g++ libstdc++ linker question.

g++ libstdc++ linker question.

[F. Heitkamp]

People will tell me to ask on matplotlib list but I believe this a more 
generic GNU C++ question.
I have been trying to run matplotlib that I built from source on my 
linux from scratch like box.

When I try to run an example I get:

bash-4.2$ python2.6 matplotlib-ex1.py
Traceback (most recent call last):
   File "matplotlib-ex1.py", line 13, in <module>
     import matplotlib.pyplot as plt
   File "/usr/lib/python2.6/site-packages/matplotlib/pyplot.py", line 
23, in <module>
     from matplotlib.figure import Figure, figaspect
   File "/usr/lib/python2.6/site-packages/matplotlib/figure.py", line 
16, in <module>
     import artist
   File "/usr/lib/python2.6/site-packages/matplotlib/artist.py", line 6, 
in <module>
     from transforms import Bbox, IdentityTransform, TransformedBbox, 
TransformedPath
   File "/usr/lib/python2.6/site-packages/matplotlib/transforms.py", 
line 34, in <module>
     from matplotlib._path import affine_transform
ImportError: /usr/lib/python2.6/site-packages/matplotlib/_path.so: 
undefined symbol: 
_ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_i

I see this symbol is in 32 bits libstdc++ library, but does not seem to 
appear in 64 bits versions.

bash-4.2$ ldd /usr/lib/python2.6/site-packages/matplotlib/_path.so
     linux-gate.so.1 =>  (0xffffe000)
     libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0xf74f7000)
     libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xf74de000)
     libpthread.so.0 => /lib/libpthread.so.0 (0xf74c4000)
     libc.so.6 => /lib/libc.so.6 (0xf7367000)
     libdl.so.2 => /lib/libdl.so.2 (0xf7362000)
     libutil.so.1 => /lib/libutil.so.1 (0xf735e000)
     libm.so.6 => /lib/libm.so.6 (0xf7338000)
     /lib/ld-linux.so.2 (0xf77d1000)

libstdc++ is not shown as being linked with _path.so

Any thoughts?

Fred

Re: g++ libstdc++ linker question.

[Jonathan Wakely]

On 30 April 2012 13:39, F. Heitkamp wrote:
> People will tell me to ask on matplotlib list but I believe this a more
> generic GNU C++ question.
> I have been trying to run matplotlib that I built from source on my linux
> from scratch like box.
>
> When I try to run an example I get:
>
> bash-4.2$ python2.6 matplotlib-ex1.py
> Traceback (most recent call last):
>  File "matplotlib-ex1.py", line 13, in <module>
>    import matplotlib.pyplot as plt
>  File "/usr/lib/python2.6/site-packages/matplotlib/pyplot.py", line 23, in
> <module>
>    from matplotlib.figure import Figure, figaspect
>  File "/usr/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in
> <module>
>    import artist
>  File "/usr/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in
> <module>
>    from transforms import Bbox, IdentityTransform, TransformedBbox,
> TransformedPath
>  File "/usr/lib/python2.6/site-packages/matplotlib/transforms.py", line 34,
> in <module>
>    from matplotlib._path import affine_transform
> ImportError: /usr/lib/python2.6/site-packages/matplotlib/_path.so: undefined
> symbol:
> _ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_i
>
> I see this symbol is in 32 bits libstdc++ library, but does not seem to
> appear in 64 bits versions.

Right, the equivalent symbol in the 64-bit lib ends in _l instead of _i

> bash-4.2$ ldd /usr/lib/python2.6/site-packages/matplotlib/_path.so
>    linux-gate.so.1 =>  (0xffffe000)
>    libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0xf74f7000)
>    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xf74de000)
>    libpthread.so.0 => /lib/libpthread.so.0 (0xf74c4000)
>    libc.so.6 => /lib/libc.so.6 (0xf7367000)
>    libdl.so.2 => /lib/libdl.so.2 (0xf7362000)
>    libutil.so.1 => /lib/libutil.so.1 (0xf735e000)
>    libm.so.6 => /lib/libm.so.6 (0xf7338000)
>    /lib/ld-linux.so.2 (0xf77d1000)
>
> libstdc++ is not shown as being linked with _path.so
>
> Any thoughts?

Is _path.so a 32-bit or 64-bit library?  From the missing symbol I'm
asuming 32-bit.

