MATLAB Central Newsreader - Conflict with mcc... libstdc++.so.6

Conflict with mcc... libstdc++.so.6

spasmous — Sun, 01 Jun 2008 21:22:15 -0400

I have a Hello World program I'm attempting to compile with mcc. It
appears to compile except at the end I get the message:

/usr/bin/ld: warning: libstdc++.so.6, needed by /usr/local/matlab/bin/
glnx86/libmwmclmcrrt.so, may conflict with libstdc++.so.5

Following previous posts on here I've checked the LD_LIBRARY_PATH is
set as in the manual. It is. A binary is generated and can be called,
however the result is errors.

>> system('./hello');
free(): invalid pointer 0x808d0c8!
free(): invalid pointer 0x808d348!
./hello: Segmentation fault

I'm stuck as to what to do now.

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Re: Conflict with mcc... libstdc++.so.6

Sebastiaan — Mon, 02 Jun 2008 12:00:05 -0400

spasmous <spasmous@gmail.com> wrote in message
<431d112e-2cfc-4e5e-8b68-e2dcac8b7008@w5g2000prd.googlegroups.com>...
> I have a Hello World program I'm attempting to compile
with mcc. It
> appears to compile except at the end I get the message:
>
> /usr/bin/ld: warning: libstdc++.so.6, needed by
/usr/local/matlab/bin/
> glnx86/libmwmclmcrrt.so, may conflict with libstdc++.so.5
>
Probably your system uses so.5 while Matlab comes with .so.6.

Did you compile with -L/opt/matlab/2007b/sys/os/glnxa64/
-lstdc++ ? What does 'ldd hello' give? And when executed
from Matlab (system('ldd hello'))?

Sebastiaan

Re: Conflict with mcc... libstdc++.so.6

spasmous — Mon, 02 Jun 2008 17:03:33 -0400

On Jun 2, 5:00=A0am, "Sebastiaan "
<s.breedv...@erasmusmc.REMOVE.BOO.BOO.nl> wrote:
> spasmous<spasm...@gmail.com> wrote in message
>
> <431d112e-2cfc-4e5e-8b68-e2dcac8b7...@w5g2000prd.googlegroups.com>...> I h=
ave a Hello World program I'm attempting to compile
> with mcc. It
> > appears to compile except at the end I get the message:
>
> > /usr/bin/ld: warning: libstdc++.so.6, needed by
>
> /usr/local/matlab/bin/> glnx86/libmwmclmcrrt.so, may conflict with libstdc=
++.so.5
>
> Probably your system uses so.5 while Matlab comes with .so.6.
>
> Did you compile with -L/opt/matlab/2007b/sys/os/glnxa64/
> -lstdc++ =A0? What does 'ldd hello' give? And when executed
> from Matlab (system('ldd hello'))?
>

Sebastian - by responding you are saving my life :) Thank you!
The result of ldd hello is:

        linux-gate.so.1 =3D> (0xffffe000)
        libmwmclmcrrt.so =3D> /usr/local/matlab/bin/glnx86/
libmwmclmcrrt.so (0x40001000)
        libm.so.6 =3D> /lib/tls/libm.so.6 (0x42e08000)
        libstdc++.so.5 =3D> /usr/lib/libstdc++.so.5 (0x439b9000)
        libpthread.so.0 =3D> /lib/tls/libpthread.so.0 (0x42f20000)
        libc.so.6 =3D> /lib/tls/libc.so.6 (0x42cea000)
        libdl.so.2 =3D> /lib/libdl.so.2 (0x42e2d000)
        libstdc++.so.6 =3D> /usr/local/matlab/bin/glnx86/../../sys/os/
glnx86/libstdc++.so.6 (0x40069000)
        libgcc_s.so.1 =3D> /usr/local/matlab/bin/glnx86/../../sys/os/
glnx86/libgcc_s.so.1 (0x40146000)
        /lib/ld-linux.so.2 =3D> /lib/ld-linux.so.2 (0x42cd1000)

So it looks like my platform uses libstdc++.so.5. Is there any
solution where I can tell MATLAB to use .so.6?

