Opened 3 years ago

Closed 3 years ago

#6893 closed defect (can't reproduce)

QOpenGLFramebufferObject errors as "alphafold predict" finishes

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.4rc202205140117 (2022-05-14 01:17:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x00004674 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00006750 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001c70 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003ad4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000035c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002200 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005458 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003b9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000652c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00006394 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001f78 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002ae8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\site-packages\ChimeraX_main.py", line 870 in init
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\site-packages\ChimeraX_main.py", line 1021 in 
  File "C:\Program Files\ChimeraX 1.4rc202205140117\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4rc202205140117\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  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> alphafold predict
> MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPLTLRQHRISATSSSEESSNKGQRQLTVS

Running AlphaFold prediction  

> alphafold predict
> MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPLTLRQHRISATSSSEESSNKGQRQLTVS

Running AlphaFold prediction  

> alphafold predict
> MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVTDRLASVETDMPLTLRQHRISATSSSEESSNKGQRQLTVS

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in C:\Users\zhuli/Downloads\ChimeraX\AlphaFold\prediction_1  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
QOpenGLFramebufferObject: An undefined error has occurred: 1285  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  

QOpenGLFramebufferObject: An undefined error has occurred: 1285  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  


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

Log:
UCSF ChimeraX version: 1.4rc202205140117 (2022-05-14)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 30.0.100.9955
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp65001
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 3420
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 8,316,026,880
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205140117
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.2.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → QOpenGLFramebufferObject errors as "alphafold predict" finishes

comment:2 by Tom Goddard, 3 years ago

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

These are all OpenGL errors from Qt 6.3.0 not from ChimeraX use of OpenGL.

One way I could imagine them happening is if Qt calls into ChimeraX when the AlphaFold job finishes and the result is downloaded from Google Colab, then ChimeraX might render the scene, and maybe Qt had its own OpenGL context active and ChimeraX switched to its OpenGL rendering context, and then when Qt got control back it assumed its OpenGL context was current and tried to do OpenGL operations using the ChimeraX context producing a stream of errors. A problem with this theory is that ChimeraX should only render its graphics from the Qt event loop, not in a callback. But maybe opening the AlphaFold PDB model causes a file history entry to be added with a thumbnail image that is captured when the open occurs, not sure.

We see lots of Windows crash reports where AlphaFold prediction was running. But we don't see these on Mac or Linux, so there may be a Windows-specific Qt bug here.

QOpenGLFramebufferObject: An undefined error has occurred: 1285  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  

QOpenGLFramebufferObject: An undefined error has occurred: 1285  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)
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