Opened 3 months ago

Closed 3 months ago

#18169 closed defect (nonchimerax)

Crash changing volume level

Reported by: mohammad.bahar@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.119.1.el7.x86_64-x86_64-with-glibc2.38
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f4d85f12740 (most recent call first):
  File "/app/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2772 in draw_elements
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1749 in draw
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 852 in _draw_geometry
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
  File "/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1579 in draw_depth
  File "/app/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1647 in use_multishadow_map
  File "/app/lib/python3.11/site-packages/chimerax/graphics/view.py", line 633 in _compute_shadowmaps
  File "/app/lib/python3.11/site-packages/chimerax/graphics/view.py", line 227 in _draw_scene
  File "/app/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/app/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
  File "/app/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/app/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_linux, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics (total: 48)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> camera ortho

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/cryosparc_P1039_J107_008_volume_map_sharp.mrc

Opened cryosparc_P1039_J107_008_volume_map_sharp.mrc as #1, grid size
896,896,896, pixel 0.73, shown at step 1, values float32  

> volume #1 region 0,0,0,895,895,895 step 4

> ui mousemode right zoom

> view orient

> volume #1 step 1

> volume #1 sdLevel 4

> surface dust #1 size 7.3

> volume #1 sdLevel 3

> set bgColor white

> lighting soft

> volume #1 sdLevel 2

> volume #1 sdLevel 2.5

> volume #1 sdLevel 3

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/locres/cryosparc_P62_J118_map_locres.mrc

Opened cryosparc_P62_J118_map_locres.mrc as #2, grid size 896,896,896, pixel
0.73, shown at step 1, values float32  

> volume #2 region 0,0,0,895,895,895 step 4

> ui tool show "Surface Color"

> color sample #1.2 map #1 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface "surface": minimum 0.3181, mean 0.3182, maximum 0.3184  

> color sample #1.2 map #2 palette
> 0.3181,#0000ff:0.3182,#7f7fff:0.3182,#ffffff:0.3183,#ff7f7f:0.3184,#ff0000

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:2,#7f7fff:2.3,#ffffff:11.67,#ff7f7f:15.56,#ff0000

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.8,#7f7fff:1.9,#ffffff:2,#ff7f7f:2.1,#ff0000

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> color single #1.2

> color sample #1.2 map #2 palette
> #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000:#808080:#808080

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.75,#7f7fff:1.8,#ffffff:1.85,#ff7f7f:1.9,#ff0000:1.95,#808080:2,#808080

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  

> ui tool show "Side View"

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.72,#5555ff:1.74,#aaaaff:1.76,#ffffff:1.78,#ffa9a9:1.8,#ff5555:1.82,#ff0000

Map values for surface "surface": minimum 0, mean 1.551, maximum 15.56  
Map values for surface "cap far": minimum 1.718, mean 1.72, maximum 2.1  
Map values for surface "cap near": minimum 1.718, mean 1.72, maximum 1.981  

> view orient

> color single #1.2

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/locres/cryosparc_P62_J113_map_locres.mrc

Opened cryosparc_P62_J113_map_locres.mrc as #3, grid size 896,896,896, pixel
0.73, shown at step 1, values float32  

> color sample #1.2 map #3 palette
> 1.7,#0000ff:1.72,#5555ff:1.74,#aaaaff:1.76,#ffffff:1.78,#ffa9a9:1.8,#ff5555:1.82,#ff0000

Map values for surface "surface": minimum 0, mean 1.503, maximum 18.67  

> color sample #1.2 map #3 palette
> 1.7,#0000ff:1.75,#5555ff:1.8,#aaaaff:1.85,#ffffff:1.9,#ffa9a9:1.95,#ff5555:2,#ff0000

Map values for surface "surface": minimum 0, mean 1.503, maximum 18.67  

> color sample #1.2 map #3 palette
> 1.7,#0fc6ce:1.75,#5fd9de:1.8,#afecee:1.85,#ffffff:1.9,#deb4c9:1.95,#be6a93:2,#9e1f5e

Map values for surface "surface": minimum 0, mean 1.503, maximum 18.67  

> volume #1 sdLevel 1


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> camera ortho

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce GTX 745/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:99.0
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Freedesktop SDK 23.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       1.7Gi        29Gi       163Mi       781Mi        29Gi
	Swap:           15Gi       916Mi        14Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 745] [10de:1382] (rev a2)	
	Subsystem: NVIDIA Corporation Device [10de:1065]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    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-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    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: 1.2.7
    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: 1.0.5
    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: 1.8
    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: 1.2.4
    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-LinuxSupport: 1.0.1
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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-OpenCommand: 1.13.5
    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: 3.0.15
    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: 1.16.5
    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: 1.4.3
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    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
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    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: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    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
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    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: 4.0.11

Change History (2)

comment:1 by pett, 3 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash changing volume level

Reported by Moh Bahar

comment:2 by Tom Goddard, 3 months ago

Resolution: → nonchimerax
Status: assigned → closed

ChimeraX crashed in the OpenGL graphics driver drawing map surfaces. This is probably because the 11 year old Nvidia GTX 745 is poorly supported by current Nvidia drivers. Another possibility is you appear to be using remote display (DISPLAY=:99.0) and OpenGL is especially buggy with X11 remote display. We discourage remote display with ChimeraX for reason.

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