[Paraview] Segfault in Python when importing paraview.servermanager and vtk in the wrong order

Thu Jan 31 05:52:37 EST 2013

Hi Pat!

[Apologies for sending you this twice, I accidentally didn't hit 'reply
all'.]

Many thanks for the detailed reply! Indeed, I'm suspecting a conflict
between different vtk versions, but I don't know which ones could be the
culprits. I'm not sure the issue is actually related to the FEniCS package,
but will have to find a computer that doesn't have any FEniCS-related
packages installed to be sure. The reason why I'm saying that is because
the segfault already happens when I say:

>>> import vtk
>>> import paraview.servermanager

and the following indicates that it loads the system-wide vtk module (not
one that comes with FEniCS):

>>> print vtk.__file__
/usr/lib/pymodules/python2.7/
vtk/__init__.pyc

Out of interest, can you reproduce the segfault on your machine? I presume
you don't have FEniCS installed?

The hints in your email are very helpful, and based on them I'll try to put
some more debugging info together as soon as I can (I won't be able to do
it before next week, however). Just to answer your questions about my setup:

I run my scripts from a regular python interpreter on the command line (not
from ParaView's python console or via pvpython). The output of sys.path is
attached below. I'll try the LD_DEBUG=lib approach next week and will
report if I can find anything.

Many thanks again and kind regards,
Max

------------------------------
Output of sys.path:

['',
'/usr/lib/python2.7',
'/usr/lib/python2.7/plat-linux2',
'/usr/lib/python2.7/lib-tk',
'/usr/lib/python2.7/lib-old',
'/usr/lib/python2.7/lib-dynload',
'/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages/PIL',
'/usr/lib/python2.7/dist-packages/gst-0.10',
'/usr/lib/python2.7/dist-packages/gtk-2.0',
'/usr/lib/pymodules/python2.7',
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-control-panel',
'/usr/lib/python2.7/dist-packages/ubuntuone-couch',
'/usr/lib/python2.7/dist-packages/ubuntuone-installer',
'/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol',
'/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode']

