can't find hdf5.h when build caffe
tangshi opened this issue · 26 comments
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
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 -lhdf5so sad...
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.soTHX a lot, works for me on Ubuntu 15.04~
See also issue BVLC/caffe#2690
Thanks a lot...... worked in Ubuntu 16......
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/
YAY, thanks a lot! Worked on my Linux Mint 18(guess it's Sarah) too.
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
thank you. had the same problem.
thank you worked for me.
ubuntu 16.04
diff --git a/Makefile b/Makefile
index 65d08f7..6c6c9f3 100644
--- a/Makefile
+++ b/Makefile
@@ -178,7 +178,8 @@ ifneq ($(CPU_ONLY), 1)
LIBRARIES := cudart cublas curand
endif
-LIBRARIES += glog gflags protobuf boost_system boost_filesystem m hdf5_hl hdf5
+LIBRARIES += glog gflags protobuf boost_system boost_filesystem m
+LIBRARIES += hdf5_serial hdf5_serial_hl
Thanks. Awesome community. This worked on Ubuntu 16.04!
Be aware of what you are trying to simlink to
I have libhdf5_serial.so.10 not libhdf5_serial.so.8.0.2
See @jeremy-rutman's comment above.
Caffe compilation is now happily eating up my macbook's cycles.
ln: fallo al crear el enlace simbólico '/usr/lib/x86_64-linux-gnu/libhdf5.so': El archivo ya existe
Basically it fails to create the simlink because it states that the file already exists. Still, i keep getting the /usr/bin/ld: cannot find -lhdf5_serial_hl error...
https://ahmedibrahimvt.wordpress.com/2017/02/19/fatal-error-hdf5-h-no-such-file-or-directory/
The most perfect answer I have seen
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
export CPATH="/usr/include/hdf5/serial/"
Thank you @bucketzxm. It works like a charm!
Worked on ubuntu 16.04 LTS for me. Thanks!
You should use CMAKE and not Make if you are compiling with the solution above
worked on ubuntu 16.04 LTS
thank you @bucketzxm
Worked on ubuntu 18.04, thanks
Note - I had to change:
sudo ln -s libhdf5_serial.so.8.0.2 libhdf5.so
sudo ln -s libhdf5_serial_hl.so.8.0.2 libhdf5_hl.so
to
sudo ln -s libhdf5_serial.so.100.0.0 libhdf5.so
sudo ln -s libhdf5_serial.so.100.0.1 libhdf5_hl.so
install opencv:
apt-get install libopencv-dev
And had to remove the following lines from the makefile since I am on cuda 9.0:
-gencode arch=compute_20,code=sm_20
-gencode arch=compute_20,code=sm_21
export CPATH="/usr/include/hdf5/serial/"
Thanks @loretoparisi this worked for me!
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 export CPATH="/usr/include/hdf5/serial/"
Thank you! This worked for me
This helped me
https://askubuntu.com/a/645089/266204
Tried to do the symbolic link, those didn't work. This worked for me. Thanks. (i still have the symbolic links added too)
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/
where to find MakeFile.config?