Matlab R2009b, Lucid Lynx
My version of gcc (4.4) is too high for Matlab R2009b (4.1 and 4.2), and Matlab chokes on it. The solution is as follows:
Install gcc-4.2:
sudo apt-get install gcc-4.2 sudo apt-get install g++-4.2
In matlab, run mex -setup and select the GCC compiler (I believe you will have to have sudo’d into Matlab for this to work). Next, at the command line:
sudo gedit ~/.matlab/R2009b/mexopts.sh
Replace all instances of CC=’gcc’ with CC=’gcc-4.2′. While you’re at it, replace -ansi with -std=c99 if you want to be able to use C++ style // comments.
DON’T RERUN mex -setup, since this overwrites mexopts.sh. That’s all.
Matlab R2011a, Natty Narwhal
There is a similar issue with newer versions of Matlab and Ubuntu (R2011a requires gcc 4.3). gcc-4.3 is not currently available as a package for Natty, you must first add the appropriate repository from Maverick. Thus:
Go to System > Administration > Synaptic Package Manager, then Settings > Repositories > Other Software, and click Add… In the box, write:
deb http://archive.ubuntu.com/ubuntu maverick universe
OK, close, Reload, then exit.
Then follow the instructions for R2009b, replacing 4.2 with 4.3. Should work as is. However, in my setup Matlab was giving me a weird error when starting it from the command line:
/usr/local/MATLAB/R2011a/bin/util/oscheck.sh: 605: /lib64/libc.so.6: not found
I don’t think this is a common error, but rather is due to my upgrade path. In any case, creating these two symlinks fixed the issue:
sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6
sudo ln -s /lib/x86_64-linux-gnu/libgcc_s.so.1 /lib64/libgcc_s.so.1
xcorr: AI & neuro 
11 responses to “Getting gcc to work with Matlab in Ubuntu to compile mex files”
I did what you said above ,but It didn’t work!My matlab error still exist:matlab/bin/util/oschec/sh:605:/lib/libc.so.6: not found.
By the way,after I did this “sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6”,I found that their link target didn’t change ,both of them link to “lib/x86_64-linux-gnu//libc.2.13”,can you tell me why?
I am no expert in Linux but I would just rm the symlink then recreate it with the ln line.
I have a new problem now though when i edited the gcc options file in order for matlab 2009b to recognise gcc 4.2 but i get this error.
I followed your instructions
My Error:
cc1plus: warning: command line option ‘-std=c99’ is valid for C/ObjC but not for C++ [enabled by default]
Any help is appreciated! Thanks!
That’s not an error, that’s just a warning. Everything should still compile.
Thanks a lot for this! When I tried compiling mex-files with Ubuntu 11.10 and Matlab 2011b I got similar complaints about the version of gcc. I also got errors of the kind “error: expected expression before ‘/’ token”, which I didn’t really understand until I read your post. After changing the occurences of -ansi with -std=c99 in the mexopts.sh file, the files finally compiled! It turned out that for my case, the version of gcc wasn’t really a problem – only the C++ comments were.
===that’s right! thanks
Thanks!!!
Thanks a lot for this! When I tried compiling mex-files with Ubuntu 11.10 and Matlab 2011b I got similar complaints about the version of gcc. I also got errors of the kind “error: expected expression before ‘/’ token”, which I didn’t really understand until I read your post. After changing the occurences of -ansi with -std=c99 in the mexopts.sh file, the files finally compiled! It turned out that for my case, the version of gcc wasn’t really a problem – only the C++ comments were.
I have no idea what that error means. Sorry I can’t be of more help.
I did it as you say,but I got “can’t start matlab engine” error again!!…what should I do now??:(..
It’s not mex-setup, it’s mex -setup (with a space). This may not have been obvious with the font I was using, so I changed the formatting on the post.
Hi,
I’ve had the same problem as you had, but I can’t download the package gcc-4.2 with synpatic because it said that there’s no link to download it, so I downloaded it from other sites and installed it manually. Now I’ve no idea how to run mex-setup!! Did you mean the mex_setup.m file which exist in matlab directory??…how can I select the gcc compiler for that file??…cause when I run this file I’ve got nothing and it ain’t make any sense.