faulthandler tracebacks with no ChimeraX crash

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
While testing the Open file dialog to see if faulthandler would save any tracebacks while using it, I got other event_loop tracebacks saved in the file that appear unrelated to the open file dialog.  I got 3 of these tracebacks in about 10 minutes.  They seemed spontaneous.  The first one I had left the computer for 5 miniutes and came back it was there, and the next two also arrived after leaving the computer for 5 minutes.

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3dwt format mmcif fromDatabase pdb

3dwt title:  
Structure of CabBCII-10 nanobody [more info...]  
  
Chain information for 3dwt #1  
---  
Chain | Description  
A B C D E F G H | cAbBCII-10  
  
Non-standard residues in 3dwt #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
3dwt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
5| author_and_software_defined_assembly  
6| author_and_software_defined_assembly  
7| author_and_software_defined_assembly  
8| author_and_software_defined_assembly  
  

> info path

system versioned config directory: C:\ProgramData\UCSF\ChimeraX\1.2  
system versioned data directory: C:\ProgramData\UCSF\ChimeraX\1.2  
system unversioned config directory: C:\ProgramData\UCSF\ChimeraX  
system unversioned data directory: C:\ProgramData\UCSF\ChimeraX  
user versioned cache directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache\1.2  
user versioned config directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2  
user versioned data directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2  
user versioned log directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2\Logs  
user versioned state directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\1.2  
user unversioned cache directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Cache  
user unversioned config directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX  
user unversioned data directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX  
user unversioned log directory:
C:\Users\goddard\AppData\Local\UCSF\ChimeraX\Logs  
user unversioned state directory: C:\Users\goddard\AppData\Local\UCSF\ChimeraX  

> open "C:/Users/goddard/Desktop/laptop manual.pdf"

Unrecognized file suffix '.pdf'  

> open D:/vrdemos/opioids-vr-2018/pdbs/carfentanil-muor.pdb

Summary of feedback from opening D:/vrdemos/opioids-vr-2018/pdbs/carfentanil-
muor.pdb  
---  
warnings | Ignored bad PDB record found on line 4  
HELIX 1 1 MET A 65 ARG A 95 1 Generated by MOE 31  
  
Ignored bad PDB record found on line 5  
HELIX 2 2 ALA A 102 THR A 118 1 Generated by MOE 17  
  
Ignored bad PDB record found on line 6  
HELIX 3 3 LEU A 121 LEU A 129 1 Generated by MOE 9  
  
Ignored bad PDB record found on line 7  
HELIX 4 4 GLY A 136 CYS A 170 1 Generated by MOE 35  
  
Ignored bad PDB record found on line 8  
HELIX 5 5 PRO A 172 PHE A 178 1 Generated by MOE 7  
  
22 messages similar to the above omitted  
  
Chain information for carfentanil-muor.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open C:/Users/goddard/Desktop/test2/emd_1080.map

Opened emd_1080.map as #3, grid size 100,100,100, pixel 2.7, shown at level
1.68, step 1, values float32  

> open C:/Users/goddard/Desktop/test3/emd_1080.map

Opened emd_1080.map as #4, grid size 100,100,100, pixel 2.7, shown at level
1.68, step 1, values float32  

> open E:/ForTom/r12c09f01p01-ch1sk1fk1fl1.tiff

Opened r12c09f01p01-ch1sk1fk1fl1.tiff as #5, grid size 1080,1080,1, pixel 1,
shown at step 1, values uint16  

> open E:/ForTom/r12c09f01p01-ch1sk3fk1fl1.tiff

Opened r12c09f01p01-ch1sk3fk1fl1.tiff as #6, grid size 1080,1080,1, pixel 1,
shown at step 1, values uint16  

> open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/casein-beta.pdb

Chain information for casein-beta.pdb #7  
---  
Chain | Description  
A | No description available  
  

QWindowsNativeFileDialogBase::shellItem : Unhandled scheme: "data"  

> open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/casein-beta3.pdb

Chain information for casein-beta3.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/goddard/Desktop/vrdemos/milk-oct2019/pdbtojson.py~

Unrecognized file suffix '.py~'  




OpenGL version: 3.3.0 NVIDIA 398.35
OpenGL renderer: GeForce GTX 1070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GS65 Stealth Thin 8RF
OS: Microsoft Windows 10 Pro (Build 19041)
Memory: 34,195,668,992
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    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: 2.0.1
    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: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
File attachment: crash_traceback.txt

crash_traceback.txt​

[goddard@…]

Added by email2trac

[Tom Goddard]

I attached the faulthandler output file.

[Tom Goddard]

The tracebacks say

"Windows fatal exception: code 0x800706ba"

and googling reports that error code is the following

"Error code 0x800706BA indicates that the remote procedure call (RPC) server is unavailable."

[Tom Goddard]

These faulthandler tracebacks were encountered testing the open file dialog for ticket #5348.

[Tom Goddard]

This is the only ChimeraX ticket that has the error code 0x800706ba in it. So it does not seem to be the root of the ChimeraX show_open_file_dialog crash reports. But it does show that fault handler can report "Windows fatal exception" and in fact ChimeraX has not crashed nor has any user-visible error occurred.

[Tom Goddard]

Apparently faulthandler appears not intended to guarantee that only tracebacks resulting in crashes are reported. So we will just have to keep this in mind when analyzing ChimeraX crash reports on Windows that only the final traceback is likely to be the cause of the crash.