It would appear it wasn't correctly linked, so its dependency on
libstdc++.so isn't recorded in the library by a DT_NEEDED entry.

Does it help if you tell the dynamic linker to preload libstdc++.so?

LD_PRELOAD=/usr/lib/libstdc++.so python2.6 matplotlib-ex1.py

Re: g++ libstdc++ linker question.

[Jonathan Wakely]

On 30 April 2012 18:28, Jonathan Wakely <jwakely.gcc@gmail.com> wrote:
> On 30 April 2012 13:39, F. Heitkamp wrote:
>> People will tell me to ask on matplotlib list but I believe this a more
>> generic GNU C++ question.
>> I have been trying to run matplotlib that I built from source on my linux
>> from scratch like box.
>>
>> When I try to run an example I get:
>>
>> bash-4.2$ python2.6 matplotlib-ex1.py
>> Traceback (most recent call last):
>>  File "matplotlib-ex1.py", line 13, in <module>
>>    import matplotlib.pyplot as plt
>>  File "/usr/lib/python2.6/site-packages/matplotlib/pyplot.py", line 23, in
>> <module>
>>    from matplotlib.figure import Figure, figaspect
>>  File "/usr/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in
>> <module>
>>    import artist
>>  File "/usr/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in
>> <module>
>>    from transforms import Bbox, IdentityTransform, TransformedBbox,
>> TransformedPath
>>  File "/usr/lib/python2.6/site-packages/matplotlib/transforms.py", line 34,
>> in <module>
>>    from matplotlib._path import affine_transform
>> ImportError: /usr/lib/python2.6/site-packages/matplotlib/_path.so: undefined
>> symbol:
>> _ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_i
>>
>> I see this symbol is in 32 bits libstdc++ library, but does not seem to
>> appear in 64 bits versions.
>
> Right, the equivalent symbol in the 64-bit lib ends in _l instead of _i
>
>> bash-4.2$ ldd /usr/lib/python2.6/site-packages/matplotlib/_path.so
>>    linux-gate.so.1 =>  (0xffffe000)
>>    libpython2.6.so.1.0 => /usr/lib/libpython2.6.so.1.0 (0xf74f7000)
>>    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xf74de000)
>>    libpthread.so.0 => /lib/libpthread.so.0 (0xf74c4000)
>>    libc.so.6 => /lib/libc.so.6 (0xf7367000)
>>    libdl.so.2 => /lib/libdl.so.2 (0xf7362000)
>>    libutil.so.1 => /lib/libutil.so.1 (0xf735e000)
>>    libm.so.6 => /lib/libm.so.6 (0xf7338000)
>>    /lib/ld-linux.so.2 (0xf77d1000)
>>
>> libstdc++ is not shown as being linked with _path.so
>>
>> Any thoughts?
>
> Is _path.so a 32-bit or 64-bit library?  From the missing symbol I'm
> asuming 32-bit.
>
> It would appear it wasn't correctly linked, so its dependency on
> libstdc++.so isn't recorded in the library by a DT_NEEDED entry.

P.S. you can check the DT_NEEDED tags by running:

readelf -d  /usr/lib/python2.6/site-packages/matplotlib/_path.so


> Does it help if you tell the dynamic linker to preload libstdc++.so?
>
> LD_PRELOAD=/usr/lib/libstdc++.so python2.6 matplotlib-ex1.py

The matplotlib I use is built with:

python setupegg.py build_ext \
  --rpath=/opt/gcc-4.4.3/lib64
python setupegg.py build
python setupegg.py install --user

The --rpath option ensures the right libstdc++.so is found at runtime
(we have several installed).  That build works here, and is linked to
libstdc++.so.  Unfortunately it builds matplotlib as a python egg,
which is a very annoying package format.  I'd rather not install it
via egg, but have no experience doing so and can't suggest why your
build was not linked to libstdc++.

Re: g++ libstdc++ linker question.

