Thread Subject: problem with Matlab 2009a on x64 Ubuntu intrepid

I have been using the latest version of matlab(2009a) on x64 ubuntu 8.10 for a couple of weeks now.
Every thing works fine but I can't make the matlab compile my C files into Matlab mex(using mex function). Intrepid is shipped with gcc 4.3.2 while the latest version that matlab supports is still gcc 4.2.3 so I think this should be the source of the problem.
When I mex a script, matlab warns me about the wrong version of the GCC and then the mex-ed file does not work properly. I get odd errors like "out of memory" or the mex ed function returns an incorrect value. The script works fine when I mex it on another computer with an older version of Linux(opensuse 10.3) which has a compatible GCC.

I tried to install an older version of GCC on intrepid but I either did it wrong or it didn't solve my problem.

I would appreciate if anyone have any idea/experience about solving this problem.

amin

Hi Amin,

I have a similar problem too. I run R2009a on a Mac Intel machine and mex-ing my C code with mex wrappers seem to work fine. I also discovered MATLAB supports up to gcc 4.2. Apple's OS X still ships with gcc-4.1 so it worked fine. I tried compiling with mex on another x86 PC running Ubuntu 9.04 Jaunty (having install and changed the symbolic link of gcc to gcc-4.1 and also gcc-4.2 in two separate tests) and this is the verbose error message I get:

# mex -v vech.c
-> mexopts.sh sourced from directory (DIR = $HOME/.matlab/$REL_VERSION)
   FILE = /root/.matlab/R2009a/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /usr/local/matlab/R2009a
-> CC = gcc
-> CC flags:
         CFLAGS = -ansi -D_GNU_SOURCE -fPIC -pthread -m32 -fexceptions -D_FILE_OFFSET_BITS=64
         CDEBUGFLAGS = -g
         COPTIMFLAGS = -O -DNDEBUG
         CLIBS = -Wl,-rpath-link,/usr/local/matlab/R2009a/bin/glnx86 -L/usr/local/matlab/R2009a/bin/glnx86 -lmx -lmex -lmat -lm -lstdc++
         arguments = -DMX_COMPAT_32
-> CXX = g++
-> CXX flags:
         CXXFLAGS = -ansi -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread
         CXXDEBUGFLAGS = -g
         CXXOPTIMFLAGS = -O -DNDEBUG
         CXXLIBS = -Wl,-rpath-link,/usr/local/matlab/R2009a/bin/glnx86 -L/usr/local/matlab/R2009a/bin/glnx86 -lmx -lmex -lmat -lm
         arguments = -DMX_COMPAT_32
-> FC = g95
-> FC flags:
         FFLAGS = -fexceptions -fPIC
         FDEBUGFLAGS = -g
         FOPTIMFLAGS = -O
         FLIBS = -Wl,-rpath-link,/usr/local/matlab/R2009a/bin/glnx86 -L/usr/local/matlab/R2009a/bin/glnx86 -lmx -lmex -lmat -lm
         arguments = -DMX_COMPAT_32
-> LD = gcc
-> Link flags:
         LDFLAGS = -pthread -shared -m32 -Wl,--version-script,/usr/local/matlab/R2009a/extern/lib/glnx86/mexFunction.map -Wl,--no-undefined
         LDDEBUGFLAGS = -g
         LDOPTIMFLAGS = -O
         LDEXTENSION = .mexglx
         arguments =
-> LDCXX =
-> Link flags:
         LDCXXFLAGS =
         LDCXXDEBUGFLAGS =
         LDCXXOPTIMFLAGS =
         LDCXXEXTENSION =
         arguments =
----------------------------------------------------------------

-> gcc -c -I/usr/local/matlab/R2009a/extern/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fPIC -pthread -m32 -fexceptions -D_FILE_OFFSET_BITS=64 -DMX_COMPAT_32 -O -DNDEBUG "vech.c"

vech.c:77:2: warning: no newline at end of file
-> gcc -O -pthread -shared -m32 -Wl,--version-script,/usr/local/matlab/R2009a/extern/lib/glnx86/mexFunction.map -Wl,--no-undefined -o "vech.mexglx" vech.o -Wl,-rpath-link,/usr/local/matlab/R2009a/bin/glnx86 -L/usr/local/matlab/R2009a/bin/glnx86 -lmx -lmex -lmat -lm -lstdc++

/usr/bin/ld: cannot find -lstdc++
collect2: ld returned 1 exit status

    mex: link of ' "vech.mexglx"' failed.

Any luck with advice?

Cheers,
Tim

"Amin " <azandvak@aecom.yu.edu> wrote in message <gua17m$m72$1@fred.mathworks.com>...
> I have been using the latest version of matlab(2009a) on x64 ubuntu 8.10 for a couple of weeks now.
> Every thing works fine but I can't make the matlab compile my C files into Matlab mex(using mex function). Intrepid is shipped with gcc 4.3.2 while the latest version that matlab supports is still gcc 4.2.3 so I think this should be the source of the problem.
> When I mex a script, matlab warns me about the wrong version of the GCC and then the mex-ed file does not work properly. I get odd errors like "out of memory" or the mex ed function returns an incorrect value. The script works fine when I mex it on another computer with an older version of Linux(opensuse 10.3) which has a compatible GCC.
>
> I tried to install an older version of GCC on intrepid but I either did it wrong or it didn't solve my problem.
>
> I would appreciate if anyone have any idea/experience about solving this problem.
>
> amin

Hey,

I am having a similar problem. I'm running R2009a on Ubuntu 9.1 (karmic koala). Did you ever fix it? I also tried creating symbolic links, which stopped Matlab moaning about the GCC version, but they would compile and I got strange errors, that I didn't get using R2007a on a Mac running OS X 10.5 and Xcode.

Thanks,

Chris

Hey,

I am having a similar problem. I'm running R2009a on Ubuntu 9.1 (karmic koala). Did you ever fix it? I also tried creating symbolic links, which stopped Matlab moaning about the GCC version, but they would compile and I got strange errors, that I didn't get using R2007a on a Mac running OS X 10.5 and Xcode.

Thanks,

Chris

Well I've got pretty close: I installed gcc-4.2 etc and changed the symlinks in /usr/bin to point to them (as opposed to gcc-4.4 etc) and created a symlinks named 'glnxa64' pointing to 'glnx86' in the following directories:
$matlabroot/extern/lib
$matlabroot/bin

My main problem now seems to revolve around the 'ld' library in /usr/bin. Specifically I get the following error:

/usr/bin/ld: skipping incompatible $matlabroot/bin/glnxa64/libmx.so when searching for -lmx

which, due to the aforementioned symlink, is actually in
$matlabroot/bin/glnx86/libmx.so

So now I'm stumped! I guess it's some 32/64 bit incompatibility but I have no idea where to begin trying to fix it!

Chris

Oh and I also edited:

~/.matlab/R2009a/mexopts.sh

and commented out the line

CFLAGS='-ansi -D_GNU_SOURCE'

in the 'glnxa64' section, per this post:

http://forums.opensuse.org/programming-scripting/396126-gcc-matlab-opensuse-11-a.html#post1875821

Chris