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conda-forge / vtk-feedstock

A conda-smithy repository for vtk.
BSD 3-Clause "New" or "Revised" License
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segfault #13

Closed dfroger closed 7 years ago

dfroger commented 7 years ago

VTK is installed with:

conda create -n vtk -c conda-forge vtk=7.0.0 python=3.5
source activate vtk

This segfaults:

import vtk
obj = vtk.vtkRenderingLICPython.vtkLineIntegralConvolution2D()
obj.GetCommunicator()
dfroger commented 7 years ago

backtrace in GDB:

#0  0x00007ffff55d17cb in vtkPythonUtil::FindNearestBaseClass(vtkObjectBase*) ()
   from /data/miniconda3/envs/vtk/lib/python3.5/site-packages/vtk/../../../libvtkWrappingPython35Core-7.0.so.1
#1  0x00007ffff55d368d in vtkPythonUtil::GetObjectFromPointer(vtkObjectBase*) ()
   from /data/miniconda3/envs/vtk/lib/python3.5/site-packages/vtk/../../../libvtkWrappingPython35Core-7.0.so.1
#2  0x00007fffc7cc9d1f in PyvtkLineIntegralConvolution2D_GetCommunicator(_object*, _object*) ()
   from /data/miniconda3/envs/vtk/lib/python3.5/site-packages/vtk/../../../libvtkRenderingLICPython35D-7.0.so.1
#3  0x00007ffff7979609 in PyCFunction_Call (func=func@entry=0x7fffec0fe288, args=args@entry=0x7ffff7fb6048, kwds=kwds@entry=0x0) at Objects/methodobject.c:109
#4  0x00007ffff7a12773 in call_function (oparg=<optimized out>, pp_stack=0x7fffffffdd20) at Python/ceval.c:4705
#5  PyEval_EvalFrameEx (f=f@entry=0x6c9828, throwflag=throwflag@entry=0) at Python/ceval.c:3236
#6  0x00007ffff7a14af6 in _PyEval_EvalCodeWithName (_co=_co@entry=0x7ffff6907c00, globals=globals@entry=0x7ffff6996448, locals=locals@entry=0x7ffff6996448, 
    args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0, kwdefs=kwdefs@entry=0x0, 
    closure=closure@entry=0x0, name=name@entry=0x0, qualname=qualname@entry=0x0) at Python/ceval.c:4018
#7  0x00007ffff7a14be8 in PyEval_EvalCodeEx (_co=_co@entry=0x7ffff6907c00, globals=globals@entry=0x7ffff6996448, locals=locals@entry=0x7ffff6996448, 
    args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0, kwdefs=kwdefs@entry=0x0, 
    closure=closure@entry=0x0) at Python/ceval.c:4039
#8  0x00007ffff7a14c2b in PyEval_EvalCode (co=co@entry=0x7ffff6907c00, globals=globals@entry=0x7ffff6996448, locals=locals@entry=0x7ffff6996448) at Python/ceval.c:777
#9  0x00007ffff7a447f3 in run_mod (arena=0x7044b0, flags=0x7fffffffe030, locals=0x7ffff6996448, globals=0x7ffff6996448, filename=0x7ffff69511f0, mod=0x7353a0)
    at Python/pythonrun.c:976
#10 PyRun_InteractiveOneObject (fp=fp@entry=0x7ffff6d818a0 <_IO_2_1_stdin_>, filename=filename@entry=0x7ffff69511f0, flags=flags@entry=0x7fffffffe030)
    at Python/pythonrun.c:233
#11 0x00007ffff7a44abe in PyRun_InteractiveLoopFlags (fp=fp@entry=0x7ffff6d818a0 <_IO_2_1_stdin_>, filename_str=filename_str@entry=0x7ffff7ae1d56 "<stdin>", 
    flags=flags@entry=0x7fffffffe030) at Python/pythonrun.c:112
#12 0x00007ffff7a4527e in PyRun_AnyFileExFlags (fp=fp@entry=0x7ffff6d818a0 <_IO_2_1_stdin_>, filename=0x7ffff7ae1d56 "<stdin>", closeit=closeit@entry=0, 
    flags=flags@entry=0x7fffffffe030) at Python/pythonrun.c:74
#13 0x00007ffff7a61d96 in run_file (p_cf=0x7fffffffe030, filename=0x0, fp=0x7ffff6d818a0 <_IO_2_1_stdin_>) at Modules/main.c:318
#14 Py_Main (argc=argc@entry=1, argv=argv@entry=0x602010) at Modules/main.c:768
#15 0x0000000000400a64 in main (argc=1, argv=<optimized out>) at ./Programs/python.c:65
dfroger commented 7 years ago

Seems to be this VTK bug, fixed in this pull request merged here

dfroger commented 7 years ago

Note: the segfault occurs when I try to build mayavi using this recipe, more details here

dfroger commented 7 years ago

I tried this patch, but still segfaults. I give up.

dfroger commented 7 years ago

VTK 7.1.0 has been released, I'm going to see if it fix the segfault.

ivoflipse commented 7 years ago

If so, feel free to submit a PR against the feedstock to update the recipe. It might have problems with the build times again, but it would be good to have available

dfroger commented 7 years ago

Argh, it still segfaults... I will PR to update the recipe.

dfroger commented 7 years ago

I think that's a VTK bug, not related to the conda packaging. I'll report it to VTK devs.

Korijn commented 7 years ago

Is this resolved with 7.1.0?

dfroger commented 7 years ago

No, it isn't resolve in 7.1.0.

I opened this VTK issue. Hope it will be fixed soon!

Korijn commented 7 years ago

Ok, thanks for leaving a trail for others to follow. :+1:

dfroger commented 7 years ago

I created this merge request in VTK to fix the segmentation fault.

If the merge request is accepted by VTK developpers, we may want to backport the patch here, so that we will have a working conda package for mayavi.

dfroger commented 7 years ago

Created PR #15 to fix this issue.