"undefined symbol: _ZNK6google8protobuf7Message11GetTypeNameEv", g++-4.9

[hughperkins]

Installed as follows, on ubuntu 15.10:

export CC=gcc-4.9
export CXX=g++-4.9
sudo apt-get install -y libprotobuf-dev protobuf-c-compiler protobuf-compiler
luarocks install loadcaffe

Test as follows:

luajit -l loadcaffe

What I expect to happen:

• silently runs, no error messages

What actually happens:

luajit: /home/ubuntu/torch/install/share/lua/5.1/loadcaffe/ffi.lua:10: /home/ubuntu/torch/install/lib/lua/5.1/libloadcaffe.so: undefined symbol: _ZNK6google8protobuf7Message11GetTypeNameEv
stack traceback:
    [C]: in function 'load'
    /home/ubuntu/torch/install/share/lua/5.1/loadcaffe/ffi.lua:10: in main chunk
    [C]: in function 'dofile'
    /home/ubuntu/torch/install/share/lua/5.1/torch/init.lua:49: in function 'include'
    /home/ubuntu/torch/install/share/lua/5.1/loadcaffe/init.lua:3: in main chunk
    [C]: at 0x0046b7a0
    [C]: at 0x00406670

[hughperkins]

Gist of build and output here: https://gist.github.com/hughperkins/da764a09b37a84e67684

Edit: protobuf version:

dpkg -l libprotobuf-dev | grep ii
ii  libprotobuf-dev:amd64 2.6.1-1.2    amd64        protocol buffers C++ library (development files)

[hughperkins]

Oh... looks like since protobuf is a c++ library, needs gcc-5 to build it, on ubuntu 15.10. (Different from the cuda libraries, which needs 4.9 to build, since cuda toolkit doesnt work with gcc-5).

CC=
CXX=
rm -Rf build
luarocks make loadcaffe-1.0.0-rockspec
luajit -l loadcaffe

=> works ok

[jayanthkoushik]

Hi, I'm having the same issue even with gcc-5.4.0. Any ideas? It's the exact same issue. https://gist.github.com/jayanthkoushik/6b90eaad95ced5b7d0aa0762b34d60bf.

[jayanthkoushik]

Ah, I think I see the problem. It sets the runtime path to $ORIGIN/../lib. But protobuf isn't there. Is there any way to change this?

[andrefaraujo]

@jayanthkoushik were you able to solve this? My error message is exactly the same as yours. I'd think the linking would work correctly, since this is what I get when I do an "ldd" on libloadcaffe:

$ ldd /home/afaraujo/torch/install/lib/lua/5.1/libloadcaffe.so
linux-vdso.so.1 =>  (0x00007fff985f8000)
libTH.so => /home/afaraujo/torch/install/lib/libTH.so (0x00007fb949ca0000)
libprotobuf.so.9 => /share/sw/free/protobuf/2.6.1rc1/lib/libprotobuf.so.9 (0x00007fb949820000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fb9495ea000)
libblas.so.3 => /usr/lib64/libblas.so.3 (0x00007fb949393000)
liblapack.so.3 => /usr/lib64/liblapack.so.3 (0x00007fb948b81000)
librt.so.1 => /lib64/librt.so.1 (0x00007fb948979000)
libstdc++.so.6 => /share/sw/free/gcc/5.3.0/lib64/libstdc++.so.6 (0x00007fb9485eb000)
libm.so.6 => /lib64/libm.so.6 (0x00007fb948366000)
libgcc_s.so.1 => /share/sw/free/gcc/5.3.0/lib64/libgcc_s.so.1 (0x00007fb948150000)
libc.so.6 => /lib64/libc.so.6 (0x00007fb947dbc000)
libgomp.so.1 => /share/sw/free/gcc/5.3.0/lib64/libgomp.so.1 (0x00007fb947b9a000)
/lib64/ld-linux-x86-64.so.2 (0x0000003711a00000)
libz.so.1 => /lib64/libz.so.1 (0x00007fb947984000)
libgfortran.so.3 => /share/sw/free/gcc/5.3.0/lib64/libgfortran.so.3 (0x00007fb947663000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fb94745f000)
libquadmath.so.0 => /share/sw/free/gcc/5.3.0/lib/../lib64/libquadmath.so.0 (0x00007fb947220000)

libprotobuf has the correct path, but still "luajit -l loadcaffe" fails exactly like it fails for you... any help would be appreciated!

[jayanthkoushik]

@andrefaraujo No, I was not :-(

[andrefaraujo]

@jayanthkoushik I was able to fix this by installing the most recent protobuf library (I cloned to a local directory from github here). I followed these instructions, except that I installed it to my home folder instead of to the default location. This is done by using the prefix option when issuing the configure command:

./configure --prefix=/home/afaraujo/protobuf

After building this new protobuf version, you can actually see that the "_ZNK6google8protobuf7Message11GetTypeNameB5cxx11Ev" symbol is there!

