Crash opening session

[carmen@…]

The following bug report has been submitted:
Platform:        Linux-5.13.0-37-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4.dev202203290305 (2022-03-29 03:05:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f821a2fd700 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/threading.py", line 1284 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f82bdb41740 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/ui/widgets/item_chooser.py", line 484 in check_and_execute
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open tmp/relion_it025_class001.mrc

Opened relion_it025_class001.mrc as #1, grid size 120,120,120, pixel 1.38,
shown at level 0.00714, step 1, values float32  

> open tmp/relion_it025_class002.mrc

Opened relion_it025_class002.mrc as #2, grid size 120,120,120, pixel 1.38,
shown at level 0.00879, step 1, values float32  

> open tmp/relion_it025_class003.mrc

Opened relion_it025_class003.mrc as #3, grid size 120,120,120, pixel 1.38,
shown at level 0.00826, step 1, values float32  

> open tmp/relion_it025_class004.mrc

Opened relion_it025_class004.mrc as #4, grid size 120,120,120, pixel 1.38,
shown at level 0.00939, step 1, values float32  

> open tmp/relion_it025_class005.mrc

Opened relion_it025_class005.mrc as #5, grid size 120,120,120, pixel 1.38,
shown at level 0.00855, step 1, values float32  

> open tmp/relion_it025_class006.mrc

Opened relion_it025_class006.mrc as #6, grid size 120,120,120, pixel 1.38,
shown at level 0.00905, step 1, values float32  

> open tmp/relion_it025_class007.mrc

Opened relion_it025_class007.mrc as #7, grid size 120,120,120, pixel 1.38,
shown at level 0.0091, step 1, values float32  

> open tmp/relion_it025_class008.mrc

Opened relion_it025_class008.mrc as #8, grid size 120,120,120, pixel 1.38,
shown at level 0.0097, step 1, values float32  

> open tmp/relion_it025_class009.mrc

Opened relion_it025_class009.mrc as #9, grid size 120,120,120, pixel 1.38,
shown at level 0.00892, step 1, values float32  

> tile

9 models tiled  

> tile spacingFactor 5

9 models tiled  

> tile spacingFactor 2

9 models tiled  

> tile spacingFactor 1

9 models tiled  

> tile spacingFactor 1.2

9 models tiled  

> ui tool show "Surface Color"

> color radial #1.1 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000 center
> 82.11,80.634,104.6

> color radial #1.1 palette
> 6.409,#0000ff:28.53,#00ffff:50.65,#00ff00:72.77,#ffff00:94.89,#ff0000 center
> 82.11,80.634,104.6

> ~tile

> color radial all palette
> 6.409,#0000ff:28.53,#00ffff:50.65,#00ff00:72.77,#ffff00:94.89,#ff0000 center
> 82.11,80.634,104.6

> tile

9 models tiled  

> volume all

> volume all level 0.02

> volume all level 0.002

> ~tile

> color radial all palette
> 6.409,#0000ff:28.53,#00ffff:50.65,#00ff00:72.77,#ffff00:94.89,#ff0000 center
> 82.11,80.634,104.6

> tile

9 models tiled  

> ui tool show "Side View"

> ui mousemode right "contour level"

> volume #1 level 0.003915

> volume #2 level 0.004253

> volume #3 level 0.003975

> volume #4 level 0.00424

> volume #5 level 0.004119

> volume #6 level 0.004317

> volume #7 level 0.004121

> volume #8 level 0.00424

> volume #9 level 0.004241

> ~tile

> color radial all palette
> 6.409,#0000ff:28.53,#00ffff:50.65,#00ff00:72.77,#ffff00:94.89,#ff0000 center
> 82.11,80.634,104.6

> tile

9 models tiled  

> ui mousemode right "move planes"

> volume #5 region 0,0,0,119,119,119

> ui mousemode right clip

> open
> /home/carmen/ScipionUserData/projects/Alphafold/Runs/000002_ProtImportAtomStructAlphafold/extra/SESSION.cxs
> format session

opened ChimeraX session  


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

Log:
UCSF ChimeraX version: 1.4.dev202203290305 (2022-03-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 510.54
OpenGL renderer: NVIDIA GeForce GTX 1650 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.6
Locale: en_US.UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20V3
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi        10Gi       3.2Gi        61Mi       1.5Gi       4.3Gi
	Swap:         2.0Gi       1.5Gi       508Mi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics [8086:9bc4] (rev 05)	
	Subsystem: Lenovo Device [17aa:3f95]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.3
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203290305
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.5
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.31.2
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Carmen,

Thanks for reporting this problem. Does that session file (/home/carmen/ScipionUserData/projects/Alphafold/Runs/000002_ProtImportAtomStructAlphafold/extra/SESSION.cxs) crash ChimeraX every time you open it, or was it just in the context of that one use of ChimeraX? If it crashes every time, is there any way you could provide the session file to us?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[carmen@…]

Hi, it crashed just that single time. I had previously killed a "heavy",
frozen session with several maps located in a sshfs mounted drive. Not sure
if that had something to do. This particular session seems quite innocent
(attached).

Regards,

CarmenSM


On Tue, Mar 29, 2022 at 6:50 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

SESSION.cxs​

[carmen@…]

Added by email2trac

[Eric Pettersen]

Hi Carmen,

Thanks for getting back to me. I am able to reproduce the crash. You have to have the Surface Color tool open when restoring the session to produce the crash. I will look into fixing this.

--Eric

[Eric Pettersen]

Again, thanks for reporting this. It will be fixed in tomorrow's build.

--Eric