Yade does not start on Natty 11.04

Bug #707966 reported by Anton Gladky
8
This bug affects 1 person
Affects Status Importance Assigned to Milestone
Yade
Fix Released
Undecided
Unassigned

Bug Description

Compiles normally, but during start:

0.60 release:
=================================================
./../build/bin/yade-cleanComp
Welcome to Yade 0.60
Traceback (most recent call last):
  File "./../build/bin/yade-cleanComp", line 105, in <module>
    import yade
  File "/home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
    import boot
ImportError: /home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/../../lib/../lib/libyade-support.so: undefined symbol: _ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
=================================================
Latest trunk:
=================================================
Welcome to Yade bzr2679
Traceback (most recent call last):
  File "./../build/bin/yade-cleanComp", line 115, in <module>
    import yade
  File "/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
    import boot
ImportError: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/py/yade/../../lib/../lib/libyade-support.so: undefined symbol: _ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
=================================================

Revision history for this message
Anton Gladky (gladky-anton) wrote : Re: [Bug 707966] [NEW] Yade does not start on Natty 11.04

The problem can be in gcc-4.5, used in Natty by default.

Revision history for this message
Václav Šmilauer (eudoxos) wrote :

I was compiling with 4.5 on maverick, and never had problems. I think the problem can be that yade-support is not linked with boost libs at all (...?). You can try to go to lib/SConscript:18, and change

 LIBS=['dl','m']+[]

to

 LIBS=['dl','m']+[l for l in env['LIBS'] if l!='yade-support']

(yade-support is in env['LIBS'] so that core and all plugins link with it automatically, but yade-support cannot obviously link with itself, so it muse be filtered away, keeping the rest of env['LIBS'] (which contains all boost libs as well).

I don't have a big machine so cannot try myself, sorry.

HTH, v.

Revision history for this message
Anton Gladky (gladky-anton) wrote : Re: [Bug 707966] Re: Yade does not start on Natty 11.04

Ok, thanks for suggestion, I will try and let you know.

Anton

2011/1/26 Václav Šmilauer <email address hidden>:
> I was compiling with 4.5 on maverick, and never had problems. I think
> the problem can be that yade-support is not linked with boost libs at
> all (...?). You can try to go to lib/SConscript:18, and change
>
>  LIBS=['dl','m']+[]
>
> to
>
>  LIBS=['dl','m']+[l for l in env['LIBS'] if l!='yade-support']
>
> (yade-support is in env['LIBS'] so that core and all plugins link with
> it automatically, but yade-support cannot obviously link with itself, so
> it muse be filtered away, keeping the rest of env['LIBS'] (which
> contains all boost libs as well).
>
> I don't have a big machine so cannot try myself, sorry.
>
> HTH, v.
>
> --
> You received this bug notification because you are a direct subscriber
> of the bug.
> https://bugs.launchpad.net/bugs/707966
>
> Title:
>  Yade does not start on Natty 11.04
>
> Status in Yet Another Dynamic Engine:
>  New
>
> Bug description:
>  Compiles normally, but during start:
>
>  0.60 release:
>  =================================================
>  ./../build/bin/yade-cleanComp
>  Welcome to Yade 0.60
>  Traceback (most recent call last):
>    File "./../build/bin/yade-cleanComp", line 105, in <module>
>      import yade
>    File "/home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
>      import boot
>  ImportError: /home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/../../lib/../lib/libyade-support.so: undefined symbol: _ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
>  =================================================
>  Latest trunk:
>  =================================================
>  Welcome to Yade bzr2679
>  Traceback (most recent call last):
>    File "./../build/bin/yade-cleanComp", line 115, in <module>
>      import yade
>    File "/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
>      import boot
>  ImportError: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/py/yade/../../lib/../lib/libyade-support.so: undefined symbol: _ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
>  =================================================
>
> To unsubscribe from this bug, go to:
> https://bugs.launchpad.net/yade/+bug/707966/+subscribe
>

Revision history for this message
Anton Gladky (gladky-anton) wrote :
Download full text (3.4 KiB)

It is better now, the previous error gone. But there are some
problems with libplugins:

Welcome to Yade bzr2680
301 FATAL yade.Omega
/home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins:
/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so:
undefined symbol `GLUtils::QGLViewer::drawArrow(Eigen::Matrix<double,
3, 1, 2, 3, 1> const&, Eigen::Matrix<double, 3, 1, 2, 3, 1> const&,
float, int)'
301 FATAL yade.Omega
/home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins:
/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so:
/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so:
undefined symbol:
_ZN7GLUtils9QGLViewer9drawArrowERKN5Eigen6MatrixIdLi3ELi1ELi2ELi3ELi1EEES5_fi
301 FATAL yade.Omega
/home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins:
Bailing out.
Aborted (core dumped)

Could you not suggest where to fix it?

