[vtkusers] Fatal Python error: PyThreadState_Get: no current thread

Isaiah Norton isaiah.norton at gmail.com
Tue Apr 11 19:57:38 EDT 2017 

Another option is `DYLD_PRINT_LIBRARIES=1 (vtkpython | python3)`. This will
dump loader activity to the console. See the man page for dyld. For lldb,
you could try attaching to a running python before calling import in the
repl.

On Mon, Apr 10, 2017 at 10:11 AM, Jayson Kempinger <
jkempinger at decisionvis.com> wrote:

> Hi Isaiah,
>
> Thanks for the response!
>
> I've pasted below the output from running python3, vtkpython, and both of
> those commands under lldb.  I've never used vmmap before, so I'm not sure
> how to attach to the process after it crashes, and running vmmap on a
> running vtkpython, before importing vtk, doesn't show anything that seems
> out of the ordinary (see output at https://pastebin.com/j5ANwNpv).
>
> I'm not sure where to go from here as I get different results under lldb
> and different lldb output for running python3 and vtkpython.  I've also
> tried vtk-7.0.0 but I get the same results, just with "-7.0.0.dylib".
>
> All of the image files that weren't found do exist on the system:
>
> > find /Users/jkempinger/build -iname "libvtkCommonCorePython35D-7.1.1.dylib"
> -exec ls -l '{}' \;
> -rwxr-xr-x  1 jkempinger  staff  2964960 Apr 10 09:46
> /Users/jkempinger/build/lib/libvtkCommonCorePython35D-7.1.1.dylib
> > find /Users/jkempinger/build -iname "libvtkWrappingPython35Core-7.1.1.dylib"
> -exec ls -l '{}' \;
> -rwxr-xr-x  1 jkempinger  staff  3052644 Apr 10 09:46
> /Users/jkempinger/build/lib/libvtkWrappingPython35Core-7.1.1.dylib
>
> and I believe my environment is set correctly:
>
> > echo $DYLD_LIBRARY_PATH
> /Users/jkempinger/build/lib:/Users/jkempinger/build/Qt5.7.
> 0/5.7/clang_64/lib
> > echo $LD_LIBRARY_PATH
> /Users/jkempinger/build/lib:/Users/jkempinger/build/Qt5.7.
> 0/5.7/clang_64/lib
> > echo $PYTHONPATH
> /Users/jkempinger/build/lib/python3.5/site-packages
>
>
> When running python3:
>
> Python 3.5.2 (default, Apr  7 2017, 11:18:59)
> [GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.38)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import vtk
> Fatal Python error: PyThreadState_Get: no current thread
> zsh: abort      /Users/jkempinger/build/bin/python3
>
>
> When running vtkpython:
>
> vtk version 7.1.1
> Python 3.5.2 (default, Apr  7 2017, 11:18:59)
> [GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.38)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import vtk
> Fatal Python error: PyThreadState_Get: no current thread
> zsh: abort      /Users/jkempinger/build/bin/vtkpython
>
>
> When running python3 under lldb and importing vtk:
>
> (lldb) target create "/Users/jkempinger/build/bin/python3"
> Current executable set to '/Users/jkempinger/build/bin/python3' (x86_64).
> (lldb) run
> Process 48987 launched: '/Users/jkempinger/build/bin/python3' (x86_64)
> Python 3.5.2 (default, Apr  7 2017, 11:18:59)
> [GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.38)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import vtk
> Traceback (most recent call last):
>   File "/Users/jkempinger/build/lib/python3.5/site-packages/vtk/vtkCommonCore.py",
> line 5, in <module>
>     from .vtkCommonCorePython import *
> ImportError: dlopen(/Users/jkempinger/build/lib/python3.5/site-
> packages/vtk/vtkCommonCorePython.so, 2): Library not loaded:
> libvtkCommonCorePython35D-7.1.1.dylib
>   Referenced from: /Users/jkempinger/build/lib/
> python3.5/site-packages/vtk/vtkCommonCorePython.so
>   Reason: image not found
