Opened 5 weeks ago

Closed 5 weeks ago

#19014 closed defect (nonchimerax)

Crash gathering Linux info for bug reporter

Reported by: neha@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.14.0-33-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11.dev202510012017 (2025-10-01 20:17:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000782f589fd6c0 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/socket.py", line 974 in getaddrinfo
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/socket.py", line 839 in create_connection
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 962 in connect
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 1468 in connect
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 996 in send
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 1058 in _send_output
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 1298 in endheaders
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 1349 in _send_request
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/http/client.py", line 1303 in request
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 1348 in do_open
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 1391 in https_open
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 496 in _call_chain
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 536 in _open
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 519 in open
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/urllib/request.py", line 216 in urlopen
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 516 in reload_available
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 982 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1002 in _bootstrap

Thread 0x0000782ff1000b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/subprocess.py", line 1196 in communicate
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/subprocess.py", line 550 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/subprocess.py", line 466 in check_output
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 769 in _linux_info
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 669 in system_summary
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 121 in __init__
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 401 in show_bug_reporter
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/crash_report.py", line 219 in _show_bug_report_dialog
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bug_reporter/crash_report.py", line 45 in _report
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, psutil._psutil_linux, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 42)
===== Log before crash start =====
Startup Messages  
---  
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.  
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: 1.11.dev202510012017 (2025-10-01)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.11.dev202510012017 (2025-10-01)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Backend texture is not a Vulkan texture.  

[Repeated 2 time(s)]




OpenGL version: 4.3 (Core Profile) Mesa 25.0.7-0ubuntu0.24.04.2
OpenGL renderer: NV194
OpenGL vendor: Mesa

Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
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: Gigabyte Technology Co., Ltd.
Model: B650M D3HP AX
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 9900X 12-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            60Gi       3.4Gi        30Gi        66Mi        27Gi        56Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD104GL [RTX 4500 Ada Generation] [10de:27b1] (rev a1)	
	Subsystem: NVIDIA Corporation AD104GL [RTX 4500 Ada Generation] [10de:180c]	
	Kernel driver in use: nouveau

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.9.1
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202510012017
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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: 1.5.2
    ChimeraX-Scenes: 0.2.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    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: 1.48.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5
    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: 0.2.3
    contourpy: 1.3.3
    coverage: 7.10.7
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.1
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    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: 2.13.1
    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: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.5
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

Change History (2)

comment:1 by Eric Pettersen, 5 weeks ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash gathering Linux info for bug reporter

Reported by Neha Gandhi

comment:2 by Greg Couch, 5 weeks ago

Resolution: → nonchimerax
Status: assigned → closed

ChimeraX is not finding the Nvidia graphics driver. If you haven't installed the proprietary Nvidia driver, then do so. If you have, then double check that all of your installed Nvidia-related packages are the same version. If that doesn't fix it, I'd recommend completely uninstalling all nvidia-related packages and reinstalling.

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