Opened 21 months ago

Closed 17 months ago

#14441 closed defect (fixed)

Crash in garbage collection

Reported by: jin.zhou@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard, Tristan Croll
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-91-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x00007fbbf388f740 (most recent call first):
  Garbage-collecting
  File "/home/corp1588/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/molobject.py", line 5656 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 167 in __getitem__
  File "/home/corp1588/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/molobject.py", line 680 in get_dihedral
  File "/home/corp1588/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/molarray.py", line 187 in restore_snapshot
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 747 in restore
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 60)
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/corp1588/Documents/Chimerax/mDISC1_aa322_722_tetramer_interface_110124.cxs
> format session

Opened cryosparc_P15_J41_010_volume_map_deepemhancer_default.mrc as #2.1.1.1,
grid size 448,448,448, pixel 1.06, shown at level 0.15, step 1, values float32  
Opened cryosparc_P15_J41_010_volume_map_deepemhancer_highres.mrc as #2.1.1.2,
grid size 448,448,448, pixel 1.06, shown at level 0.1, step 1, values float32  
Opened P15_J39_csparc_autosharpened.mrc as #2.1.1.3, grid size 448,448,448,
pixel 1.06, shown at level 0.426, step 1, values float32  
Restoring stepper: mDISC1_model_real_space_refined_033_corrected_v6b.pdb  
opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain /C /D

Alignment identifier is 2  

> select /A-B:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> select /A-B:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> ui mousemode right swapaa

> select H

9848 atoms, 464 pseudobonds, 1216 residues, 3 models selected  

> hide (#!2.2 & sel) target a

> select clear

> select /A-B:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> select /A-B:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> ui tool show "Volume Viewer"

> ui mousemode right "bond rotation"

> ui mousemode right swapaa

> swapaa mousemode /A:362 GLU

> swapaa mousemode /A:371 VAL

> swapaa mousemode /A:377 LYS

> swapaa mousemode /A:374 ALA

> select clear

> select /A:371@CA

1 atom, 1 residue, 1 model selected  

> swapaa mousemode /A:371 ALA

> select clear

> select /C-D:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> select /C-D:371

42 atoms, 42 bonds, 2 residues, 1 model selected  

> swapaa mousemode /C:371 ALA

> save
> /home/corp1588/Documents/phenix/DISC1/PDB/Kamel/mDISC1_model_real_space_refined_033_corrected_v6b_mutated.pdb
> relModel #2.1.1.2

> close session

> open
> /home/corp1588/Documents/phenix/DISC1/PDB/Kamel/mDISC1_model_real_space_refined_033_corrected_v6b_mutated.pdb
> format pdb

Chain information for
mDISC1_model_real_space_refined_033_corrected_v6b_mutated.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> close session

> open
> /home/corp1588/Documents/Chimerax/mDISC1_aa322_722_tetramer_interface_110124.cxs
> format session


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

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 495.29.05
OpenGL renderer: NVIDIA GeForce RTX 3060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi       4.0Gi       114Gi        40Mi       6.8Gi       120Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2504] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:4071]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    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-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    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: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (5)

comment:1 by pett, 21 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: crash in get_dihedral while restoring session

Reported by Jin Chuan Zhou

comment:2 by Tristan Croll, 21 months ago

Hmm... the last call in the stack (before the "Garbage-collecting" entry - I can't recall seeing that before in a segmentation fault traceback?) is in c_ptr_to_py_inst() (defined in ISOLDE's molobject.py at ​https://github.com/tristanic/isolde/blob/64e692c04ea01136139e6ed0cad723bb9f6f9c4b/isolde/src/molobject.py#L5656, but functionally equivalent to the official version). Eric, I believe that was your code: any suggestions on what kinds of problems could cause a segmentation fault there?

Jin: does this happen reproducibly when you attempt to open this .cxs file?

comment:3 by jin.zhou@…, 21 months ago 

Dear Tristan,

Many thanks for your message! I think this was a rare instance where Chimerax crashed after attempting to load a saved session with ISOLDE. Otherwise, both Chimerax and ISOLDE have been running very smoothly on my local machine. I have since opened this and other .cxs files multiple times with no issues.

Regards,

Jin

From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, 22 January 2024 at 19:49
To: Jin Zhou <jin.zhou@bioch.ox.ac.uk>, tcroll@altoslabs.com <tcroll@altoslabs.com>
Subject: Re: [ChimeraX] #14441: ISOLDE: crash in get_dihedral while restoring session
#14441: ISOLDE: crash in get_dihedral while restoring session
----------------------------------+---------------------------
          Reporter:  jin.zhou@…   |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Comment (by Tristan Croll):

 Hmm... the last call in the stack (before the "Garbage-collecting" entry -
 I can't recall seeing that before in a segmentation fault traceback?) is
 in `c_ptr_to_py_inst()` (defined in ISOLDE's `molobject.py` at
 https://github.com/tristanic/isolde/blob/64e692c04ea01136139e6ed0cad723bb9f6f9c4b/isolde/src/molobject.py#L5656,
 but functionally equivalent to the official version). Eric, I believe that
 was your code: any suggestions on what kinds of problems could cause a
 segmentation fault there?

 Jin: does this happen reproducibly when you attempt to open this .cxs
 file?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/14441#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:4 by pett, 21 months ago

Cc: Tom Goddard Tristan Croll added
Component: Third Party → Core
Owner: changed from Tristan Croll to pett
Summary: ISOLDE: crash in get_dihedral while restoring session → Crash in garbage collection

The fact that garbage collection was occurring when it crashed really means that the stack trace was very little to do with the root cause of the crash, so I am reclassifying this ticket -- putting it with the roughly 20 tickets we already have for garbage collection crashes in 1.7. We are definitely looking to try to track down the cause of the problem, but garbage-collection crashes are notoriously difficult to debug. We have some avenues of attack we intend to try.

comment:5 by pett, 17 months ago

Resolution: → fixed
Status: assigned → closed

Fixed in 1.8 release candidate

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