I'm not sure I understand what you meant by compiling with -L/opt/
matlab/2007b/sys/os/glnxa64/-lstdc++. There is not -L flag with mcc
that I can see.

Re: Conflict with mcc... libstdc++.so.6

Sebastiaan — Mon, 02 Jun 2008 18:16:02 -0400

> Sebastian - by responding you are saving my life :) Thank you!
> The result of ldd hello is:
>
> linux-gate.so.1 =3D> (0xffffe000)
> libmwmclmcrrt.so =3D> /usr/local/matlab/bin/glnx86/
> libmwmclmcrrt.so (0x40001000)
> libm.so.6 =3D> /lib/tls/libm.so.6 (0x42e08000)
> libstdc++.so.5 =3D> /usr/lib/libstdc++.so.5
(0x439b9000)
> libpthread.so.0 =3D> /lib/tls/libpthread.so.0
(0x42f20000)
> libc.so.6 =3D> /lib/tls/libc.so.6 (0x42cea000)
> libdl.so.2 =3D> /lib/libdl.so.2 (0x42e2d000)
> libstdc++.so.6 =3D>
/usr/local/matlab/bin/glnx86/../../sys/os/
> glnx86/libstdc++.so.6 (0x40069000)
> libgcc_s.so.1 =3D>
/usr/local/matlab/bin/glnx86/../../sys/os/
> glnx86/libgcc_s.so.1 (0x40146000)
> /lib/ld-linux.so.2 =3D> /lib/ld-linux.so.2
(0x42cd1000)
>
> So it looks like my platform uses libstdc++.so.5. Is there any
> solution where I can tell MATLAB to use .so.6?
>
> I'm not sure I understand what you meant by compiling with
-L/opt/
> matlab/2007b/sys/os/glnxa64/-lstdc++. There is not -L flag
with mcc
> that I can see.

Funny, it is actually linked to .so.5 and .so.6. Seems
strange, but I am not an expert on this.

I also have no experience with mcc, only with mex files.

From
http://www.gravity.psu.edu/~s4/software/MATLAB-R2006a/Compiling_MATLAB_Release_2006a.html
it seems that you have to edit bin/mbuildopts.sh (or better:
~/.matlab/R2007b/mbuildopts.sh which is the one you can and
should edit) and change:
CLIBS="$RPATH $MLIBS -lm $TMW_ROOT/sys/os/$Arch/libstdc++.so.6""

in the section belonging to your architecture (seems glnx86).

Does it work?

