Opened 2 years ago

Closed 23 months ago

Last modified 23 months ago

#10273 closed defect (can't reproduce)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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-6.2.0-36-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7rc202311302110 (2023-11-30 21:10:26 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f8c4bf87640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f8e77a1eb80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/ast.py", line 92 in copy
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
  File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 679 in _choice
  File "/usr/lib/ucsf-chimerax/lib/python3.11/contextlib.py", line 137 in __enter__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 370 in _residue_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 359 in block7
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 361 in _chain_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 323 in block0
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 325 in _model_parts_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 200 in _model_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 157 in block0
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 159 in _model_list_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 136 in _as_term_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 93 in _atom_specifier_
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/grako/contexts.py", line 206 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 192 in _parse_unquoted
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 121 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
  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/shortcuts/shortcuts.py", line 525 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  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, chimerax.pdb_lib._load_libs, chimerax.map._map, 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, chimerax.surface._surface, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 55)
===== Log before crash start =====
UCSF ChimeraX version: 1.7rc202311302110 (2023-11-30)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/mnt1/zjtdata/PDB_Final/FIPV79_N_NTD_FINAL/ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb
> format pdb

ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb title:  
\--- [more info...]  
  
Chain information for ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting shadows true

> lighting shadows false

> lighting flat

> mlp

Map values for surface "ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb_A SES
surface": minimum -26.73, mean -5.059, maximum 21.79  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb_A SES surface
#1.1: minimum, -11.05, mean 2.30, maximum 14.71  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide surfaces

> coulombic

Coulombic values for ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb_A SES surface
#1.1: minimum, -11.05, mean 2.30, maximum 14.71  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide cartoons

> show cartoons

> hide surfaces

> open 7act fromDatabase pdb format mmcif

Summary of feedback from opening 7act fetched from pdb  
---  
note | Fetching compressed mmCIF 7act from
http://files.rcsb.org/download/7act.cif  
  
7act title:  
The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with
10mer ssRNA [more info...]  
  
Chain information for 7act  
---  
Chain | Description | UniProt  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | Nucleoprotein |
NCAP_SARS2 44-180  
2.1/B 2.2/B 2.3/B 2.4/B 2.5/B 2.6/B 2.7/B 2.8/B 2.9/B 2.10/B | ssRNA |  
  

> lighting soft

> lighting simple

> ui tool show "Side View"

> view

> view orient

> graphics silhouettes false

> lighting shadows true

> lighting flat

> lighting full

> hide #!1 target m

> set bgColor white

> volume step 2

No volumes specified  

> volume region all imageMode "full region"

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 10 atomic
models, 0 maps.  

Hide dust shortcut requires a displayed map surface  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 10 atomic models, 0 maps.  

> close #1

> select add #2

23900 atoms, 24420 bonds, 1470 residues, 11 models selected  

> select subtract #2

Nothing selected  

> select add #2

23900 atoms, 24420 bonds, 1470 residues, 11 models selected  

> close

> open
> /home/mnt1/zjtdata/PDB_Final/FIPV79_N_NTD_FINAL/ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb
> format pdb

ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb title:  
\--- [more info...]  
  
Chain information for ZJT_FIPV_N_refine_38_refmac1-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
  

> coulombic


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

Log:
UCSF ChimeraX version: 1.7rc202311302110 (2023-11-30)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.5 (Core Profile) Mesa 23.0.4-0ubuntu1~22.04.1
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.11.2
Locale: en_US.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: Supermicro
Model: Super Server
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 128 Intel(R) Xeon(R) Platinum 8336C CPU @ 2.30GHz
Cache Size: 55296 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi       3.2Gi        14Gi       116Mi       234Gi       246Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52)	
	DeviceName: Aspeed Video 2600	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.13.1
    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: 12.1.2
    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-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: 1.7rc202311302110
    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-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: 4.45.1
    funcparserlib: 2.0.0a0
    glfw: 2.6.3
    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: 5.5.0
    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: 2.8.7
    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: 4.0.0
    prompt-toolkit: 3.0.41
    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: 25.1.1
    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: 4.8.0
    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 (8)

comment:1 by Eric Pettersen, 23 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 23 months ago

Was parsing defattr atom specs used by coulombic under the hood to assign amber_type residue attributes or atom charge and gaff_type attributes.

comment:3 by Eric Pettersen, 23 months ago

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

comment:4 by Tom Goddard, 23 months ago

I vaguely sense a connection between weird garbage collection crashes and having run coulombic. Maybe a search for bug report crashes involving coulombic would suggest a connection, or maybe I am just imagining things.

comment:5 by Eric Pettersen, 23 months ago

Of the 6 garbage-collection crashes reported in the last 3 months, this is the only one involving coulombic.

comment:6 by Tom Goddard, 23 months ago

Ok. Sorry to send you on a goose chase. It may be I made this association just because I see coulombic in logs in crash reports a good bit because it simply is used a good bit.

comment:7 by Tom Goddard, 23 months ago

I was wondering if I just made this up. But I see these 5 garbage collection crashes in the past 4 months that have coulombic in the log.

#9993 #9858 #9549 #9530 #9432

That is about 1/3 of the garbage collection crashes. Maybe just statistical noise. Given the frequency of garbage collection crashes I suspect some code, probably ours, did not do an incref somewhere resulting in a Python object being freed before and later the garbage collector reaching it.

comment:8 by Eric Pettersen, 23 months ago

I see, I searched for "garbage collection" in the summary, which produced a different set of tickets (#9788 #9839 #9844 #10150 #10215 #10273). For those, coulombic was only in one.

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