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.mar...@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.alb...@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.alb...@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 () >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://www.paraview.org/mailman/listinfo/paraview >> > >
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