Greetz,
Sebastiaan

Re: Conflict with mcc... libstdc++.so.6

spasmous — Mon, 02 Jun 2008 18:59:02 -0400

On Jun 2, 11:16=A0am, "Sebastiaan "
<s.breedv...@erasmusmc.REMOVE.BOO.BOO.nl> wrote:
> > Sebastian - by responding you are saving my life :) Thank you!
> > The result of ldd hello is:
>
> > =A0 =A0 =A0 =A0 linux-gate.so.1 =3D3D> =A0(0xffffe000)
> > =A0 =A0 =A0 =A0 libmwmclmcrrt.so =3D3D> /usr/local/matlab/bin/glnx86/
> > libmwmclmcrrt.so (0x40001000)
> > =A0 =A0 =A0 =A0 libm.so.6 =3D3D> /lib/tls/libm.so.6 (0x42e08000)
> > =A0 =A0 =A0 =A0 libstdc++.so.5 =3D3D> /usr/lib/libstdc++.so.5
> (0x439b9000)
> > =A0 =A0 =A0 =A0 libpthread.so.0 =3D3D> /lib/tls/libpthread.so.0
> (0x42f20000)
> > =A0 =A0 =A0 =A0 libc.so.6 =3D3D> /lib/tls/libc.so.6 (0x42cea000)
> > =A0 =A0 =A0 =A0 libdl.so.2 =3D3D> /lib/libdl.so.2 (0x42e2d000)
> > =A0 =A0 =A0 =A0 libstdc++.so.6 =3D3D>
>
> /usr/local/matlab/bin/glnx86/../../sys/os/> glnx86/libstdc++.so.6 (0x40069=
000)
> > =A0 =A0 =A0 =A0 libgcc_s.so.1 =3D3D>
>
> /usr/local/matlab/bin/glnx86/../../sys/os/
>
> > glnx86/libgcc_s.so.1 (0x40146000)
> > =A0 =A0 =A0 =A0 /lib/ld-linux.so.2 =3D3D> /lib/ld-linux.so.2
> (0x42cd1000)
>
> > So it looks like my platform uses libstdc++.so.5. Is there any
> > solution where I can tell MATLAB to use .so.6?
>
> > I'm not sure I understand what you meant by compiling with
> -L/opt/
> > matlab/2007b/sys/os/glnxa64/-lstdc++. There is not -L flag
> with mcc
> > that I can see.
>
> Funny, it is actually linked to .so.5 and .so.6. Seems
> strange, but I am not an expert on this.
>
> I also have no experience with mcc, only with mex files.
>
> Fromhttp://www.gravity.psu.edu/~s4/software/MATLAB-R2006a/Compiling_MATLA.=
..
> it seems that you have to edit bin/mbuildopts.sh (or better:
> ~/.matlab/R2007b/mbuildopts.sh which is the one you can and
> should edit) and change:
> CLIBS=3D"$RPATH $MLIBS -lm $TMW_ROOT/sys/os/$Arch/libstdc++.so.6""
>
> in the section belonging to your architecture (seems glnx86).
>
> Does it work?

Interesting. I changed my mbuildopts.sh file as you suggested and it
does work. But only calling from the MATLAB prompt via system('./
hello'). Calling from the bash shell gives the error

=2E/hello: error while loading shared libraries: libmwmclmcrrt.so:
cannot open shared object file: No such file or directory

