Opened 3 years ago
Closed 3 years ago
#6893 closed defect (can't reproduce)
QOpenGLFramebufferObject errors as "alphafold predict" finishes
Reported by: | 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 , 3 years ago
Component: | Unassigned → Structure Prediction |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → QOpenGLFramebufferObject errors as "alphafold predict" finishes |
comment:2 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | assigned → closed |
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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.