[F. Heitkamp]

On 04/30/12 13:28, Jonathan Wakely wrote:
> On 30 April 2012 13:39, F. Heitkamp wrote:
>> People will tell me to ask on matplotlib list but I believe this a more
>> generic GNU C++ question.
>> I have been trying to run matplotlib that I built from source on my linux
>> from scratch like box.
>>
>> When I try to run an example I get:
>>
>> bash-4.2$ python2.6 matplotlib-ex1.py
>> Traceback (most recent call last):
>>   File "matplotlib-ex1.py", line 13, in<module>
>>     import matplotlib.pyplot as plt
>>   File "/usr/lib/python2.6/site-packages/matplotlib/pyplot.py", line 23, in
>> <module>
>>     from matplotlib.figure import Figure, figaspect
>>   File "/usr/lib/python2.6/site-packages/matplotlib/figure.py", line 16, in
>> <module>
>>     import artist
>>   File "/usr/lib/python2.6/site-packages/matplotlib/artist.py", line 6, in
>> <module>
>>     from transforms import Bbox, IdentityTransform, TransformedBbox,
>> TransformedPath
>>   File "/usr/lib/python2.6/site-packages/matplotlib/transforms.py", line 34,
>> in<module>
>>     from matplotlib._path import affine_transform
>> ImportError: /usr/lib/python2.6/site-packages/matplotlib/_path.so: undefined
>> symbol:
>> _ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_i
>>
>> I see this symbol is in 32 bits libstdc++ library, but does not seem to
>> appear in 64 bits versions.
> Right, the equivalent symbol in the 64-bit lib ends in _l instead of _i
>
>> bash-4.2$ ldd /usr/lib/python2.6/site-packages/matplotlib/_path.so
>>     linux-gate.so.1 =>    (0xffffe000)
>>     libpython2.6.so.1.0 =>  /usr/lib/libpython2.6.so.1.0 (0xf74f7000)
>>     libgcc_s.so.1 =>  /lib/libgcc_s.so.1 (0xf74de000)
>>     libpthread.so.0 =>  /lib/libpthread.so.0 (0xf74c4000)
>>     libc.so.6 =>  /lib/libc.so.6 (0xf7367000)
>>     libdl.so.2 =>  /lib/libdl.so.2 (0xf7362000)
>>     libutil.so.1 =>  /lib/libutil.so.1 (0xf735e000)
>>     libm.so.6 =>  /lib/libm.so.6 (0xf7338000)
>>     /lib/ld-linux.so.2 (0xf77d1000)
>>
>> libstdc++ is not shown as being linked with _path.so
>>
>> Any thoughts?
> Is _path.so a 32-bit or 64-bit library?  From the missing symbol I'm
> asuming 32-bit.
>
> It would appear it wasn't correctly linked, so its dependency on
> libstdc++.so isn't recorded in the library by a DT_NEEDED entry.
>
> Does it help if you tell the dynamic linker to preload libstdc++.so?
>
> LD_PRELOAD=/usr/lib/libstdc++.so python2.6 matplotlib-ex1.py
The answers to your questions are bellow.
The LD_PRELOAD comand worked (after changing the backend to PyQT4).
bash-4.2$ file /usr/lib/python2.6/site-packages/matplotlib/_path.so
/usr/lib/python2.6/site-packages/matplotlib/_path.so: ELF 32-bit LSB 
shared object, Intel 80386, version 1 (GNU/Linux), dynamically linked, 
not stripped


bash-4.2$ readelf -d  /usr/lib/python2.6/site-packages/matplotlib/_path.so

Dynamic section at offset 0xfb980 contains 26 entries:
   Tag        Type                         Name/Value
  0x00000001 (NEEDED)                     Shared library: 
[libpython2.6.so.1.0]
  0x00000001 (NEEDED)                     Shared library: [libgcc_s.so.1]
  0x00000001 (NEEDED)                     Shared library: [libpthread.so.0]
  0x00000001 (NEEDED)                     Shared library: [libc.so.6]
  0x0000000c (INIT)                       0x53d18
  0x0000000d (FINI)                       0xdaba8
  0x00000019 (INIT_ARRAY)                 0xfc1c8
  0x0000001b (INIT_ARRAYSZ)               36 (bytes)
  0x00000004 (HASH)                       0xd4
  0x00000005 (STRTAB)                     0x1261c
  0x00000006 (SYMTAB)                     0x552c
  0x0000000a (STRSZ)                      142332 (bytes)
  0x0000000b (SYMENT)                     16 (bytes)
  0x00000003 (PLTGOT)                     0xfcc88
  0x00000002 (PLTRELSZ)                   2160 (bytes)
  0x00000014 (PLTREL)                     REL
  0x00000017 (JMPREL)                     0x534a8
  0x00000011 (REL)                        0x36d08
  0x00000012 (RELSZ)                      116640 (bytes)
  0x00000013 (RELENT)                     8 (bytes)
  0x00000016 (TEXTREL)                    0x0
  0x6ffffffe (VERNEED)                    0x36c38
  0x6fffffff (VERNEEDNUM)                 3
  0x6ffffff0 (VERSYM)                     0x35218
  0x6ffffffa (RELCOUNT)                   1709

