Opened 22 months ago

Closed 22 months ago

Last modified 22 months ago

#10422 closed defect (can't reproduce)

Crash in garbage collection while adding hydrogens during coulombic

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core 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-5.15.0-91-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.8.dev202312290130 (2023-12-29 01:30:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fa8b0c1f700 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007fa998755740 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 1014 in to_h36
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 1082 in _h_name
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 949 in new_hydrogen
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 910 in add_altloc_hyds
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 909 in _attach_hydrogens
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 225 in add_hydrogens
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 184 in hbond_add_hydrogens
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 95 in assign_charges
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 102 in cmd_coulombic
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax-daily/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, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 54)
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202312290130 (2023-12-29)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/satya/Satya_continuum/ASGARD/PDB/LOKI2.pdb

Summary of feedback from opening
/media/satya/Satya_continuum/ASGARD/PDB/LOKI2.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 216 UNP A0A0F8XFT2 A0A0F8XFT2_LOKSG 1 216  
  
LOKI2.pdb title:  
Alphafold monomer V2.0 prediction for bar domain-containing protein
(A0A0F8XFT2) [more info...]  
  
Chain information for LOKI2.pdb #1  
---  
Chain | Description  
A | bar domain-containing protein  
  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for LOKI2.pdb_A SES surface #1.1: minimum, -15.09, mean
-1.71, maximum 20.01  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for LOKI2.pdb_A SES surface #1.1: minimum, -15.09, mean
-1.71, maximum 20.01  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close

> open /media/satya/Satya_continuum/ASGARD/PDB/7d6d_chain_A_B.pdb

Chain information for 7d6d_chain_A_B.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> coulombic


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

Log:
UCSF ChimeraX version: 1.8.dev202312290130 (2023-12-29)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/satya/Satya_continuum/ASGARD/PDB/7d6d_chain_A_B.pdb

Chain information for 7d6d_chain_A_B.pdb #1  
---  
Chain | Description  
A B | No description available  
  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 7d6d_chain_A_B.pdb_A SES surface #1.1: minimum, -21.56,
mean -0.52, maximum 14.32  
Coulombic values for 7d6d_chain_A_B.pdb_B SES surface #1.2: minimum, -18.31,
mean -0.53, maximum 14.25  
To also show corresponding color key, enter the above coulombic command and
add key true  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_IN.ISO8859-1
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=:0
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       7.9Gi       1.0Gi       1.2Gi       6.5Gi       5.7Gi
	Swap:         2.0Gi       688Mi       1.3Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop 9 Series) [8086:3e98] (rev 02)	
	DeviceName: Onboard - Video	
	Subsystem: Dell UHD Graphics 630 (Desktop 9 Series) [1028:092e]

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: 1.5.14
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.52
    ChimeraX-AtomicLibrary: 12.1.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.11
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    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: 1.8.dev202312290130
    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
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    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: 1.5.15
    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: 1.1
    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: 1.0.4
    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: 1.2.1
    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: 1.14.1
    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: 1.33.5
    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: 5.6.1
    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
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    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 (3)

comment:1 by pett, 22 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection while adding hydrogens during coulombic

comment:2 by pett, 22 months ago

Resolution: → can't reproduce
Status: accepted → closed

Tried coulombic on 7d6d chain A a few times and it always worked.

comment:3 by Tom Goddard, 22 months ago

I think we talked about coulombic being related to the garbage collection crashes before. Probably the relation is that coulombic often triggers garbage collection so that is where we see the crash. We also often see the crash in numpy, and I think that case is almost surely because garbage collection happens often in those specific numpy calls.

Note: See TracTickets for help on using tickets.