Re: Conflict with mcc... libstdc++.so.6

spasmous — Mon, 02 Jun 2008 19:16:11 -0400

On Jun 2, 11:59=A0am, spasmous <spasm...@gmail.com> wrote:
> On Jun 2, 11:16=A0am, "Sebastiaan "
>
>
>
> <s.breedv...@erasmusmc.REMOVE.BOO.BOO.nl> wrote:
> > > Sebastian - by responding you are saving my life :) Thank you!
> > > The result of ldd hello is:
>
> > > =A0 =A0 =A0 =A0 linux-gate.so.1 =3D3D> =A0(0xffffe000)
> > > =A0 =A0 =A0 =A0 libmwmclmcrrt.so =3D3D> /usr/local/matlab/bin/glnx86/
> > > libmwmclmcrrt.so (0x40001000)
> > > =A0 =A0 =A0 =A0 libm.so.6 =3D3D> /lib/tls/libm.so.6 (0x42e08000)
> > > =A0 =A0 =A0 =A0 libstdc++.so.5 =3D3D> /usr/lib/libstdc++.so.5
> > (0x439b9000)
> > > =A0 =A0 =A0 =A0 libpthread.so.0 =3D3D> /lib/tls/libpthread.so.0
> > (0x42f20000)
> > > =A0 =A0 =A0 =A0 libc.so.6 =3D3D> /lib/tls/libc.so.6 (0x42cea000)
> > > =A0 =A0 =A0 =A0 libdl.so.2 =3D3D> /lib/libdl.so.2 (0x42e2d000)
> > > =A0 =A0 =A0 =A0 libstdc++.so.6 =3D3D>
>
> > /usr/local/matlab/bin/glnx86/../../sys/os/> glnx86/libstdc++.so.6 (0x400=
69000)
> > > =A0 =A0 =A0 =A0 libgcc_s.so.1 =3D3D>
>
> > /usr/local/matlab/bin/glnx86/../../sys/os/
>
> > > glnx86/libgcc_s.so.1 (0x40146000)
> > > =A0 =A0 =A0 =A0 /lib/ld-linux.so.2 =3D3D> /lib/ld-linux.so.2
> > (0x42cd1000)
>
> > > So it looks like my platform uses libstdc++.so.5. Is there any
> > > solution where I can tell MATLAB to use .so.6?
>
> > > I'm not sure I understand what you meant by compiling with
> > -L/opt/
> > > matlab/2007b/sys/os/glnxa64/-lstdc++. There is not -L flag
> > with mcc
> > > that I can see.
>
> > Funny, it is actually linked to .so.5 and .so.6. Seems
> > strange, but I am not an expert on this.
>
> > I also have no experience with mcc, only with mex files.
>
> > Fromhttp://www.gravity.psu.edu/~s4/software/MATLAB-R2006a/Compiling_MATL=
A...
> > it seems that you have to edit bin/mbuildopts.sh (or better:
> > ~/.matlab/R2007b/mbuildopts.sh which is the one you can and
> > should edit) and change:
> > CLIBS=3D"$RPATH $MLIBS -lm $TMW_ROOT/sys/os/$Arch/libstdc++.so.6""
>
> > in the section belonging to your architecture (seems glnx86).
>
> > Does it work?
>
> Interesting. I changed my mbuildopts.sh file as you suggested and it
> does work. But only calling from the MATLAB prompt via system('./
> hello'). Calling from the bash shell gives the error
>
> ./hello: error while loading shared libraries: libmwmclmcrrt.so:
> cannot open shared object file: No such file or directory

Whoops, my error. I opened an xterm without updating the
LD_LIBRARY_PATH variable. After doing that it works as advertised from
the command line. Thanks again. Wow, it works.

Re: Conflict with mcc... libstdc++.so.6

Jack Yu — Wed, 23 Jul 2008 14:11:05 -0400

Hello,
I think I have a similar, if not the same, problem. The
version of Matlab I am using is: 7.0.0.19901 (R14). And the
problem is when I use mcc -m to compile a certain function,
I get the following warning message:

/usr/bin/ld: warning: libstdc++.so.5, needed by
/usr/local/matlab/bin/glnx86/libmwmclmcrrt.so, may conflict
with libstdc++.so.6
Warning: Objects of uiundo.FunctionCommand class exist - not
clearing this class
or any of its super-classes.
Warning: Objects of uiundo.CommandManager class exist - not
clearing this class
or any of its super-classes.
Warning: Objects of uitools.FigureToolManager class exist -
not clearing this class
or any of its super-classes.

So, I tried to solve it by changing my mbuildopts.sh as follows:

# CLIBS = "$RPATH $MLIBS -lm -lstdc++"
CLIBS = "$RPATH $MLIBS -lm
$TMW_ROOT/sys/os/$Arch/libstdc++.so.5""

where I've commented out the old CLIBS and inserted what I
think I should according to this discussion. But now, I get
an error:

Warning: an error occurred while parsing class
dspopts.abstractspectrum:
Undefined function or variable 'check_integer'.
Warning: an error occurred while parsing class
dspopts.pseudospectrum:
Invalid superclass handle.
??? Unable to create a class array for class
dspopts.pseudospectrum

Warning: Objects of uiundo.FunctionCommand class exist - not
clearing this class
or any of its super-classes.
Warning: Objects of uiundo.CommandManager class exist - not
clearing this class
or any of its super-classes.
Warning: Objects of uitools.FigureToolManager class exist -
not clearing this class
or any of its super-classes.
??? Depfun error: 'Unable to create a class array for class
dspopts.pseudospectrum
'

