Opened 10 months ago

Last modified 10 months ago

#16454 assigned defect

Crash in event loop

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-48-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.9.dev202409120541 (2024-09-12 05:41:30 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000078f756a00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f757400640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f757e00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/selectors.py", line 415 in select
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f760c00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f761600640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f762000640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f762a00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f763400640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f763e00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76cc00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76d600640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76e000640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76ea00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76f400640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f76fe00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f778c00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f779600640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f77a000640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f77aa00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f77b400640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f77be00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f784c00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f785600640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f786000640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f786a00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f787400640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f787e00640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000078f791600640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x000078f8353e4b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

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.surface._surface, chimerax.pdb_lib._load_libs, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 43)
===== Log before crash start =====
Startup Messages  
---  
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: 1.9.dev202409120541 (2024-09-12)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QObject::killTimer: Timers cannot be stopped from another thread  

QObject::~QObject: Timers cannot be stopped from another thread  

QMutex: destroying locked mutex  


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9.dev202409120541 (2024-09-12)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: AMD Radeon RX 6500 (navi24, LLVM 15.0.7, DRM 3.57, 6.8.0-48-generic)
OpenGL vendor: AMD

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: OptiPlex Tower Plus 7010
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 13th Gen Intel(R) Core(TM) i7-13700
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        10Gi       1.6Gi       1.2Gi        50Gi        49Gi
	Swap:          2.0Gi       699Mi       1.3Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:a780] (rev 04)	
	Subsystem: Dell Device [1028:0bcc]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    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: 2.14
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.6
    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
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.3.4
    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: 1.9.dev202409120541
    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-DeepMutationalScan: 1.0
    ChimeraX-Dicom: 1.2.5
    ChimeraX-DiffPlot: 1.0
    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-Foldseek: 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-Label: 1.1.11
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 1.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3
    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: 3.2.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.13
    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-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: 1.40.1
    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: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.5
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.53.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.8
    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: 2.1.5
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.8
    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: 4.3.2
    prompt_toolkit: 3.0.47
    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
    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: 3.1.4
    pyproject_hooks: 1.1.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.2
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.2
    PyQt6-WebEngineSubwheel-Qt6: 6.7.2
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.1
    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: 2024.1
    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 (5)

comment:1 by pett, 10 months ago

Cc: chimera-programmers added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by pett, 10 months ago

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

Not sure how a timer could be being stopped from another thread at startup

comment:3 by Tom Goddard, 10 months ago

It would be super useful to know how any Qt is being executed in a separate thread. I guess it is in the multiprocessing/_handle_results call, and it is happening at startup. Perhaps it is related to the check for updates code? Any use of Qt in another thread is likely to cause a crash, and I believe we have seen a number of those crash at startup reports.

comment:4 by Tom Goddard, 10 months ago

Resolution: can't reproduce
Status: closed → reopened

comment:5 by Tom Goddard, 10 months ago

Owner: changed from pett to Greg Couch
Status: reopened → assigned

Greg, can you check that ChimeraX check for updates which I believe is asynchronous does not attempt any Qt (like saying an update is available) in another thread? We have dozens of mysterious crashes on startup in the past year and this report clearly says it was trying to use Qt from a different thread and the user was just starting ChimeraX.

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