glTexImage2D: out of memory while drawing silhouettes /selection outline

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9rc202411272016 (2024-11-27 20:16:15 UTC)
Description
Frozen, won't respond


Log:
Startup Messages  
---  
warning | Unknown Vendor ID: "0x4d4f4351"  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411272016 (2024-11-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\\\Users\\\megan\\\OneDrive\\\Desktop\\\Hexameric_YME1L.pdb

Chain information for Hexameric_YME1L.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
  

> open "C:/Users/megan/Downloads/fold_2024_12_18_16_17
> (7)/fold_2024_12_18_16_17_model_0.cif"

Chain information for fold_2024_12_18_16_17_model_0.cif #2  
---  
Chain | Description  
A B | .  
  
Computing secondary structure  

> open "C:/Users/megan/Downloads/fold_2024_12_18_16_17
> (8)/fold_2024_12_18_16_17_model_0.cif"

Chain information for fold_2024_12_18_16_17_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> mmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Hexameric_YME1L.pdb, chain A (#1) with
fold_2024_12_18_16_17_model_0.cif, chain A (#2), sequence alignment score =
2196.5  
RMSD between 115 pruned atom pairs is 0.428 angstroms; (across all 442 pairs:
18.214)  
  

> mmaker #3 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Hexameric_YME1L.pdb, chain A (#1) with
fold_2024_12_18_16_17_model_0.cif, chain A (#3), sequence alignment score =
2212.7  
RMSD between 430 pruned atom pairs is 0.905 angstroms; (across all 442 pairs:
1.092)  
  

> select #1

36530 atoms, 37245 bonds, 4640 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> ~select

Nothing selected  

> select #1

36530 atoms, 37245 bonds, 4640 residues, 1 model selected  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\std_commands\select.py", line 62, in select  
report_selection(session)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\std_commands\select.py", line 192, in report_selection  
session.logger.status(', '.join(lines) + ' selected', log = True)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\core\logger.py", line 522, in status  
StatusLogger.status(self, msg, **kw)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\core\logger.py", line 220, in status  
if l.status(msg, color, secondary) and getattr(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\ui\gui.py", line 1048, in status  
sbar.status(msg, color, secondary)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 155, in status  
self._draw_text(msg, color, secondary)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 165, in _draw_text  
draw_overlays(dlist, self._renderer)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1608, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 780, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 826, in _draw_geometry  
t.bind_texture()  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3177, in bind_texture  
self.fill_opengl_texture()  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3214, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "C:\Program Files\ChimeraX 1.9rc202411272016\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3097, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
585,  
33,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
)  
)  
  
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 24.3.0-devel (git-370ac36d5d)
OpenGL renderer: D3D12 (Qualcomm(R) Adreno(TM) X1-85 GPU)
OpenGL vendor: Microsoft Corporation

Python: 3.11.4
Locale: en_CA.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Microsoft Surface Laptop, 7th Edition
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,761,454,592
MaxProcessMemory: 137,438,953,344
CPU: 12 Snapdragon(R) X 12-core X1E80100 @ 3.40 GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411272016
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.4
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Tom Goddard]

Mesa 24.3.0 ran out of memory allocating about 15 Kbytes for a texture. Not sure what could cause that, possibly a driver bug. The 24.3.0 release notes (Nov 21, 2024) say you shouldn't use that version if you are concerned with stability.