Logger collapse similar causes thread related crashes

[Tom Goddard]

Andreas Prlic's image capture script was causing numerous thread related crashes because of a thread safety problem in Logger collapse similar. The crashes occur in many places varying each run, but the following traceback points to the lines in core/logger.py

self._sim_timer = Timer(0.5, self._sim_timer_cb)
self._sim_timer.start()

perhaps because the callback function is called in a different thread.

I've disabled this code by making Logger.collapse_similar.setter return without enabling collapse mode until this bug can be fixed.

Fatal Python error: Segmentation fault

Thread 0x00000001303cc000 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 297 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 559 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 1187 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 923 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 891 in _bootstrap

Current thread 0x00000001243cb000 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/graphics/opengl.py", line 1388 in delete_buffer
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/graphics/opengl.py", line 1381 in del
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 345 in notify
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 362 in notify_all
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 520 in set
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 1190 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 923 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 891 in _bootstrap

Thread 0x000000012773f000 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 297 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 556 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 1187 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 923 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 891 in _bootstrap

Thread 0x00007fff728e1300 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 307 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 556 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 858 in start
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/logger.py", line 370 in _log
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/logger.py", line 311 in warning
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/pdb.py", line 24 in open_pdb
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versionsp/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 513 in open_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 554 in open_multiple_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 278 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 65 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1823 in execute
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/run.py", line 22 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/scripting.py", line 110 in open_command_script
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 511 in open_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/io.py", line 554 in open_multiple_data
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/models.py", line 281 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/open.py", line 65 in open
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1823 in execute
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 121 in on_enter
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 61 in forwarded_keystroke
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/ui/gui.py", line 106 in forward_keystroke
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/wx/core.py", line 1893 in MainLoop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/ui/gui.py", line 98 in event_loop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/ChimeraX_main.py", line 414 in init
File "main.py", line 3 in <module>

Segmentation fault: 11

[Tom Goddard]

Script from Andreas Prlic that demonstrates crash.

[Tom Goddard]

PDB file from Andreas Prlic used by script that causes crash.

[pett]

I believe this problem is fixed because log-collapsing no longer uses timers.