FS#52771 - mayavi does not start when vtk is installed

Attached to Project: Community Packages
Opened by Johannes E (JohannesE) - Monday, 30 January 2017, 08:24 GMT
Last edited by Doug Newgard (Scimmia) - Wednesday, 01 February 2017, 15:17 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To No-one
Architecture x86_64
Severity Medium
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:
If vtk-7.1.0-2 is installed mayavi crashes on startup with the following error:

% mayavi2
Traceback (most recent call last):
File "/usr/bin/mayavi2", line 11, in <module>
load_entry_point('mayavi==4.5.0', 'gui_scripts', 'mayavi2')()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 560, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2642, in load_entry_point
return ep.load()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2296, in load
return self.resolve()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2302, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/lib/python2.7/site-packages/mayavi/scripts/mayavi2.py", line 460, in <module>
raise ImportError(msg)
ImportError: /opt/vtk6/lib/libvtkRenderingOpenGL.so.1: undefined symbol: _ZN19vtkImageSliceMapper6UpdateEi
________________________________________________________________________________
Do you have vtk installed properly?
VTK (and build instructions) can be obtained from http://www.vtk.org


Additional info:
- mayavi version 4.5.0-4


Steps to reproduce:
- Install mayavi
- Install vtk-7.1.0-2
- Run mayavi (fails)
- Remove vtk-7.1.0-2
- Run mayavi (works)
This task depends upon

Closed by  Doug Newgard (Scimmia)
Wednesday, 01 February 2017, 15:17 GMT
Reason for closing:  Duplicate
Additional comments about closing:   FS#51611 
Comment by Doug Newgard (Scimmia) - Tuesday, 31 January 2017, 15:45 GMT
Can you give us the output of `ldd /opt/vtk6/lib/libvtkRenderingOpenGL.so.1`, as well as the version of vtk6?
Comment by Johannes E (JohannesE) - Tuesday, 31 January 2017, 16:21 GMT
revelation ~ % ldd /opt/vtk6/lib/libvtkRenderingOpenGL.so.1
linux-vdso.so.1 (0x00007ffe88b2c000)
libvtkRenderingCore.so.1 => /usr/lib/libvtkRenderingCore.so.1 (0x00007faf9015f000)
libvtkImagingHybrid.so.1 => /usr/lib/libvtkImagingHybrid.so.1 (0x00007faf8fee7000)
libGL.so.1 => /usr/lib/libGL.so.1 (0x00007faf8fc75000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x00007faf8f936000)
libXt.so.6 => /usr/lib/libXt.so.6 (0x00007faf8f6cd000)
libvtkIOImage.so.1 => /usr/lib/libvtkIOImage.so.1 (0x00007faf8f329000)
libvtkCommonExecutionModel.so.1 => /usr/lib/libvtkCommonExecutionModel.so.1 (0x00007faf8f080000)
libvtkCommonDataModel.so.1 => /usr/lib/libvtkCommonDataModel.so.1 (0x00007faf8ead9000)
libvtkCommonTransforms.so.1 => /usr/lib/libvtkCommonTransforms.so.1 (0x00007faf8e8a8000)
libvtkCommonMath.so.1 => /usr/lib/libvtkCommonMath.so.1 (0x00007faf8e685000)
libvtkCommonSystem.so.1 => /usr/lib/libvtkCommonSystem.so.1 (0x00007faf8e471000)
libvtksys.so.1 => /usr/lib/libvtksys.so.1 (0x00007faf8e224000)
libvtkCommonCore.so.1 => /usr/lib/libvtkCommonCore.so.1 (0x00007faf8dca2000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007faf8d91a000)
libm.so.6 => /usr/lib/libm.so.6 (0x00007faf8d616000)
libc.so.6 => /usr/lib/libc.so.6 (0x00007faf8d278000)
libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007faf8d061000)
libvtkCommonColor.so.1 => /usr/lib/libvtkCommonColor.so.1 (0x00007faf8ce44000)
libvtkFiltersGeometry.so.1 => /usr/lib/libvtkFiltersGeometry.so.1 (0x00007faf8cbbd000)
libvtkFiltersSources.so.1 => /usr/lib/libvtkFiltersSources.so.1 (0x00007faf8c921000)
libvtkFiltersGeneral.so.1 => /usr/lib/libvtkFiltersGeneral.so.1 (0x00007faf8c429000)
libvtkFiltersCore.so.1 => /usr/lib/libvtkFiltersCore.so.1 (0x00007faf8bd4d000)
libvtkCommonComputationalGeometry.so.1 => /usr/lib/libvtkCommonComputationalGeometry.so.1 (0x00007faf8bb17000)
libvtkImagingCore.so.1 => /usr/lib/libvtkImagingCore.so.1 (0x00007faf8b66b000)
libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00007faf8b43f000)
libxcb-dri3.so.0 => /usr/lib/libxcb-dri3.so.0 (0x00007faf8b23c000)
libxcb-present.so.0 => /usr/lib/libxcb-present.so.0 (0x00007faf8b039000)
libxcb-sync.so.1 => /usr/lib/libxcb-sync.so.1 (0x00007faf8ae32000)
libxshmfence.so.1 => /usr/lib/libxshmfence.so.1 (0x00007faf8ac2f000)
libglapi.so.0 => /usr/lib/libglapi.so.0 (0x00007faf8aa00000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x00007faf8a7ec000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x00007faf8a5e9000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x00007faf8a3e3000)
libX11-xcb.so.1 => /usr/lib/libX11-xcb.so.1 (0x00007faf8a1e1000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007faf89fb8000)
libxcb-glx.so.0 => /usr/lib/libxcb-glx.so.0 (0x00007faf89d9c000)
libxcb-dri2.so.0 => /usr/lib/libxcb-dri2.so.0 (0x00007faf89b95000)
libXxf86vm.so.1 => /usr/lib/libXxf86vm.so.1 (0x00007faf8998f000)
libdrm.so.2 => /usr/lib/libdrm.so.2 (0x00007faf8977f000)
libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007faf89562000)
libdl.so.2 => /usr/lib/libdl.so.2 (0x00007faf8935e000)
libSM.so.6 => /usr/lib/libSM.so.6 (0x00007faf89156000)
libICE.so.6 => /usr/lib/libICE.so.6 (0x00007faf88f37000)
libvtkDICOMParser.so.1 => /usr/lib/libvtkDICOMParser.so.1 (0x00007faf88d1b000)
libvtkmetaio.so.1 => /usr/lib/libvtkmetaio.so.1 (0x00007faf88a7d000)
libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0x00007faf88813000)
libpng16.so.16 => /usr/lib/libpng16.so.16 (0x00007faf885dd000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007faf883c6000)
libtiff.so.5 => /usr/lib/libtiff.so.5 (0x00007faf88140000)
libvtkCommonMisc.so.1 => /usr/lib/libvtkCommonMisc.so.1 (0x00007faf87f26000)
/usr/lib64/ld-linux-x86-64.so.2 (0x00005618d2930000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x00007faf87d22000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007faf87b1c000)
libuuid.so.1 => /usr/lib/libuuid.so.1 (0x00007faf87915000)
liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007faf876ef000)
0revelation ~ % pacman -Q vtk6
vtk6 6.3.0-5
0revelation ~ % pacman -Q vtk
vtk 7.1.0-2
0revelation ~ % pacman -Q mayavi
mayavi 4.5.0-4
0revelation ~ % mayavi2
Traceback (most recent call last):
File "/usr/bin/mayavi2", line 11, in <module>
load_entry_point('mayavi==4.5.0', 'gui_scripts', 'mayavi2')()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 560, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2642, in load_entry_point
return ep.load()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2296, in load
return self.resolve()
File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2302, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/lib/python2.7/site-packages/mayavi/scripts/mayavi2.py", line 460, in <module>
raise ImportError(msg)
ImportError: /opt/vtk6/lib/libvtkRenderingOpenGL.so.1: undefined symbol: _ZN19vtkImageSliceMapper6UpdateEi
________________________________________________________________________________
Do you have vtk installed properly?
VTK (and build instructions) can be obtained from http://www.vtk.org

