Glue crashed when 3D volume rendering

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Suinan Zhang

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Oct 14, 2020, 10:21:43 AM10/14/20
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Hello,

I'm trying to use Glue to visualize my N2H+ data cube (exported from CASA, stokes axis dropped). The fits file is ~52 MB. I tried to open the data cube in "3D volume rendering" mode, but Glue crashed and an error reported in the terminal "Segmentation fault (core dumped)".

I found an open issue on Github reporting this problem (https://github.com/glue-viz/glue/issues/1958). It suggested to start Glue using "python -X faulthandler -m glue.main" to look at the cause of the crash. I tried and it returned:

Fatal Python error: Segmentation fault

Current thread 0x00007efcf36a1740 (most recent call first):
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 752 in _init_specific
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/vispy/app/backends/_qt.py", line 317 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/vispy/app/canvas.py", line 222 in create_native
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/vispy/app/canvas.py", line 205 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/vispy/scene/canvas.py", line 137 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue_vispy_viewers/common/vispy_widget.py", line 26 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue_vispy_viewers/common/vispy_data_viewer.py", line 45 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue_vispy_viewers/volume/volume_viewer.py", line 39 in __init__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/viewers/common/qt/data_viewer.py", line 27 in __call__
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/application_base.py", line 82 in new_data_viewer
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1010 in new_data_viewer
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/utils/matplotlib.py", line 170 in wrapper
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/command.py", line 215 in do
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/command.py", line 125 in do
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/application_base.py", line 258 in do
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1006 in choose_new_data_viewer
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/mdi_area.py", line 54 in new_layer
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/mdi_area.py", line 63 in dropEvent
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1222 in start
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 197 in start_glue
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 259 in main
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 362 in <module>
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/runpy.py", line 85 in _run_code
  File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/runpy.py", line 193 in _run_module_as_main
Segmentation fault (core dumped)

I have played with 2D data in Glue and it went well.

I'm working on a linux machine. I've tried increasing all the soft limits to hard limits using the command "limit". But this didn't solve the problem.

Does anyone have ideas about this?

Thanks,

Suinan
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