  0x00000000 (NULL)                       0x0
bash-4.2$


bash-4.2$ LD_PRELOAD=/lib/libstdc++.so python2.6 matplotlib-ex1.py
Traceback (most recent call last):
   File "matplotlib-ex1.py", line 13, in <module>
     import matplotlib.pyplot as plt
   File "/usr/lib/python2.6/site-packages/matplotlib/pyplot.py", line 
95, in <module>
     new_figure_manager, draw_if_interactive, _show = pylab_setup()
   File 
"/usr/lib/python2.6/site-packages/matplotlib/backends/__init__.py", line 
25, in pylab_setup
     globals(),locals(),[backend_name])
   File 
"/usr/lib/python2.6/site-packages/matplotlib/backends/backend_wx.py", 
line 45, in <module>
     raise ImportError(missingwx)
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8

Re: g++ libstdc++ linker question.

[F. Heitkamp]

On 04/30/12 13:47, Jonathan Wakely wrote:
> On 30 April 2012 18:28, Jonathan Wakely<jwakely.gcc@gmail.com>  wrote:
>> On 30 April 2012 13:39, F. Heitkamp wrote:
>>
> The matplotlib I use is built with:
>
> python setupegg.py build_ext \
>    --rpath=/opt/gcc-4.4.3/lib64
> python setupegg.py build
> python setupegg.py install --user
>
> The --rpath option ensures the right libstdc++.so is found at runtime
> (we have several installed).  That build works here, and is linked to
> libstdc++.so.  Unfortunately it builds matplotlib as a python egg,
> which is a very annoying package format.  I'd rather not install it
> via egg, but have no experience doing so and can't suggest why your
> build was not linked to libstdc++.
>

This last suggestion did not work for me.  I got the same undefined 
symbol error.  My linux setup is a 64 bits kernel running on sort of a 
hybrid 32/64 bits system.  By that I mean I have some 64 bits userland 
along with the 32bits.  When I configure python programs using the usual 
commands it comes back with arch x86_64.  Anyway I guess this is getting 
off topic for this list now, but suggestions are welcome nonetheless.

Fred

Re: g++ libstdc++ linker question.

[Andrew Haley]

On 05/02/2012 12:14 PM, F. Heitkamp wrote:
> On 04/30/12 13:47, Jonathan Wakely wrote:
>> On 30 April 2012 18:28, Jonathan Wakely<jwakely.gcc@gmail.com>  wrote:
>>> On 30 April 2012 13:39, F. Heitkamp wrote:
>>>
>> The matplotlib I use is built with:
>>
>> python setupegg.py build_ext \
>>    --rpath=/opt/gcc-4.4.3/lib64
>> python setupegg.py build
>> python setupegg.py install --user
>>
>> The --rpath option ensures the right libstdc++.so is found at runtime
>> (we have several installed).  That build works here, and is linked to
>> libstdc++.so.  Unfortunately it builds matplotlib as a python egg,
>> which is a very annoying package format.  I'd rather not install it
>> via egg, but have no experience doing so and can't suggest why your
>> build was not linked to libstdc++.
> 
> This last suggestion did not work for me.  I got the same undefined 
> symbol error.  My linux setup is a 64 bits kernel running on sort of a 
> hybrid 32/64 bits system.  By that I mean I have some 64 bits userland 
> along with the 32bits.  When I configure python programs using the usual 
> commands it comes back with arch x86_64.  Anyway I guess this is getting 
> off topic for this list now, but suggestions are welcome nonetheless.

We really need you to answer this question:

> Is _path.so a 32-bit or 64-bit library?  From the missing symbol I'm
> assuming 32-bit.

And if it is compiled 32-bit, we need to know why.

Andrew.

Re: g++ libstdc++ linker question.

[F. Heitkamp]

We really need you to answer this question:


> Is _path.so a 32-bit or 64-bit library?  From the missing symbol I'm
> assuming 32-bit.
And if it is compiled 32-bit, we need to know why.

It is 32 bit.  Probably because the Python it's compiled against is 32 bit?

I don't understand why the build process is not pulling in libstdc++ if _path.so needs it.

Fred