[vtkusers] Can't run build vtk from source with python wrappings

[Evgeniya Malikova]

Hello, I’m trying to run vtk with python wrappings build from source https://gitlab.kitware.com/vtk/vtk.git. Target os - MacOs, python version 3.6. The basic call of “import vtk” from python gives error that libraries can’t be loaded (python program from https://www.vtk.org/Wiki/VTK/Examples/Python/Cylinder <https://www.vtk.org/Wiki/VTK/Examples/Python/Cylinder>):


Traceback (most recent call last):
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 5, in <module>
from .vtkCommonCorePython import *
ImportError: dlopen(/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so, 2): Library not loaded: @rpath/libvtkCommonCorePython36D-8.2.1.dylib
Referenced from: /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py", line 7, in <module>
from .vtkCommonCore import *
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'

This is the error with added path to /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH variable.

Looks very much like libraries are found but can’t be loaded for some reasons. Any suggestions what can cause such an error?

Thank you very much in advance,
Best regards,
Evgeniya

[Evgeniya Malikova]

Forgot to add, main library files, like libvtkCommonCorePython36-8.2.1.dylib are in Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ folder.

Best regards,
Evgeniya

Post by Evgeniya Malikova
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 5, in <module>
from .vtkCommonCorePython import *
Referenced from: /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py", line 7, in <module>
from .vtkCommonCore import *
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'
This is the error with added path to /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH variable.
Looks very much like libraries are found but can’t be loaded for some reasons. Any suggestions what can cause such an error?
Thank you very much in advance,
Best regards,
Evgeniya

[Jean-Christophe Fillion-Robin]

Hi,

If you explicitly set or update DYLD_LIBRARY_PATH environment variable
first with the path"
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/", are you able
to import ?

While sub-optimal, knowing that this work would provide good information.

Jc

Post by Evgeniya Malikova
Forgot to add, main library files, like
libvtkCommonCorePython36-8.2.1.dylib are in
Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ folder.
Best regards,
Evgeniya
Hello, I’m trying to run vtk with python wrappings build from source
https://gitlab.kitware.com/vtk/vtk.git. Target os - MacOs, python version
3.6. The basic call of “import vtk” from python gives error that libraries
can’t be loaded (python program from
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py",
line 5, in <module>
from .vtkCommonCorePython import *
dlopen(/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so,
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py",
line 7, in <module>
from .vtkCommonCore import *
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py",
line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'
This is the error with added path to
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH
variable.
Looks very much like libraries are found but can’t be loaded for some
reasons. Any suggestions what can cause such an error?
Thank you very much in advance,
Best regards,
Evgeniya
_______________________________________________
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http://www.kitware.com/opensource/opensource.html
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https://public.kitware.com/mailman/listinfo/vtkusers

[Evgeniya Malikova]

No, looks like updating DYLS_LIBRARY_PATH didn’t solve the problem.

However, vtkpython works well. Just come across this description:
https://stackoverflow.com/questions/48148376/running-vtk-from-python-not-just-vtkpython

The similar check gives me similar list of dependencies with vtk python depending on libpython3.6m.dylib:
otool -L libvtkCommonCorePython36D-8.2.1.dylib
libvtkCommonCorePython36D-8.2.1.dylib:
@rpath/libvtkCommonCorePython36D-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)

otool -L vtkpython
vtkpython:
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkPythonInterpreter-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libpython3.6m.dylib (compatibility version 3.6.0, current version 3.6.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)

Best regards,
Evgeniya

Hi,
If you explicitly set or update DYLD_LIBRARY_PATH environment variable first with the path" /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/", are you able to import ?
While sub-optimal, knowing that this work would provide good information.
Jc
Forgot to add, main library files, like libvtkCommonCorePython36-8.2.1.dylib are in Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ folder.
Best regards,
Evgeniya

Post by Evgeniya Malikova
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 5, in <module>
from .vtkCommonCorePython import *
Referenced from: /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py", line 7, in <module>
from .vtkCommonCore import *
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'
This is the error with added path to /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH variable.
Looks very much like libraries are found but can’t be loaded for some reasons. Any suggestions what can cause such an error?
Thank you very much in advance,
Best regards,
Evgeniya

_______________________________________________
Powered by www.kitware.com <http://www.kitware.com/>
Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_FAQ <http://www.vtk.org/Wiki/VTK_FAQ>
Search the list archives at: http://markmail.org/search/?q=vtkusers <http://markmail.org/search/?q=vtkusers>
https://public.kitware.com/mailman/listinfo/vtkusers <https://public.kitware.com/mailman/listinfo/vtkusers>

[Jean-Christophe Fillion-Robin]

Hi,

I see. As an alternative approach, you could also look into building VTK
python package using https://github.com/jcfr/VTKPythonPackage

This is what is used to build the VTK python wheels. That said, note that
we are are not yet officially supporting VTK python wheels.

