Caffe didn't see hdf5.h when compiling

Question

I am having trouble when installing Caffe Deep Learning Framework on Python:

When I run make command at caffe directory, it says

Answer 1

This solution worked for me on the Ubuntu16.04LTS

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

Answer 2

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.

Answer 3

It did not work for me on Ubuntu16.04 LTS.

So I had to

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

Now do this

export CPATH="/usr/include/hdf5/serial/"

Answer 4

On RHEL7, I got tired of hunting for specific hdf5 RPMs and ran:

sudo yum install *hdf5*

and these are what I have:

hdf5-openmpi3-static-1.8.12-11.el7.x86_64
hdf5-1.8.12-11.el7.x86_64
hdf5-openmpi-static-1.8.12-11.el7.x86_64
hdf5-openmpi3-devel-1.8.12-11.el7.x86_64
hdf5-openmpi3-1.8.12-11.el7.x86_64
hdf5-mpich-devel-1.8.12-11.el7.x86_64
hdf5-devel-1.8.12-11.el7.x86_64
hdf5-openmpi-devel-1.8.12-11.el7.x86_64
hdf5-mpich-static-1.8.12-11.el7.x86_64
hdf5-mpich-1.8.12-11.el7.x86_64
hdf5-openmpi-1.8.12-11.el7.x86_64

Thanks to @loretoparisi, I was able to figure out where I had the header file I was missing and the problem went away.

$ find /usr -iname "*hdf5.h*"
/usr/include/openmpi-x86_64/hdf5.h
/usr/include/hdf5.h
/usr/include/mpich-x86_64/hdf5.h
/usr/include/openmpi3-x86_64/hdf5.h

Answer 5

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.