ParaView 5.7 doesn't work scipy internal python module

MBG · January 6, 2020, 6:24am

MacOS ParaView 5.6.2

>>> from scipy.spatial import cKDTree

>>>

MacOS ParaView 5.7

from scipy.spatial import cKDTree
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/__init__.py", line 100, in <module>
    from .qhull import *
ImportError: dlopen(/Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so, 2): Symbol not found: _main
  Referenced from: /Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so
  Expected in: flat namespace
 in /Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so

And I can’t load external scipy module because the internal one exists.

MBG · January 6, 2020, 6:52am

The recent night build ParaView-5.7.0-936-ga45459775a.app:

from scipy.spatial import cKDTree
Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/Applications/ParaView-5.7.0-936-ga45459775a.app/Contents/Python/scipy/spatial/__init__.py", line 100, in <module>
    from .qhull import *
ImportError: dlopen(/Applications/ParaView-5.7.0-936-ga45459775a.app/Contents/Python/scipy/spatial/qhull.so, 2): Symbol not found: _main
  Referenced from: /Applications/ParaView-5.7.0-936-ga45459775a.app/Contents/Python/scipy/spatial/qhull.so
  Expected in: flat namespace
 in /Applications/ParaView-5.7.0-936-ga45459775a.app/Contents/Python/scipy/spatial/qhull.so

mwestphal · January 6, 2020, 9:30am

Are you using our release from https://www.paraview.org/download/

Works fine on linux here.

mwestphal · January 6, 2020, 9:30am

@cory.quammen

MBG · January 6, 2020, 10:07am

MacOS is not equal to Linux. Try MacOS build by your link.

cory.quammen · January 6, 2020, 1:48pm

I am able to run from scipy.spatial import cKDTree with the Kitware binaries of 5.7.0.

MBG · January 6, 2020, 2:03pm

cory.quammen · January 6, 2020, 2:51pm

What version of macOS are you running? Since 5.7 uses the system Python, that could explain the difference. I am running macOS 10.14.6.

MBG · January 6, 2020, 2:56pm

MacOS 10.14.6 (18G2022)

ParaView Python Library Path: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7

ParaView Python Library Version: 2.7.16 (default, Oct 16 2019, 00:34:56)
[GCC 4.2.1 Compatible Apple LLVM 10.0.1 (clang-1001.0.37.14)]

cory.quammen · January 6, 2020, 6:05pm

Strange, I have the same Python version and Path on my system.

I don’t know why it is looking for a main function in qhull.so on your system but not mine.

Can you run

/Applications/ParaView-5.7.0.app/Contents/MacOS/paraview -dr

to try running with a default environment and settings?

MBG · January 6, 2020, 6:24pm

I uninstalled and installed ParaView 5.7 again and the issue is the same and it’s not depends of PYTHONPATH env variable:

unset PYTHONPATH; /Applications/ParaView-5.7.0.app/Contents/MacOS/paraview -dr

from scipy.spatial import cKDTree

Traceback (most recent call last):
  File "<console>", line 1, in <module>
  File "/Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/__init__.py", line 100, in <module>
    from .qhull import *
ImportError: dlopen(/Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so, 2): Symbol not found: _main
  Referenced from: /Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so
  Expected in: flat namespace
 in /Applications/ParaView-5.7.0.app/Contents/Python/scipy/spatial/qhull.so

cory.quammen · January 6, 2020, 6:38pm

Thanks for trying. Thoughts, @ben.boeckel?

MBG · January 13, 2020, 5:25pm

Maybe the issue is not so important if we will have soon ParaView 5.8 with Python 3:

ben.boeckel · January 14, 2020, 3:26pm

Very strange. I don’t know what would cause it to happen on one machine and not another, sorry. Looking for main is very odd (macOS mangling involves putting a leading _ on symbols).