id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17626 ArtiaX: glTexImage3D: out of memory pavol.harar@… Utz Ermel "{{{ The following bug report has been submitted: Platform: Linux-6.11.0-25-generic-x86_64-with-glibc2.39 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Download 649.mrc (rsync -avzh --progress rsync://ftp.ebi.ac.uk/empiar/world_availability/11830/data/cryocare_bin4/649.mrc) Start ChimeraX Launch ArtiaX Open tomogram... Browse and choose the 649.mrc file Then this error appears. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 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 tomo_0649_2gb.mrc as #1.1.1, grid size 1024,1024,512, pixel 7.84, shown at level 324, 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, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ) ) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/updateloop.py"", line 84, in draw_new_frame view.draw(check_for_changes = False) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 259, in _draw_scene draw_opaque(r, opaque_drawings) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1554, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1567, in _draw_multiple d.draw(renderer, draw_pass) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 933, in draw drawing = self._update_view_axis(renderer) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 659, in _update_view_axis pd = self._update_3d_texture_planes(view_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 711, in _update_3d_texture_planes pd = self._texture_3d_planes() ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 721, in _texture_3d_planes pd = Texture3dPlanes(self) ^^^^^^^^^^^^^^^^^^^^^ File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1548, in __init__ self._fill_textures() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/map/image3d.py"", line 1665, in _fill_textures t.reload_texture(td, now=True) File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 3204, in reload_texture self.fill_opengl_texture() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 3214, in fill_opengl_texture self.initialize_texture(size, format, iformat, tdtype, ncomp, data) File ""/usr/lib/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 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 ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/OpenGL/platform/baseplatform.py"", line 415, in __call__ return self( *args, **named ) ^^^^^^^^^^^^^^^^^^^^^^ File ""src/errorchecker.pyx"", line 58, 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, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ), cArgs = ( GL_TEXTURE_3D, 0, GL_R32F, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ), cArguments = ( GL_TEXTURE_3D, 0, GL_R32F, 1024, 1024, 512, 0, GL_RED, GL_FLOAT, array([[[ 54.29878 , 105.903275 , 108.21507 , ..., 88.76678 , 50.011986 , -4.6252937 ], ..., ) ) Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1217, in __del__ self.delete() File ""/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/graphics/drawing.py"", line 1237, 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: Traceback (most recent call last): File ""/usr/lib/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: 4.6 (Core Profile) Mesa 24.2.8-1ubuntu1~24.04.1 OpenGL renderer: Mesa Intel(R) Graphics (MTL) OpenGL vendor: Intel Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: xcb XDG_SESSION_TYPE=wayland DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME GNOME_SETUP_DISPLAY=:1 DISPLAY=:0 WAYLAND_DISPLAY=wayland-0 Manufacturer: LENOVO Model: 21KCCTO1WW OS: Ubuntu 24.04 Architecture: 64bit ELF Virtual Machine: none CPU: 14 Intel(R) Core(TM) Ultra 7 155U Cache Size: 12288 KB Memory: total used free shared buff/cache available Mem: 30Gi 16Gi 7.0Gi 2.6Gi 10Gi 13Gi Swap: 8.0Gi 502Mi 7.5Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Meteor Lake-P [Intel Graphics] [8086:7d45] (rev 08) Subsystem: Lenovo Meteor Lake-P [Intel Graphics] [17aa:231e] Kernel driver in use: i915 Installed Packages: alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.7.0 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: 3.0.0 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-ArtiaX: 0.6.0 ChimeraX-Atomic: 1.58.8 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: 3.0.0 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: 1.9 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: 1.1.14 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: 2.1.6 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: 3.5.6 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 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 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 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 19.0.1 pycollada: 0.8 pydantic: 2.11.3 pydantic_core: 2.33.1 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 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 sniffio: 1.3.1 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 starfile: 0.5.12 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-inspection: 0.4.0 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 }}} " defect assigned normal Third Party Tom Goddard all ChimeraX