Does anyone know how I can make this work? Any help or
hints would be very much appreciated.

cheers,

Jack

spasmous <spasmous@gmail.com> wrote in message
<9f4032f6-4871-4bae-b649-e78b2b4fa1bc@z24g2000prf.googlegroups.com>...
> On Jun 2, 11:16=A0am, "Sebastiaan "
> <s.breedv...@erasmusmc.REMOVE.BOO.BOO.nl> wrote:
> > > Sebastian - by responding you are saving my life :)
Thank you!
> > > The result of ldd hello is:
> >
> > > =A0 =A0 =A0 =A0 linux-gate.so.1 =3D3D> =A0(0xffffe000)
> > > =A0 =A0 =A0 =A0 libmwmclmcrrt.so =3D3D>
/usr/local/matlab/bin/glnx86/
> > > libmwmclmcrrt.so (0x40001000)
> > > =A0 =A0 =A0 =A0 libm.so.6 =3D3D> /lib/tls/libm.so.6
(0x42e08000)
> > > =A0 =A0 =A0 =A0 libstdc++.so.5 =3D3D>
/usr/lib/libstdc++.so.5
> > (0x439b9000)
> > > =A0 =A0 =A0 =A0 libpthread.so.0 =3D3D>
/lib/tls/libpthread.so.0
> > (0x42f20000)
> > > =A0 =A0 =A0 =A0 libc.so.6 =3D3D> /lib/tls/libc.so.6
(0x42cea000)
> > > =A0 =A0 =A0 =A0 libdl.so.2 =3D3D> /lib/libdl.so.2
(0x42e2d000)
> > > =A0 =A0 =A0 =A0 libstdc++.so.6 =3D3D>
> >
> > /usr/local/matlab/bin/glnx86/../../sys/os/>
glnx86/libstdc++.so.6 (0x40069=
> 000)
> > > =A0 =A0 =A0 =A0 libgcc_s.so.1 =3D3D>
> >
> > /usr/local/matlab/bin/glnx86/../../sys/os/
> >
> > > glnx86/libgcc_s.so.1 (0x40146000)
> > > =A0 =A0 =A0 =A0 /lib/ld-linux.so.2 =3D3D>
/lib/ld-linux.so.2
> > (0x42cd1000)
> >
> > > So it looks like my platform uses libstdc++.so.5. Is
there any
> > > solution where I can tell MATLAB to use .so.6?
> >
> > > I'm not sure I understand what you meant by compiling with
> > -L/opt/
> > > matlab/2007b/sys/os/glnxa64/-lstdc++. There is not -L flag
> > with mcc
> > > that I can see.
> >
> > Funny, it is actually linked to .so.5 and .so.6. Seems
> > strange, but I am not an expert on this.
> >
> > I also have no experience with mcc, only with mex files.
> >
> >
Fromhttp://www.gravity.psu.edu/~s4/software/MATLAB-R2006a/Compiling_MATLA.=
> ..
> > it seems that you have to edit bin/mbuildopts.sh (or better:
> > ~/.matlab/R2007b/mbuildopts.sh which is the one you can and
> > should edit) and change:
> > CLIBS=3D"$RPATH $MLIBS -lm
$TMW_ROOT/sys/os/$Arch/libstdc++.so.6""
> >
> > in the section belonging to your architecture (seems
glnx86).
> >
> > Does it work?
>
>
> Interesting. I changed my mbuildopts.sh file as you
suggested and it
> does work. But only calling from the MATLAB prompt via
system('./
> hello'). Calling from the bash shell gives the error
>
> =2E/hello: error while loading shared libraries:
libmwmclmcrrt.so:
> cannot open shared object file: No such file or directory

Re: Conflict with mcc... libstdc++.so.6

Sebastiaan — Wed, 13 Aug 2008 09:13:01 -0400

What does ldd give you, before and after the change in the
CLIBS?