2013/1/30 Pat Marion <pat.marion at kitware.com>

> Hi,
>
> It sounds like you probably have multiple versions of the vtk libraries
> installed someplace in your path.  Maybe the FEniCS package ships it's own
> version of the vtk libraries?  If FEniCS imports a different version of
> vtk, then paraview won't be able to import vtk within the same memory
> space, or maybe you can build FEniCS and ParaView to use the same version
> of vtk.
>
> Are you running this script in ParaView's python console, or from the
> command line?  If command line, what interpreter are you using, pvpython,
> or regular python?
>
> To collect some more debugging info, in the interpreter print out sys.path
> and tell us what that says.  Normally, you can't import vtk from the
> paraview console, you have to import paraview.vtk.  So if you can import
> vtk, it's probably grabbing it from a third party location, not the vtk
> installed with paraview.
>
> Also, try exporting LD_DEBUG=libs and then run paraview, that will print a
> lot of information to the terminal, it will tell you which libraries are
> being loaded.  See if any vtk libs are loaded from a location that is
> different than where paraview is installed.
>
> Pat
>
>
>
> On Wed, Jan 30, 2013 at 10:20 AM, Maximilian Albert <
> maximilian.albert at gmail.com> wrote:
>
>> Hi,
>>
>> apologies for bumping my own message, but looking at the thread view
>> [1] of the mailing list archives I just realised that strangely my
>> email was filed under a completely unrelated thread (even though I
>> hadn't replied to any messages) and maybe this is why it got lost in
>> people's inboxes.
>>
>> So hopefully you won't mind me asking for help again - if anybody has
>> any thoughts on the paraview/vtk segfault described below, this would
>> be very much appreciated.
>>
>> Many thanks and kind regards,
>> Max
>>
>> [1] http://www.paraview.org/pipermail/paraview/2013-January/thread.html
>>
>>
>> 2013/1/21 Maximilian Albert <maximilian.albert at gmail.com>:
>> > Hi all,
>> >
>> > since this is my first post here, let me take the opportunity to thank
>> > all the developers for their hard work and and for an immensely useful
>> > piece of software! :)
>> >
>> > I'm writing becasue I am having a problem with a very annoying
>> > segfault related to Paraview scripting and hope someone can help me.
>> > The following two lines when executed in a Python interpreter lead to
>> > a segfault:
>> >
>> >>>> import vtk
>> >>>> import paraview.servermanager
>> > Segmentation fault (core dumped)
>> >
>> > However, if I do the imports the other way around then it works fine.
>> >
>> >>>> import paraview.servermanager
>> > paraview version 3.14.1, Date: 2012-02-17
>> >>>> import vtk
>> >>>>
>> >
>> > This looks like it should be a very common bug to hit, but I couldn't
>> > find anything on the web that looked similar. Does anybody have an
>> > idea what could be causing this and how to work around it? It is quite
>> > annoying because I'm using the FEniCS package [1] to run simulations
>> > that I would like to visualize using Paraview, but FEniCS internally
>> > imports vtk, so now all my simulation scripts have stopped working and
>> > produce crashes. So any help would be much appreciated.
>> >
>> > For the record, I am using Ubuntu 12.04.1 LTS with the standard
>> > Paraview version 3.14.1 that is shipped with it, but I also tried it
>> > on another computer with version 3.98.0 from the PPA [2], and the
>> > segfault also happens there. The backtrace from the coredump is
>> > attached below in case it can be of any help.
>> >
>> > Many thanks and best regards,
>> > Max
>> >
>> > [1] http://fenicsproject.org/
>> > [2] http://ppa.launchpad.net/gladky-anton/paraview/ubuntu
>> >
>> >
>> > === Gdb session output with backtrace ===
>> >
>> > $ GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
>> > Copyright (C) 2012 Free Software Foundation, Inc.
>> > License GPLv3+: GNU GPL version 3 or later <
>> http://gnu.org/licenses/gpl.html>
>> > This is free software: you are free to change and redistribute it.
>> > There is NO WARRANTY, to the extent permitted by law.  Type "show
>> copying"
>> > and "show warranty" for details.
>> > This GDB was configured as "x86_64-linux-gnu".
>> > For bug reporting instructions, please see:
>> > <http://bugs.launchpad.net/gdb-linaro/>...
>> > Reading symbols from /usr/bin/python...Reading symbols from
>> > /usr/lib/debug/usr/bin/python2.7...done.
>> > done.
>> > [New LWP 20514]
>> >
>> > warning: Can't read pathname for load map: Input/output error.
>> > [Thread debugging using libthread_db enabled]
>> > Using host libthread_db library
>> "/lib/x86_64-linux-gnu/libthread_db.so.1".
>> > Core was generated by `python'.
>> > Program terminated with signal 11, Segmentation fault.
>> > #0  0x0000000000000000 in ?? ()
>> > (gdb) bt
>> > #0  0x0000000000000000 in ?? ()
>> > #1  0x00007f7ad64812ff in
>> > vtkTCPNetworkAccessManager::vtkTCPNetworkAccessManager() () from
>> > /usr/lib/paraview/libvtkPVClientServerCore.so
>> > #2  0x00007f7ad648136d in vtkTCPNetworkAccessManager::New() () from
>> > /usr/lib/paraview/libvtkPVClientServerCore.so
>> > #3  0x00007f7ad6475a92 in vtkProcessModule::vtkProcessModule() () from
>> > /usr/lib/paraview/libvtkPVClientServerCore.so
>> > #4  0x00007f7ad6475b6d in vtkProcessModule::New() () from
>> > /usr/lib/paraview/libvtkPVClientServerCore.so
>> > #5  0x00007f7ad6475e1b in
>> > vtkProcessModule::Initialize(vtkProcessModule::ProcessTypes, int&,
>> > char**&) () from /usr/lib/paraview/libvtkPVClientServerCore.so
>> > #6  0x00007f7acc4e987c in vtkInitializationHelper::Initialize(int,
>> > char**, int, vtkPVOptions*) () from
>> > /usr/lib/paraview/libvtkPVServerManager.so
>> > #7  0x00007f7acc4ea62e in vtkInitializationHelper::Initialize(char
>> > const*, int, vtkPVOptions*) () from
>> > /usr/lib/paraview/libvtkPVServerManager.so
>> > #8  0x00007f7acc8d8b45 in ?? () from
>> > /usr/lib/python2.7/dist-packages/vtkPVServerManagerPython.so
>> > #9  0x0000000000497ea4 in PyEval_EvalFrameEx ()
>> > #10 0x000000000049f1c0 in PyEval_EvalCodeEx ()
>> > #11 0x00000000004a7f18 in PyImport_ExecCodeModuleEx ()
>> > #12 0x000000000053cde1 in load_source_module.39052 ()
>> > #13 0x000000000053d7db in import_submodule.39106 ()
>> > #14 0x00000000004fc1a3 in load_next.39111 ()
>> > #15 0x000000000053e266 in import_module_level.isra.3.39132 ()
>> > #16 0x00000000004c2e6b in builtin___import__.32787 ()
>> > #17 0x00000000004e9f36 in PyObject_Call ()
>> > #18 0x00000000004ea396 in PyEval_CallObjectWithKeywords ()
>> > #19 0x000000000049a4ed in PyEval_EvalFrameEx ()
>> > #20 0x000000000049f1c0 in PyEval_EvalCodeEx ()
>> > #21 0x00000000004a9d0f in PyRun_InteractiveOneFlags ()
>> > #22 0x00000000004aa075 in PyRun_InteractiveLoopFlags ()
>> > #23 0x00000000004aa328 in PyRun_AnyFileExFlags ()
>> > #24 0x00000000004aa8bd in Py_Main ()
>> > #25 0x00007f7af885f76d in __libc_start_main () from
>> > /lib/x86_64-linux-gnu/libc.so.6
>> > #26 0x000000000041b9b1 in _start ()
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