"Access violation" getting StructureDatas._graphics_changeds

[chimerax-bug-report@…]

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
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Current thread 0x00003cc8 (most recent call first):
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\numpy\core\_internal.py", line 282 in data_as
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\molc.py", line 320 in pointer
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\molc.py", line 195 in get_prop
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\atomic\structure.py", line 1577 in _update_graphics_if_needed
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 130 in invoke
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 213 in _activate
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 182 in activate
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\triggerset.py", line 350 in activate_trigger
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\graphics\view.py", line 269 in check_for_drawing_change
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 65 in draw_new_frame
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 138 in _redraw_timer_callback
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Users\ekatpe\Programs\ChimeraX 1.2.5\bin\lib\runpy.py", line 194 in _run_module_as_main


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
> C:\Users\ekatpe\ownCloud\Experiments\Proteomics\Structure_HBV\EMD_maps\emd_0271.map
> format ccp4

Opened emd_0271.map as #1, grid size 512,512,512, pixel 1.04, shown at level
5.95, step 2, values float32  




OpenGL version: 3.3.0 NVIDIA 452.69
OpenGL renderer: Quadro P1000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP ZBook Studio G5
OS: Microsoft Windows 10 Education (Build 19042)
Memory: 16,981,991,424
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
OSLanguage: en-US
Locale: ('en_150', '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-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
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    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
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    Jinja2: 2.11.2
    jupyter-client: 6.1.7
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    numpydoc: 1.1.0
    openvr: 1.14.1501
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    PyOpenGL-accelerate: 3.1.5
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    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
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    WMI: 1.5.1

[Tom Goddard]

It was trying to call our C++ structure_graphics_change() function but crashed before it called it while creating the numpy array of int32 return values that is passed as an argument. It crashed in numpy in the second line of these two

cty = numpy_type_to_ctype[a.dtype.type]
p = a.ctypes.data_as(ctypes.POINTER(cty))

That code was in the numpy ctypes.data_as() method executing the second of these two lines

ptr = self._ctypes.cast(self._data, obj)
ptr._arr = self._arr

Here self is a _ctypes Python class instance. ptr is a c_void_p.value. Seem like this would only crash if the numpy object was used after being deallocated. But this numpy array was just created for holding the returned _graphics_change values. It does not seem possible that it could be deallocated.

[Tom Goddard]

Same crash is #4530 in ChimeraX 1.1 where it was simply opening an mmCIF model and autostyling it. The current report it was simply redrawing the graphics. These seem to be the only two reported crashes in numpy data_as().

Don't have enough clues to debug it.

[Tom Goddard]

Very likely a crash in Python garbage collection, see #5115 on Mac where C++ stack shows this.