Opened 11 months ago

Closed 11 months ago

#16318 closed defect (can't reproduce)

Crash at startup

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411150349 (2024-11-15 03:49:13 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x0000000294117000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000029310b000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002920ff000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002910f3000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002900e7000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028f0db000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028e0cf000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028d0c3000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028c0b7000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028b0ab000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028a09f000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000289093000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000288087000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000028707b000 (most recent call first):
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1134 in read
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1278 in recv_into
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706 in readinto
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 279 in _read_status
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 318 in begin
  File "/private/var/folders/m6/06crnjsx3_n1hm_j9ns2fsd40000gn/T/AppTranslocation/9F8F2F88-FE49-4511-80F3-3D6A8DE350BD/d/ChimeraX-1.9-rc2024.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1378 in getresponse
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Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 44)


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    "path" : "\/private\/var\/folders\/*\/ChimeraX-1.9-rc2024.11.15.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
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    "path" : "\/private\/var\/folders\/*\/ChimeraX-1.9-rc2024.11.15.app\/Contents\/MacOS\/ChimeraX",
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    "path" : "\/usr\/lib\/dyld",
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    "arch" : "arm64e",
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},
  "vmSummary" : "ReadOnly portion of Libraries: Total=608K resident=0K(0%) swapped_out_or_unallocated=608K(100%)\nWritable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 4032K        4 \nCG image                            96K        4 \nColorSync                          608K       26 \nCoreAnimation                      224K       11 \nCoreGraphics                        32K        2 \nCoreUI image data                 2512K       15 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                           352.2M       77 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         816.0M        7         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        784K       49 \nStack                            431.2M       50 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      165.2M      128 \nVM_ALLOCATE (reserved)           224.0M        5         reserved VM address space (unallocated)\n__DATA                              16K        1 \n__DATA_CONST                        96K        1 \n__LINKEDIT                         224K        1 \n__TEXT                             384K        1 \ndyld private memory               1072K        3 \nmapped file                      485.6M      609 \nshared memory                     5328K       27 \n===========                     =======  ======= \nTOTAL                              2.9G     1045 \nTOTAL, minus reserved VM space     1.5G     1045 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000448
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    }
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  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
warning | QCoreApplication::postEvent: Unexpected null receiver  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9rc202411150349 (2024-11-15)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411150349 (2024-11-15)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 42 days 14:36

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411150349
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

Change History (2)

comment:1 by pett, 11 months ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash at startup

comment:2 by pett, 11 months ago

Resolution: → can't reproduce
Status: accepted → closed

Looks like it crashed in the Chromium process

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