glTexImage3D: out of memory after "artiax view xy"

[huirene@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-553.82.1.el8_10.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
ArtiaX open tomogram failed

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
Opened 240426_TS_072_10.00Apx_lp60.mrc as #1.1.1, grid size 1242,1242,606,
pixel 10, shown at level 2.31, step 1, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
)  
)  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84,
in draw_new_frame  
view.draw(check_for_changes = False)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188, in
draw  
self._draw_scene(camera, drawings)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259, in
_draw_scene  
draw_opaque(r, opaque_drawings)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line
1559, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line
1572, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 936, in
draw  
drawing = self._update_view_axis(renderer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 662, in
_update_view_axis  
pd = self._update_3d_texture_planes(view_dir)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 714, in
_update_3d_texture_planes  
pd = self._texture_3d_planes()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 724, in
_texture_3d_planes  
pd = Texture3dPlanes(self)  
^^^^^^^^^^^^^^^^^^^^^  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1551, in
__init__  
self._fill_textures()  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/map/image3d.py", line 1668, in
_fill_textures  
t.reload_texture(td, now=True)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3210,
in reload_texture  
self.fill_opengl_texture()  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3220,
in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3100,
in initialize_texture  
GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2],  
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/OpenGL/platform/baseplatform.py", line
487, in __call__  
return self(*args, **named)  
^^^^^^^^^^^^^^^^^^^^  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1242,  
1242,  
606,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[-4.36224528e-02, 4.00447287e-04, 2.31746033e-01, ...,  
1.51411295e-01, 1.68809578e-01, 5.750086...,  
)  
)  
  
Exception ignored in: <function Drawing.__del__ at 0x7f0d34a1bba0>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line
1222, in __del__  
self.delete()  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line
1242, in delete  
raise RuntimeError("Don't have opengl context needed to delete texture from
drawing '%s' because drawing was never drawn" % self.name)  
RuntimeError: Don't have opengl context needed to delete texture from drawing
'Image3D 3d texture planes' because drawing was never drawn  
Exception ignored in: <function Texture.__del__ at 0x7f0d3039b380>  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.10.1_c8/libexec/UCSF-
ChimeraX/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 3165,
in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  




OpenGL version: 4.5 (Core Profile) Mesa 23.1.4
OpenGL renderer: llvmpipe (LLVM 17.0.6, 256 bits)
OpenGL vendor: Mesa

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb

XDG_SESSION_TYPE=
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:10.0
Manufacturer: ASUSTeK COMPUTER INC.
Model: ESC4000-E11
OS: Red Hat Enterprise Linux 8.10
Architecture: 64bit ELF
Virtual Machine: none
CPU: 64 INTEL(R) XEON(R) GOLD 6526Y
Cache Size: 38400 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi        15Gi       141Gi       420Mi        93Gi       232Gi
	Swap:         4.0Gi       342Mi       3.7Gi

Graphics:
	0000:02:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52)	
	DeviceName: ASPEED 2600	
	Subsystem: ASUSTeK Computer Inc. Device [1043:87ed]

Installed Packages:
    alabaster: 1.0.0
    annotated-types: 0.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.6.0
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 2.5.1
    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: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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: 1.19.1
    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: 2.5.2
    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: 1.45.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    geomdl: 5.4.0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    pandas: 2.3.3
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pyarrow: 22.0.0
    pycollada: 0.8
    pydantic: 2.12.3
    pydantic_core: 2.41.4
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    starfile: 0.5.13
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Reported by Irene Hu

Apparent duplicate of #18150

[Tom Goddard]

ArtiaX is trying to display your tomogram of size 1242,1242,606 at full resolution and the error says there is not enough graphics memory. ArtiaX should check for this error and probably show a subsampled map when this happens.