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

hdf5.h:no such directory

The steps I have done:

Update and upgrade my Ubuntu Server
Install Python 2.7
Having all of the dependencies base on http://caffe.berkeleyvision.org/install_apt.html
Run cp cp Makefile.config.example Makefile.config
Uncomment cpu_only = 1 in Makefile.config

I will be grateful if someone can help me.

Error message:

CXX src/caffe/util/hdf5.cpp
in file include from src/caffe/util/hdf5.cpp:1:0:
./include/caffe/util/hdf5.hpp:6:18: fatal error: hdf5.h: No such file or directory
compilation terminated 

Makefile:572 recipe for target '.build_release/src/caffe/util/hdf5.o'       
failed Make:*** [.build_release/src/caffe/util/hdf5.o] Error 1

welcome to SO. please do not post screenshots, but rather copy-paste (and format) the error message to your question: this way search engines can better locate this thread in the future. — Shai, May 03 '16 at 15:07
have you installed hdf5? look at http://caffe.berkeleyvision.org/install_apt.html: `sudo apt-get install libhdf5-serial-dev` — Shai, May 03 '16 at 15:10
oh sorry about that i'm new, i will change the screenshots. thank you for notifying me. yes i already installed hdf5. — kelvin, May 05 '16 at 02:24
Do you have `hdf5.h` on your system somewhere? Try a command like `locate hdf5.h` to find out where it is, and post that here. — John Zwinck, May 05 '16 at 02:58
hi, i try to write `locate hdf5.h` as you suggest in my ubuntu terminal but nothing happen. so, i run another comment `find ~/ -type f -name "hdf5.h"` an the result is `/home/kelvin/opencv-3.1.0/modules/flann/include/opencv2/flann/hdf5.h`. Thank you — kelvin, May 05 '16 at 05:25

score 64 · Answer 1 · answered May 05 '16 at 18:03

64

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.

answered May 05 '16 at 18:03

alfakini

4,635
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sorry for my late response, thank you for your help i already fix the problem by moving my hdf5 to the directory. – kelvin May 08 '16 at 06:37
1

Thanks. That saves me time! – tobe Jul 01 '16 at 01:49
1

This is the solution that worked for me! Thanhs a lot! – Dang Manh Truong Sep 24 '16 at 04:29
This answer is indeed the best solution (i.e. instead of moving the hdf5 dir.) @kelvin : Could you mark this answer as correct? – MarvMind Nov 12 '16 at 14:43
I just added 'LIBRARIES += ' string. I don't have any and it seems working. – XuMuK Dec 08 '16 at 15:53
Thanks a lot. Solved my problem – user3304797 Jun 13 '17 at 18:22
1

This worked on Ubuntu 18.04 without adding the LIBRARIES part. – jfleach Aug 17 '18 at 15:25
indeed! Might also be worth to check [this answer](https://superuser.com/a/1276813/1732034), as MMV depending on system, some ln might be needed – M.K Sep 20 '22 at 13:54

score 30 · Answer 2 · answered Jul 04 '17 at 18:37

30

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/"

answered Jul 04 '17 at 18:37

loretoparisi

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3

Worked for me too! – O. Edholm Aug 25 '17 at 09:12
2

Worked for me three! – Neo li Apr 23 '18 at 09:27
just `sudo apt-get install libhdf5-10 libhdf5-serial-dev` worked for me – Tony Z May 14 '18 at 22:49

score 4 · Answer 3 · answered May 24 '16 at 06:29

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.

score 4 · Answer 4 · answered Aug 09 '20 at 10:09

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/"

score 1 · Answer 5 · answered Jul 14 '20 at 15:27

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

Caffe didn't see hdf5.h when compiling

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