can't find hdf5.h when build caffe

[tangshi]

I want to install digits on my debian jessie.
When I build caffe(NVIDIA's fork), I got errors complaining that hdf5.h could not be found.

I'm sure I had installed libhdf5-serial-dev and libhdf5-dev, and I found the header file in /usr/include/hdf5/serial and its libs in /usr/lib/x86_64-linux-gnu.

So, what's wrong? Some one help me?

The build error message show below:

(venv)➜  caffe  make all --jobs=4
CXX src/caffe/layer_factory.cpp
CXX src/caffe/util/insert_splits.cpp
CXX src/caffe/util/db.cpp
CXX src/caffe/util/upgrade_proto.cpp
In file included from src/caffe/util/upgrade_proto.cpp:10:0:
./include/caffe/util/io.hpp:8:18: fatal error: hdf5.h: no such file or directory
 #include "hdf5.h"
                  ^
compilation terminated.
Makefile:512: recipe for target '.build_release/src/caffe/util/upgrade_proto.o' failed
make: *** [.build_release/src/caffe/util/upgrade_proto.o] Error 1
make: *** 正在等待未完成的任务....
In file included from ./include/caffe/common_layers.hpp:10:0,
                 from ./include/caffe/vision_layers.hpp:10,
                 from src/caffe/layer_factory.cpp:6:
./include/caffe/data_layers.hpp:9:18: fatal error: hdf5.h: no such file or directory
 #include "hdf5.h"
                  ^
compilation terminated.
Makefile:512: recipe for target '.build_release/src/caffe/layer_factory.o' failed
make: *** [.build_release/src/caffe/layer_factory.o] Error 1

[tangshi]

I solved the header file problem according to here.

But there is another problem:

/usr/bin/ld: cannot find -lhdf5_hl
/usr/bin/ld: cannot find -lhdf5

so sad...

[tangshi]

Lucky! I solved the second problem!

The lib names of hdf5 on debian have a postfix "serial", therefore -lhdf5 and -lhdf5_hl cannot be found.

To solve it, I created two symbolics:

cd /usr/lib/x86_64-linux-gnu
sudo ln -s libhdf5_serial.so.8.0.2 libhdf5.so
sudo ln -s libhdf5_serial_hl.so.8.0.2 libhdf5_hl.so

[chenyang-charles]

THX a lot, works for me on Ubuntu 15.04~

[dgorissen]

See also issue BVLC/caffe#2690

[minemeraj]

Thanks a lot...... worked in Ubuntu 16......

[bucketzxm]

after do the two steps @tangshi mentioned, I continued to add the following lines in MakeFile.config
INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/ and
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/lib/x86_64-linux-gnu/hdf5/serial/

[coelho-oliva]

YAY, thanks a lot! Worked on my Linux Mint 18(guess it's Sarah) too.

[jeremy-rutman]

the lbhdf5 you actually have will determine what symlink to do - so after ls /usr/lib/x86_64-linux-gnu to see what version you have, do the symlink taking that into account. (.e.g i had v10 not v8 as in post above)

$ sudo ln -s /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10 /usr/lib/x86_64-linux-gnu/libhdf5.so
$ sudo ln -s /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10 /usr/lib/x86_64-linux-gnu/libhdf5_hl.so