$ grep _ZNK6google8protobuf7Message11GetTypeNameB5cxx11Ev /home/afaraujo/protobuf/lib/libprotobuf.so
Binary file /home/afaraujo/protobuf/lib/libprotobuf.so matches

In the CMakeLists.txt for the loadcaffe package, make sure to add the following lines (of course, change the path accordingly):

SET(PROTOBUF_LIBRARY "/home/afaraujo/protobuf/lib/libprotobuf.so")
SET(PROTOBUF_INCLUDE_DIR "/home/afaraujo/protobuf/include/")
SET(PROTOBUF_PROTOC_EXECUTABLE "/home/afaraujo/protobuf/bin/protoc")

Then, in the loadcaffe path, run:

luarocks make loadcaffe-1.0-0.rockspec

and then it works :) hopefully this works for you too...

[hughperkins]

I think the issue is caused by a mismatch between the g++ version used to build the protobuf library, and that used to build loadcaffe.

Installing the latest version of protobuf, as per @andrefaraujo , my guess is, solves the issue, becuase the library is being rebuilt with the same version of g++ as loadcaffe? It's not certain, but I feel it could be a hypothesis worth double-checking perhaps?

[victoriastuart]

I had this issue. I generally use Anaconda virtual environments to isolate packages/installs, but got lazy and for convenience had caffe, and then later tensorflow installed in a py27 venv. The problem is multiply-present "protobuf" installs; in my case, via pip and conda.

On my Arch Linux system I needed the pip-installed protobuf ("pip install protobuf") for my caffe install,

pip list | grep -i protobuf
    protobuf (3.1.0.post1)

but tensoflow (installed via "conda install -c conda-forge tensorflow") installed the following:

protobuf:   3.0.0-py27_0  conda-forge
tensorflow: 0.11.0-py27_0 conda-forge

Go ahead and remove all those protobuf versions

pip uninstall  protobuf
conda uninstall protobuf
conda uninstall libprotobuf    ## if present

then delete and reinstall caffe:

git clone https://github.com/BVLC/caffe
cd caffe
# edit "Makefile.config" file per your system, needs
make all -j8    ## 8 cores on my Intel CPU
# add pycaffe your $PYTHONPATH
export PYTHONPATH=${PYTHONPATH}:/mnt/Vancouver/apps/caffe/python/
#  can also add to ~/.bashrc or your preferred "$PYTHONPATH" file ..
make pycaffe
pip install protobuf

I am again able to import caffe in my py27 venv, without the "undefined symbol: _ZNK6google8protobuf7Message11GetTypeNameEv..." error.

I just then went ahead and reinstalled tensorflow,

conda install -c conda-forge tensorflow

with the caveat that on on subsequent caffe or tensorflow updates I may need to repeat this process; due to this mess:

pip list | grep -i protobuf
    protobuf (3.1.0.post1)

conda list | grep -i protobuf
    protobuf                  3.1.0.post1               <pip>
    protobuf                  3.0.0                    py27_0    conda-forge

Meh ! :-/

But I can import my packages, again:

>>> import caffe
>>> import tensorflow
>>> tensorflow.__version__
    '0.11.0'
>>> import cv2
>>> import keras
    Using Theano backend.
>>> import scipy
>>> import theano
>>> import numpy
>>> ## ...

[archenroot]

Same happened here on Gentoo system with gcc 6.2.0, I just reinstalled latest version -> dev-libs/protobuf-3.1.0::gentoo

And now the error dissapeared.

[b4zz4]

sudo $(which luarocks) install loadcaffe
I use this and fix

[lijiansong]

We can install loadcaffe from the original source code, by

git clone https://github.com/szagoruyko/loadcaffe.git
cd loadcaffe
luarocks make loadcaffe-1.0-0.rockspec

if you have some problems as @andrefaraujo mentioned， you have to build libprotobuf from its source code, set libprotobuf path in the CMakeLists.txt for this loadcaffe package, then

cd loadcaffe
luarocks make loadcaffe-1.0-0.rockspec

[hlnull]

Share my solution first. These two commands solved my problem.

sudo apt-get install protobuf-compiler
sudo $(which luarocks) install loadcaffe

Hi, sudo $(which luarocks) install loadcaffe did solve this problem on my computer. Thanks.

I checked the logs of sudo $(which luarocks) install loadcaffe and luarocks install loadcaffe and found a little difference:

sudo $(which luarocks) install loadcaffe:

-- Set runtime path of "/home/name/torch/install/lib/luarocks/rocks/loadcaffe/1.0-0/lib/libloadcaffe.so" to "$ORIGIN/../lib:/home/name/torch/install/lib"

luarocks install loadcaffe:

-- Set runtime path of "/home/name/torch/install/lib/luarocks/rocks/loadcaffe/1.0-0/lib/libloadcaffe.so" to "$ORIGIN/../lib:/home/name/torch/install/lib:/home/name/anaconda2/lib"

Running luarocks without sudo include /home/name/anaconda2/lib. It is weird since loadcaffe shall have nothing to do with anaconda2, which is used in python. Then I remembered I installed protobuf in the anaconda2 environment. It seems luajit found the protobuf.lib in /home/name/anaconda2/lib instead of correct lib.

So check the logs and make sure nothing weird happens.

Besides, there might be some methods in lua to find which protobuf I am using, right? Does anyone knows the answer?

[xingdi1990]

Tried all the methods mentioned above, does not work for me. :(