Thanks

Anton

On Wed, Jan 26, 2011 at 3:19 PM, Anton Gladky <email address hidden> wrote:
> Ok, thanks for suggestion, I will try and let you know.
>
> Anton
>
>
>
>
> 2011/1/26 Václav Šmilauer <email address hidden>:
>> I was compiling with 4.5 on maverick, and never had problems. I think
>> the problem can be that yade-support is not linked with boost libs at
>> all (...?). You can try to go to lib/SConscript:18, and change
>>
>>  LIBS=['dl','m']+[]
>>
>> to
>>
>>  LIBS=['dl','m']+[l for l in env['LIBS'] if l!='yade-support']
>>
>> (yade-support is in env['LIBS'] so that core and all plugins link with
>> it automatically, but yade-support cannot obviously link with itself, so
>> it muse be filtered away, keeping the rest of env['LIBS'] (which
>> contains all boost libs as well).
>>
>> I don't have a big machine so cannot try myself, sorry.
>>
>> HTH, v.
>>
>> --
>> You received this bug notification because you are a direct subscriber
>> of the bug.
>> https://bugs.launchpad.net/bugs/707966
>>
>> Title:
>>  Yade does not start on Natty 11.04
>>
>> Status in Yet Another Dynamic Engine:
>>  New
>>
>> Bug description:
>>  Compiles normally, but during start:
>>
>>  0.60 release:
>>  =================================================
>>  ./../build/bin/yade-cleanComp
>>  Welcome to Yade 0.60
>>  Traceback (most recent call last):
>>    File "./../build/bin/yade-cleanComp", line 105, in <module>
>>      import yade
>>    File "/home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
>>      import boot
>>  ImportError: /home/gladk/dem/yade/060/build/lib/yade-cleanComp/py/yade/../../lib/../lib/libyade-support.so: undefined symbol: _ZN5boost11basic_regexIcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE9do_assignEPKcS7_j
>>  =================================================
>>  Latest trunk:
>>  =================================================
>>  Welcome to Yade bzr2679
>>  Traceback (most recent call last):
>>    File "./../build/bin/yade-cleanComp", line 115, in <module>
>>      import yade
>>    File "/home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/py/yade/__init__.py", line 58, in <module>
>>      import boot
>>  ImportError: /home/gladk/dem/yade/cleanComp/build/lib/yade-cl...

Read more...

Revision history for this message
Václav Šmilauer (eudoxos) wrote :

I adjusted the linking (yade-opengl is merged in yade-support), it should be solved now. I can't verify on natty, though, so I let you close if it is solved now.

Changed in yade:
status: New → In Progress
Revision history for this message
Anton Gladky (gladky-anton) wrote :

Unfortuntely, it is still gives an error:

Welcome to Yade bzr2700
FATAL /home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:207 loadPlugins: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/lib/lib_gts__python-module.so: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/lib/lib_gts__python-module.so: cannot open shared object file: No such file or directory .
FATAL /home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:207 loadPlugins: Bailing out.
Aborted

Also, when VTK-feature is enabled, it crashes with corresponding message (vtk-library).

Could you not, please, explain, why it links normally on other systems, but Natty gives a problem?

Thanks

Revision history for this message
Václav Šmilauer (eudoxos) wrote :

I have no idea what is it doing, perhaps post build-log so that we see what is being linked. Also, the output of "ldd home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/lib/lib_gts__python-module.so" would help. I don't have natty, so I cannot test.

Revision history for this message
Anton Gladky (gladky-anton) wrote :

The default clean compilation:
-----------------------------------------------------
./../build/bin/yade-cleanComp
Welcome to Yade bzr2705
96 FATAL yade.Omega /home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so: undefined symbol `vtkCellArray::New()'
96 FATAL yade.Omega /home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so: /home/gladk/dem/yade/cleanComp/build/lib/yade-cleanComp/plugins/libplugins.so: undefined symbol: _ZN12vtkCellArray3NewEv
96 FATAL yade.Omega /home/gladk/dem/yade/cleanComp/yade/core/Omega.cpp:204 loadPlugins: Bailing out.
Aborted

-----------------------------------------------------

Revision history for this message
Anton Gladky (gladky-anton) wrote :
Revision history for this message
Anton Gladky (gladky-anton) wrote :
Revision history for this message
Anton Gladky (gladky-anton) wrote :

build-log will be provided a little later.

Revision history for this message
Anton Gladky (gladky-anton) wrote :
Revision history for this message
Anton Gladky (gladky-anton) wrote :

It seems, it can't find vtkCommon. Will try to add /usr/lib to -Ldirs.

Revision history for this message
Anton Gladky (gladky-anton) wrote :

It did not help.

There are outputs of ldd for lucid and nattys, differences. In Lucid much more libraries are linked, than in Natty.

Revision history for this message
Anton Gladky (gladky-anton) wrote :
Revision history for this message
Anton Gladky (gladky-anton) wrote :

I deleted libraries which are persist in Natty and Lucid.

Revision history for this message
Anton Gladky (gladky-anton) wrote :

Fixed in r2707, will be backported to 0.60

Changed in yade:
status: In Progress → Fix Released
Revision history for this message
Mathan (rmsdiscover) wrote :

The latest trunk version is also showing the same problem [1] when I am trying to launch.

error : ImportError: /home2/mkr/yade-build/lib/yade-Unknown/libcore.so: undefined symbol: _ZN5boost9iostreams6detail9zlib_base8xdeflateEi

[1] https://answers.launchpad.net/yade/+question/220027

MathanK Raja

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