Crash in garbage collection when closing a tool

[cchamble@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.3.dev202109160803 (2021-09-16 08:03:16 UTC)
Description
Last time you used ChimeraX it crashed.
I was trying to select a residue, but I forgot the proper way. I was trying to right click, double click, shift click, all sorts of stuff.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000023e8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000016b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001d3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000230c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002138 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002314 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001f14 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002244 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x00001a14 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\site-packages\chimerax\ui\gui.py", line 359 in _cleanup
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\site-packages\chimerax\ui\gui.py", line 396 in cb
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\site-packages\ChimeraX_main.py", line 880 in init
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\site-packages\ChimeraX_main.py", line 1029 in 
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3.dev202109160803\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3.dev202109160803 (2021-09-16)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Chris\Downloads\6zgg.pdb format pdb

6zgg.pdb title:  
Furin cleaved spike protein of sars-cov-2 with one RBD erect [more info...]  
  
Chain information for 6zgg.pdb #1  
---  
Chain | Description | UniProt  
A | spike glycoprotein | SPIKE_SARS2  
B | spike glycoprotein | SPIKE_SARS2  
C | spike glycoprotein | SPIKE_SARS2  
  

> select sel : show atoms

> hide atoms

> show cartoons

> hide cartoons

> show cartoons

> lighting full

> ui tool show "Selection Inspector"


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

Log:
UCSF ChimeraX version: 1.3.dev202109160803 (2021-09-16)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 24.20.100.6286
OpenGL renderer: Intel(R) HD Graphics 520
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Latitude 3580
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 8,449,589,248
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-6006U CPU @ 2.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109160803
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.12.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distlib: 0.3.2
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.1
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
File attachment: 6zgg.pdb

6zgg.pdb​

[cchamble@…]

Added by email2trac

[Tom Goddard]

The stack trace shows some ChimeraX tool panel had just been closed and our code called Python garbage collection (line 359 in gui.py) and crashed. We have observed numerous crashes in Python garbage collection and do not have a clue what is causing these.

This report has 8 additional Python threads running using the Python multiprocessing module. It is unclear what created those additional threads and possibly they are connected to the crash.

[Tom Goddard]

I don't think we have any info in this bug report that can help us find the cause.

[Tom Goddard]

There are actually some interesting clues here. The log shows very little was done before this crash, opening 6zgg, selecting, showing and hiding atoms, hiding and showing cartoons, full lighting, and showing Selection inspector. Then in crashed. That is pretty small set of actions for running into the garbage collection crash which we believe may be caused by incorrect reference counting of some Python object.

Still not enough info to be able to debug it.

[pett]

Also don't understand how "select sel : show atoms" can show in the log as a command without an error message.