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Users/jkempinger/build/lib/python3.5/site-packages/vtk/__init__.py",
> line 41, in <module>
>     from .vtkCommonCore import *
>   File "/Users/jkempinger/build/lib/python3.5/site-packages/vtk/vtkCommonCore.py",
> line 9, in <module>
>     from vtkCommonCorePython import *
> ImportError: No module named 'vtkCommonCorePython'
> >>>
>
>
> When running vtkpython in lldb:
>
> (lldb) target create "/Users/jkempinger/build/bin/vtkpython"
> Current executable set to '/Users/jkempinger/build/bin/vtkpython'
> (x86_64).
> (lldb) run
> Process 49021 launched: '/Users/jkempinger/build/bin/vtkpython' (x86_64)
> dyld: Library not loaded: libvtkWrappingPython35Core-7.1.1.dylib
>   Referenced from: /Users/jkempinger/build/bin/vtkpython
>   Reason: image not found
> Process 49021 stopped
> * thread #1, stop reason = signal SIGABRT
>     frame #0: 0x00000001000359ee dyld`__abort_with_payload + 10
> dyld`__abort_with_payload:
> ->  0x1000359ee <+10>: jae    0x1000359f8               ; <+20>
>     0x1000359f0 <+12>: movq   %rax, %rdi
>     0x1000359f3 <+15>: jmp    0x100035300               ; cerror_nocancel
>     0x1000359f8 <+20>: retq
> (lldb) image list
> [  0] 08649D04-B82E-328E-AD4C-CA3C421293E5 0x0000000100000000
> /Users/jkempinger/build/bin/vtkpython
> [  1] 8239D0D7-66F6-3C44-A77F-586F74525DA3 0x000000010000c000
> /usr/lib/dyld
> (lldb)
>
>
> Any suggestions on what to try next?
>
> Thanks!
> Jayson
>
> On Apr 7, 2017, at 10:45 PM, Isaiah Norton <isaiah.norton at gmail.com>
> wrote:
>
> You could debug with vmmap, to see which shared libraries are loaded in
> the process.
> Or start under lldb and look at output of `image list` when it aborts.
>
> Isaiah
>
> On Fri, Apr 7, 2017 at 4:26 PM, Jayson Kempinger <
> jkempinger at decisionvis.com> wrote:
>
>> Hi, I’m trying to install VTK on an iMac running 10.12.  I’m using python
>> 3.5.2, compiled from source, and am compiling VTK-7.1.1 from source.
>>
>> When I run python3 (with -v and -d) and try to import vtk python crashes
>> with the following error:
>>
>> >>> import vtk
>> # /Users/username/build/lib/python3.5/site-packages/vtk/__pycache__/__init__.cpython-35.pyc
>> matches /Users/username/build/lib/python3.5/site-packages/vtk/__init__.py
>> # code object from '/Users/username/build/lib/pyt
>> hon3.5/site-packages/vtk/__pycache__/__init__.cpython-35.pyc'
>> # /Users/username/build/lib/python3.5/__pycache__/__future__.cpython-35.pyc
>> matches /Users/username/build/lib/python3.5/__future__.py
>> # code object from '/Users/username/build/lib/pyt
>> hon3.5/__pycache__/__future__.cpython-35.pyc'
>> import '__future__' # <_frozen_importlib_external.SourceFileLoader
>> object at 0x1073032e8>
>> # /Users/username/build/lib/python3.5/site-packages/vtk/__pyca
>> che__/vtkCommonCore.cpython-35.pyc matches /Users/username/build/lib/pyth
>> on3.5/site-packages/vtk/vtkCommonCore.py
>> # code object from '/Users/username/build/lib/pyt
>> hon3.5/site-packages/vtk/__pycache__/vtkCommonCore.cpython-35.pyc'
>> Fatal Python error: PyThreadState_Get: no current thread
>> zsh: abort      python3 -v -d
>>
>> From what I’ve read online it sounds like this is due to a python
>> mismatch, i.e. building VTK against a different python version than the
>> version it is run under.  I’ve searched through the advanced cmake
>> configuration and can’t find any reference to the system built-in python2
>> interpreter.
>>
>> Any suggestions on what might be going wrong?
>>
>> Thanks!
>> Jayson
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>
>
>
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