1revelation ~ %
Comment by Doug Newgard (Scimmia) - Tuesday, 31 January 2017, 16:28 GMT
Ah, yeah, you can see that that vtk6 library is linking to a number of vtk libraries in /usr/lib/. Anything in /etc/ld.so.conf.d/ or your environmental variables that would cause that? There should be a file at /etc/ld.so.conf.d/vtk6.conf that prevents this from happening.
Comment by Johannes E (JohannesE) - Tuesday, 31 January 2017, 16:39 GMT
I'm not sure, this is the list of files in /etc/ld.so.conf.d. However, I tried to move away the file /etc/ld.so.conf.d/ffmpeg2.8.conf, but the problem persists. I also made sure that LD_LIBRARY_PATH is empty...

revelation ~ % for i in /etc/ld.so.conf.d/*; do echo $i; cat $i; done
/etc/ld.so.conf.d/fakeroot.conf
/usr/lib/libfakeroot
/etc/ld.so.conf.d/ffmpeg2.8.conf
/usr/lib/
/usr/lib/ffmpeg2.8/
/etc/ld.so.conf.d/lib32-glibc.conf
/usr/lib32
/etc/ld.so.conf.d/octave.conf
/usr/lib/octave/4.2.0
/etc/ld.so.conf.d/openmpi.conf
/usr/lib/openmpi
/etc/ld.so.conf.d/vtk6.conf
/opt/vtk6/lib
Comment by Doug Newgard (Scimmia) - Wednesday, 01 February 2017, 15:17 GMT
While not exactly the same problem, I'm almost certain it has the same root cause as  FS#51611 . We can continue there.

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