[Paraview] Importing paraview.simple from python

Burlen Loring burlen.loring at gmail.com
Wed Aug 10 13:55:06 EDT 2016 

fyi, a common way to encounter
> Fatal Python error: PyThreadState_Get: no current thread
is when cmake's find Python modules mix two version of Python. this 
happen if you have two installs, one in a system location and one else 
where with interpreter in the path. You can identify it in the cmake 
cache. bug reports on this are found in the cmake Mantis tracker. The 
most informative is here <https://cmake.org/Bug/view.php?id=14809> and 
in new bug tracker here 
<https://gitlab.kitware.com/cmake/cmake/issues/14809>. I've resorted to 
using python-config in cmake to work around, but this requires the 
environment to have the desired python in the path, ld lib path, dyld 
lib path and pkg config path.

On 08/10/2016 05:33 AM, Utkarsh Ayachit wrote:
> Looks like the relative path specification has change which may make
> this tricky. Ben, can you take  a look please? Thanks
>
> Utkarsh
>
> On Wed, Aug 10, 2016 at 5:29 AM, Zhou, Fangyi
> <fangyi.zhou15 at imperial.ac.uk> wrote:
>> Thanks to previous emails I have managed to get it running on Linux, but I have the similar problem on mac
>>
>> % export DYLD_FALLBACK_FRAMEWORK_PATH=/Applications/paraview.app/Contents/Frameworks
>> % export DYLD_FALLBACK_LIBRARY_PATH=/Applications/paraview.app/Contents/Libraries
>> % export DYLD_LIBRARY_PATH=/Applications/paraview.app/Contents/Libraries/
>> % export PYTHONPATH=/Applications/paraview.app/Contents/Python:/Applications/paraview.app/Contents/Python/vtk:/Applications/paraview.app/Contents/Libraries
>>
>> Home-brew python:
>>
>> % which python
>> /usr/local/bin/python
>> % python
>> Python 2.7.12 (default, Jun 29 2016, 14:05:02)
>> [GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import paraview.simple
>> Fatal Python error: PyThreadState_Get: no current thread
>> [1]    47104 abort      python
>>
>> System python:
>>
>> % /usr/bin/python
>> Python 2.7.10 (default, Oct 23 2015, 19:19:21)
>> [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import paraview.simple
>> Error: Could not import vtkCommonComputationalGeometry
>> Traceback (most recent call last):
>>    File "<stdin>", line 1, in <module>
>>    File "/Applications/paraview.app/Contents/Python/paraview/simple.py", line 39, in <module>
>>      import servermanager
>>    File "/Applications/paraview.app/Contents/Python/paraview/servermanager.py", line 52, in <module>
>>      from paraview import vtk
>>    File "/Applications/paraview.app/Contents/Python/paraview/vtk/__init__.py", line 7, in <module>
>>      from vtkCommonCore import *
>>    File "/Applications/paraview.app/Contents/Python/paraview/vtk/vtkCommonCore.py", line 9, in <module>
>>      from vtkCommonCorePython import *
>> ImportError: dlopen(/Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so, 2): Library not loaded: @executable_path/../Libraries/libvtkCommonCorePython27D-pv5.1.1.dylib
>>    Referenced from: /Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
>>    Reason: unsafe use of @executable_path in /Applications/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so with restricted binary
>>
>> Thanks
>>
>> Fangyi
>>
>>> On 9 Aug 2016, at 17:52, Mohammad Mirzadeh <mirzadeh at gmail.com> wrote:
>>>
>>> Thanks Utkarsh. Two issues:
>>>
>>> 1- Looks like I have to use OS X provided python (2.7)? Using any other python results in
>>>
>>> Fatal Python error: PyThreadState_Get: no current thread
>>>
>>> 2- using system python I get some unresolved symbol issue with MPI.
>>> Traceback (most recent call last):
>>>    File "<stdin>", line 1, in <module>
>>>    File "/Applications/paraview.app/Contents/Python/paraview/simple.py", line 39, in <module>
>>>      import servermanager
>>>    File "/Applications/paraview.app/Contents/Python/paraview/servermanager.py", line 55, in <module>
>>>      from vtk.vtkPVServerImplementationCore import *
>>>    File "/Applications/paraview.app/Contents/Python/paraview/vtk/vtkPVServerImplementationCore.py", line 9, in <module>
>>>      from vtkPVServerImplementationCorePython import *
>>> ImportError: dlopen(/Applications/paraview.app/Contents/Libraries/vtkPVServerImplementationCorePython.so, 2): Symbol not found: _MPI_Group_size
>>>    Referenced from: /Applications/paraview.app/Contents/Libraries/libmpich.3.3.dylib
>>>    Expected in: flat namespace
>>>   in /Applications/paraview.app/Contents/Libraries/libmpich.3.3.dylib
>>>
>>> Any idea why that happens? I have open-mpi installed system-wide (/usr/local).
>>>
>>>
>>> On Tue, Aug 9, 2016 at 12:15 PM, Utkarsh Ayachit <utkarsh.ayachit at kitware.com> wrote:
>>> Attached is a script from an older email. The 5.1.* uses Python 2.7,
>>> so you'll need to update the script accordingly. I haven't tested it
>>> (as I don't have my Mac here), but it should give you some hints.
>>>
>>> Utkarsh
>>>
>>> On Tue, Aug 9, 2016 at 12:10 PM, Mohammad Mirzadeh <mirzadeh at gmail.com> wrote:
>>>> Along the same lines, is this possible with prebuilt binaries on OS X? I
>>>> have tried including
>>>>
>>>> export PYTHONPATH="$PYTHONPATH:/Applications/paraview.app/Contents/Python"
>>>> export
>>>> PYTHONPATH="$PYTHONPATH:/Applications/paraview.app/Contents/Python/vtk"
>>>> export
>>>> DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:/Applications/paraview.app/Contents/Library
>>>>
>>>> but have not been able to make it work
>>>>
>>>> On Tue, Aug 9, 2016 at 12:04 PM, Utkarsh Ayachit
>>>> <utkarsh.ayachit at kitware.com> wrote:
>>>>> Here's a sample launch script:
>>>>>
>>>>> #----------------------------------------------
>>>>> #!/usr/bin/env bash
>>>>> pvprefix=/tmp/ParaView-5.1.2-Qt4-OpenGL2-MPI-Linux-64bit/
>>>>> export
>>>>> PYTHONPATH=$pvprefix/lib/paraview-5.1/site-packages/vtk:$pvprefix/lib/paraview-5.1/site-packages
>>>>> export LD_LIBRARY_PATH=$pvprefix/lib/paraview-5.1
>>>>> python
>>>>> #----------------------------------------------
>>>>>
>>>>> Utkarsh
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
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>>>>
> _______________________________________________
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>
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>
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>
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>
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