id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16803 Graphics crash, macOS 13.7.1, M2 GPU chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.7.1-arm64-arm-64bit ChimeraX Version: 1.9.dev202405150316 (2024-05-15 03:16:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000001fbabe100 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2744 in update_buffer_data File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1912 in update_buffers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1924 in activate_bindings File 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830.7M 140 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 864.3M 762 \ndyld private memory 272K 2 \nmapped file 216.7M 59 \nshared memory 3248K 28 \n=========== ======= ======= \nTOTAL 24.8G 4365 \nTOTAL, minus reserved VM space 23.8G 4365 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6f44e54e3c98b65b5755faef888ab08d14984de9"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.9.dev202405150316 (2024-05-15) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/danny/Baker lab/Tomo Data/241127-Pal- > KO/TS02-V3/reolmts02_rec.mrc"" Opened reolmts02_rec.mrc as #1, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 > vop scale #1 shift -1 factor -1 Opened reolmts02_rec.mrc scaled as #2, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 region 0,0,0,2045,2879,120 step 4 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 change image level -172.9,0 level 348.9,0.8 level 2009,1 > volume #2 level 260.6 > volume #2 level 226.3 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > ui tool show ""Map Eraser"" > ui mousemode right ""translate selected models"" > select add #3 1 model selected > view matrix models #3,1,0,0,14741,0,1,0,52511,0,0,1,1120.8 > view matrix models #3,1,0,0,17050,0,1,0,54167,0,0,1,1152.4 > volume erase #2 center 17050,54167,1152.4 radius 9204.9 Opened reolmts02_rec.mrc scaled copy as #4, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 > show #!2 models > hide #!4 models > show #!4 models ===== Log before crash end ===== Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.9.dev202405150316 (2024-05-15) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/danny/Baker lab/Tomo Data/241127-Pal- > KO/TS02-V3/reolmts02_rec.mrc"" Opened reolmts02_rec.mrc as #1, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 region 0,0,0,2045,2879,120 step 4 [Repeated 1 time(s)] > vop scale #1 shift -1 factor -1 Opened reolmts02_rec.mrc scaled as #2, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 > show #!1 models > hide #!1 models > close #1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #2 step 8 > volume #2 level 143.6 > volume #2 level 186.4 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > save ""/Users/danny/Baker lab/Tomo Data/241127-Pal-KO/TS02-V3/reoLMTS02-Pal- > KO.cxs"" > ui mousemode right ""translate selected models"" > ui tool show ""Map Eraser"" > select add #1 1 model selected > volume erase #2 center 17156,55342,-184.49 radius 14350 Opened reolmts02_rec.mrc scaled copy as #3, grid size 2046,2880,121, pixel 26.2,26.2,26.2, shown at step 1, values int16 OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16T000JCB/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 11881.41.5 OS Loader Version: 8422.141.2.700.1 Software: System Software Overview: System Version: macOS 13.7.1 (22H221) Kernel Version: Darwin 22.6.0 Time since boot: 72 days, 7 hours, 18 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal VA2732 100Hz: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiobotocore: 2.19.0 aiohappyeyeballs: 2.4.4 aiohttp: 3.11.11 aioitertools: 0.12.0 aiosignal: 1.3.2 alabaster: 0.7.16 annotated-types: 0.7.0 anyio: 4.8.0 appdirs: 1.4.4 appnope: 0.1.4 asciitree: 0.3.3 asttokens: 2.4.1 asyncssh: 2.19.0 attrs: 25.1.0 Babel: 2.15.0 backoff: 2.2.1 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 boto3: 1.36.3 botocore: 1.36.3 build: 1.2.1 certifi: 2023.11.17 cffi: 1.17.1 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.5.0 ChimeraX-Atomic: 1.58 ChimeraX-AtomicLibrary: 14.0.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 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: 2.2.4 ChimeraX-ColorActions: 1.0.4 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-copick: 0.5.0 ChimeraX-Core: 1.9.dev202405150316 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.1 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OME-Zarr: 0.5.4 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 1.3.5 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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 click: 8.1.8 cloudpickle: 3.1.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 copick: 0.8.1 cryoet-data-portal: 4.0.0 cryptography: 44.0.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 dask: 2025.1.0 debugpy: 1.8.1 decorator: 5.1.1 deepmerge: 2.0 Deprecated: 1.2.18 distinctipy: 1.3.4 distributed: 2025.1.0 docutils: 0.20.1 executing: 2.0.1 fasteners: 0.19 filelock: 3.13.4 fonttools: 4.51.0 frozenlist: 1.5.0 fsspec: 2025.2.0 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.7.0 gql: 3.5.0 grako: 3.16.5 graphql-core: 3.2.6 h5py: 3.11.0 hatchling: 1.27.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imageio: 2.37.0 imagesize: 1.4.1 importlib-metadata: 8.6.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jmespath: 1.0.1 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 lazy-loader: 0.4 line-profiler: 4.1.2 locket: 1.0.0 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 multidict: 6.1.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numcodecs: 0.15.0 numexpr: 2.10.0 numpy: 1.26.4 ome-zarr: 0.10.3 openvr: 1.26.701 packaging: 24.2 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 partd: 1.4.2 pathspec: 0.12.1 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 pluggy: 1.5.0 prompt-toolkit: 3.0.43 propcache: 0.2.1 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pyarrow: 19.0.0 pycollada: 0.8 pycparser: 2.22 pydantic: 2.10.6 pydantic-core: 2.27.2 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 pyspnego: 0.11.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 PyYAML: 6.0.2 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 requests-toolbelt: 1.0.0 s3fs: 2025.2.0 s3transfer: 0.11.2 scikit-image: 0.25.1 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 smbprotocol: 1.15.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 sshfs: 2024.9.0 stack-data: 0.6.3 starfile: 0.5.11 strcase: 1.0.0 superqt: 0.6.3 tables: 3.8.0 tblib: 3.0.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 toolz: 1.0.0 tornado: 6.4 tqdm: 4.67.1 traitlets: 5.14.2 trimesh: 4.6.1 trove-classifiers: 2025.1.15.22 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 wrapt: 1.17.2 yarl: 1.18.3 zarr: 2.18.4 zict: 3.0.0 zipp: 3.21.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX