MEX/GCC Setup Problems

[JoelChev]

Hi all,

I'm trying to setup matconvnet on my local CPU and run the v1_testnn script. During the compile process, I keep getting the following warning:

Warning: You are using gcc version '5.4.0'. The version of gcc is not supported. The version currently supported
with MEX is '4.9.x'. For a list of currently supported compilers see:

I'm running on Ubuntu 16.04, I'm assuming my gcc is too new for installing this toolkit? When I run the v1test_nn script, I get a bunch of these errors:

Error occurred in nnsimplenn[dataType=single,device=cpu]/backPropDepth and it did not run to completion.

---------
Error ID:
---------
'MATLAB:mex:ErrInvalidMEXFile'

--------------
Error Details:
--------------
Invalid MEX-file '/home/joelchev/Documents/CSC2515/project/LRR/matconvnet/matlab/mex/vl_nnconv.mexa64': /usr/local/MATLAB/R2016b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/joelchev/Documents/CSC2515/project/LRR/matconvnet/matlab/mex/vl_nnconv.mexa64).

So again, I'm running into some type of errors with MEX files not being generated properly during compilation. Does anyone have any tips/steps to fix this? Thanks!

[peterpans01]

Followed this issues. I have same problem.

[lenck]

Hi, this is old annoying issue with MATLAB shipping with an old version of the libstdc++, even though the compiler tends to use the system, newer version...
Several solutions are proposed e.g. here.

[zchrissirhcz]

thanks@lenck

Here's my situation, hope it can be useful:

I use ubuntu16.04 with x64 architecture. I installed matlab2016b, with cuda7.5 and cudnn5 installed.
I faced with similar problem and handle it by executing these commands:(for me, default gcc is version 5.4)

cd /usr/local/MATLAB/R2016b/sys/os/glnxa64  #where I installed my matlab
sudo mv libstdc++.so.6.0.20 bak-libstdc++.so.6.0.20
sudo mv libstdc++.so.6 bak-libstdc++.so.6
sudo ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21 ./
sudo ln -sf ./libstdc++.so.6.0.21 ./libstdc++.so.6

Then reopen matlab and compile MatConvNet. Still have warning about gcc version but compiling can be done.

[SahilC]

Thanks @zchrissirhcz!! This worked for me :)

[Ashutosh1995]

Thanks a lot @zchrissirhcz ....it worked for me too :-)

[pilhoon]

Thanks a lot @zchrissirhcz !!!!!!!!!!!!

(I just removed four files :
libstdc++.so.6.0.20 libgcc_s.so.1 libgfortran.so.3.0.0 libquadmath.so.0.0.0 in the MATLAB path(usually under /usr/local/MATLAB/).
README.libstdc++file is saying these files are included for only in the event that your distribution does not provide them.
So just removing them(=making MATLAB use system default library) would enough.)

[GeneL64]

Hello all,
Trying to solve a similar problem with gcc incompatibility when running 'make matcaffe' to make a Matlab wrapper for Caffe.

Was trying to follow @zchrissirhcz recommendations. Got:
mv: cannot move 'libstdc++.so.6.0.20' to 'bak-libstdc++.so.6.0.20': Permission denied
The file has the following permissions
-r-xr-xr-x 1 support support 6814982 Jul 22 2016 libstdc++.so.6.0.20
Attempt to change those with 'chmod' failed
chmod: changing permissions of 'libstdc++.so.6.0.20': Operation not permitted

Interesting that after the warning during 'make matcaffe' I seem to be getting a successful compilation anyway:
chmod: changing permissions of 'libstdc++.so.6.0.20': Operation not permitted

However, a subsequent 'make mattest' run throws numerous errors like:
Warning: The following error was caught while executing 'caffe.Net' class destructor:
Error using caffe_
Usage: caffe_('delete_solver', hNet)
Error in caffe.Net/delete (line 72)
caffe_('delete_net', self.hNet_self);
Error in caffe.Net (line 31)
self = caffe.get_net(varargin{:});
Error in caffe.test.test_net (line 39)
self.net = caffe.Net(self.model_file, 'train');

And at the end:
Totals:
7 Passed, 0 Failed, 0 Incomplete.
0.6783 seconds testing time.

1.Are those error result from gcc incompatibility or something else?
2. If '1' is 'yes' how to solve those?

Thanks!!!

[thylacine1975]

I needed to extend the advice of @zchrissirhcz to creating a symlink in the /usr/lib/x86_64-linux-gnu directory as well pointing to a .so file without the version suffix. i.e.:

sudo ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.20 /usr/lib/x86_64-linux-gnu/libstdc++.so

..then all was happy :)

[soulslicer]

i did the above fix but I get this error:

[100%] Building Matlab interface: /home/ryaadhav/caffe/matlab/+caffe/private/caffe_.mexa64
Building with 'g++'.
Warning: You are using gcc version '5.4.0'. The version of gcc is not supported. The version currently supported with MEX is '4.9.x'. For a list of currently supported compilers see: http://www.mathworks.com/support/compilers/current_release.
In file included from /usr/local/include/caffe/common.hpp:19:0,
from /usr/local/include/caffe/blob.hpp:8,
from /usr/local/include/caffe/caffe.hpp:7,
from /home/ryaadhav/caffe/matlab/+caffe/private/caffe_.cpp:18:

[henanjun]

Thanks for your useful solution @zchrissirhcz . It works for me.

[ihnorton]

If you are on CentOS and have root or sudo, you can use these instructions to get a GCC 4.9 toolchain:

https://www.softwarecollections.org/en/scls/rhscl/devtoolset-3/

(note that only yum install devtoolset-3-toolchain is really necessary -- the other stuff in the full devtoolset-3 package is unrelated Java/IDE libraries)