. It worked fine.