glue

glue copied to clipboard

While i tried the 3d volume rendering for a 3d cube fits data glue crashed with:

anaconda3/lib/python3.6/site-packages/glue/core/component.py:79: FutureWarning:

Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.

Segmentation fault (core dumped)

The 2d slices work as expected.

@Mixpap - what kind of 3D data are you using, and how large is it?

Its a 627x497x61 fits file (82.4 Mb)

I thought i had old version issues (i am using conda) so i downloaded everything (matplotlib, numpy etc) from conda forge. Now, glue doesn't even start giving

Segmentation fault (core dumped)

Part of the conda list:

#
# Name                    Version                   Build  Channel
astropy                   3.1.1            py36h7b6447c_0 
glue-core                 0.14.2                   py36_0    glueviz
glue-vispy-viewers        0.11                       py_0    glueviz
glueviz                   0.14.0                        0    astropy
numpy                     1.15.4           py36h7e9f1db_0  
pyqt                      5.6.0                    py36_2 
qt                        5.6.2               h974d657_12  
wheel                     0.32.3                   py36_0  

@Mixpap - sorry for the delay, if you are still running into the segmentation fault, could you try starting up glue using:

python -X faulthandler -m glue.main

as this will provide more information about the cause of the crash.

Hi @astrofrog,

>>> python -X faulthandler -m glue.main
~/anaconda3/lib/python3.6/runpy.py:125: RuntimeWarning: 'glue.main' found in sys.modules after import of package 'glue', but prior to execution of 'glue.main'; this may result in unpredictable behaviour
  warn(RuntimeWarning(msg))
Fatal Python error: Segmentation fault

Current thread 0x00007f5139800740 (most recent call first):
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 922 in create_module
  File "<frozen importlib._bootstrap>", line 571 in module_from_spec
  File "<frozen importlib._bootstrap>", line 658 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 955 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 971 in _find_and_load
  File "/home/astromix/anaconda3/lib/python3.6/site-packages/qtpy/__init__.py", line 127 in <module>
  File "<frozen importlib._bootstrap>", line 219 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 678 in exec_module
  File "<frozen importlib._bootstrap>", line 665 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 955 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 971 in _find_and_load
  File "/home/astromix/anaconda3/lib/python3.6/site-packages/glue/main.py", line 141 in start_glue
  File "/home/astromix/anaconda3/lib/python3.6/site-packages/glue/main.py", line 255 in main
  File "/home/astromix/anaconda3/lib/python3.6/site-packages/glue/main.py", line 354 in <module>
  File "/home/astromix/anaconda3/lib/python3.6/runpy.py", line 85 in _run_code
  File "/home/astromix/anaconda3/lib/python3.6/runpy.py", line 193 in _run_module_as_main
Segmentation fault (core dumped)

Hi,

I've also encountered this problem. I started Glue using python -X faulthandler -m glue.main It returned: `Fatal Python error: Segmentation fault

Current thread 0x00007f854ba82740 (most recent call first): File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue_vispy_viewers/extern/vispy/app/backends/_qt.py", line 459 in event File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue_vispy_viewers/common/vispy_data_viewer.py", line 188 in show File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1014 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 216 in do File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/command.py", line 126 in do File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/core/application_base.py", line 261 in do File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1008 in choose_new_data_viewer File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/mdi_area.py", line 56 in new_layer File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/mdi_area.py", line 65 in dropEvent File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/app/qt/application.py", line 1210 in start File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 199 in start_glue File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 261 in main File "/ubuntuhome/thistle6-sz57/anaconda3/lib/python3.7/site-packages/glue/main.py", line 360 in 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) `

Any idea?

I am also encountering the segfault when trying to use the 3D plugins. Would appreciate help with this ticket.