Hth
Jc

Post by Evgeniya Malikova
No, looks like updating DYLS_LIBRARY_PATH didn’t solve the problem.
https://stackoverflow.com/questions/48148376/running-vtk-from-python-not-just-vtkpython
The similar check gives me similar list of dependencies with vtk python
otool -L libvtkCommonCorePython36D-8.2.1.dylib
@rpath/libvtkCommonCorePython36D-8.2.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version
1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
otool -L vtkpython
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version
1.0.0, current version 1.0.0)
@rpath/libvtkPythonInterpreter-8.2.1.dylib (compatibility version 1.0.0,
current version 1.0.0)
/usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libpython3.6m.dylib (compatibility version 3.6.0, current version 3.6.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
Best regards,
Evgeniya
Hi,
If you explicitly set or update DYLD_LIBRARY_PATH environment variable
first with the path"
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/", are you able
to import ?
While sub-optimal, knowing that this work would provide good information.
Jc
On Fri, Oct 26, 2018 at 8:29 AM Evgeniya Malikova <

Post by Evgeniya Malikova
Forgot to add, main library files, like
libvtkCommonCorePython36-8.2.1.dylib are in
Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ folder.
Best regards,
Evgeniya
Hello, I’m trying to run vtk with python wrappings build from source
https://gitlab.kitware.com/vtk/vtk.git. Target os - MacOs, python
version 3.6. The basic call of “import vtk” from python gives error that
libraries can’t be loaded (python program from
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py",
line 5, in <module>
from .vtkCommonCorePython import *
dlopen(/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so,
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py",
line 7, in <module>
from .vtkCommonCore import *
File
"/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py",
line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'
This is the error with added path to
/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH
variable.
Looks very much like libraries are found but can’t be loaded for some
reasons. Any suggestions what can cause such an error?
Thank you very much in advance,
Best regards,
Evgeniya
_______________________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
http://www.vtk.org/Wiki/VTK_FAQ
Search the list archives at: http://markmail.org/search/?q=vtkusers
https://public.kitware.com/mailman/listinfo/vtkusers

_______________________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
http://www.vtk.org/Wiki/VTK_FAQ
Search the list archives at: http://markmail.org/search/?q=vtkusers
https://public.kitware.com/mailman/listinfo/vtkusers

[Evgeniya Malikova]

Ok. Thank you very much.

Evgeniya

Hi,
I see. As an alternative approach, you could also look into building VTK python package using https://github.com/jcfr/VTKPythonPackage
This is what is used to build the VTK python wheels. That said, note that we are are not yet officially supporting VTK python wheels.
Hth
Jc

No, looks like updating DYLS_LIBRARY_PATH didn’t solve the problem.
https://stackoverflow.com/questions/48148376/running-vtk-from-python-not-just-vtkpython
otool -L libvtkCommonCorePython36D-8.2.1.dylib
@rpath/libvtkCommonCorePython36D-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
otool -L vtkpython
@rpath/libvtkWrappingPython36Core-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkPythonInterpreter-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libpython3.6m.dylib (compatibility version 3.6.0, current version 3.6.0)
@rpath/libvtksys-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
@rpath/libvtkCommonCore-8.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 400.9.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.0.0)
Best regards,
Evgeniya
Hi,
If you explicitly set or update DYLD_LIBRARY_PATH environment variable first with the path" /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/", are you able to import ?
While sub-optimal, knowing that this work would provide good information.
Jc

Post by Evgeniya Malikova
Forgot to add, main library files, like libvtkCommonCorePython36-8.2.1.dylib are in Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ folder.
Best regards,
Evgeniya
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 5, in <module>
from .vtkCommonCorePython import *
Referenced from: /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCorePython.so
Reason: image not found
File "/Users/evgeniya/PycharmProjects/untitled/vtk_test.py", line 1, in <module>
import vtk
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/__init__.py", line 7, in <module>
from .vtkCommonCore import *
File "/Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/vtkCommonCore.py", line 9, in <module>
from vtkCommonCorePython import *
ModuleNotFoundError: No module named ‘vtkCommonCorePython'
This is the error with added path to /Users/evgeniya/anaconda3/lib/python3.6/site-packages/vtk/ to PYTHONPATH variable.
Looks very much like libraries are found but can’t be loaded for some reasons. Any suggestions what can cause such an error?
Thank you very much in advance,
Best regards,
Evgeniya
_______________________________________________
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 VTK FAQ at: http://www.vtk.org/Wiki/VTK_FAQ
Search the list archives at: http://markmail.org/search/?q=vtkusers
https://public.kitware.com/mailman/listinfo/vtkusers

_______________________________________________
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 VTK FAQ at: http://www.vtk.org/Wiki/VTK_FAQ
Search the list archives at: http://markmail.org/search/?q=vtkusers
https://public.kitware.com/mailman/listinfo/vtkusers

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Powered by www.kitware.com

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Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_FAQ

Search the list archives at: http://markmail.org/search/?q=vtkusers

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