Opened 19 months ago

Closed 19 months ago

Last modified 19 months ago

#15015 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-6.5.0-27-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8.dev202404192135 (2024-04-19 21:35:01 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000075be0e7fc640 (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

Thread 0x000075be0f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/tasks.py", line 416 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/webservices/cxservices_job.py", line 150 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/tasks.py", line 285 in _run_function
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be0ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2cff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2d7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/selectors.py", line 415 in select
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2dffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2e7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2effd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be2ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be44bf7640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be453f8640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be45bf9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be463fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be46bfb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be473fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be47bfd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be483fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be48bff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be6abfe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be6b3ff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be88d4f640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be89550640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075be8bfff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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

Thread 0x000075bea13fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/threading.py", line 975 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 0x000075bf6f49eb80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/ctypes/__init__.py", line 512 in cast
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1895 in _update_graphics_if_needed
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath (total: 52)
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404192135 (2024-04-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Model Loops"

> cd /home/zt/workdir

Current working directory is: /home/zt/workdir  

> ui tool show "Show Sequence Viewer"

> set bgColor white

> set bgColor black

> open /home/zt/workdir/blinddock/cul1_rbx1/1ldj_prep.pdb

1ldj_prep.pdb title:  
Structure of the CUL1-RBX1-SKP1-F BOXSKP2 SCF ubiquitin ligase complex [more
info...]  
  
Chain information for 1ldj_prep.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close session

> open /home/zt/workdir/blinddock/cul5_rbx2/7oni_prep.pdb

7oni_prep.pdb title:  
Structure of neddylated CUL5 C-terminal region-RBX2-ARIH2* [more info...]  
  
Chain information for 7oni_prep.pdb #1  
---  
Chain | Description  
C | No description available  
R | No description available  
  

> close session

> open /home/zt/workdir/blinddock/cul1_rbx1/1ldj_prep.pdb format pdb

1ldj_prep.pdb title:  
Structure of the CUL1-RBX1-SKP1-F BOXSKP2 SCF ubiquitin ligase complex [more
info...]  
  
Chain information for 1ldj_prep.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /home/zt/workdir/af2/cul1.fasta

Summary of feedback from opening /home/zt/workdir/af2/cul1.fasta  
---  
notes | Alignment identifier is cul1.fasta  
Associated 1ldj_prep.pdb chain A to AF_AFQ13616F1_1|Chain A|Cullin-1|Homo
sapiens (9606) with 0 mismatches  
  
Opened 1 sequences from cul1.fasta  

> open /home/zt/workdir/af2/rbx1.fasta

Summary of feedback from opening /home/zt/workdir/af2/rbx1.fasta  
---  
notes | Alignment identifier is rbx1.fasta  
Associated 1ldj_prep.pdb chain B to AF_AFP62877F1_1|Chain A|E3 ubiquitin-
protein ligase RBX1|Homo sapiens (9606) with 0 mismatches  
  
Opened 1 sequences from rbx1.fasta  

> ui tool show "Model Loops"

> modeller refine cul1.fasta:1:all-missing numModels 2 fast false
> adjacentFlexible 1 protocol standard

Webservices job id: GNLL4IYTQUFDUB0W  


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

Log:
UCSF ChimeraX version: 1.8.dev202404192135 (2024-04-19)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.171.04
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 82RF
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       7.1Gi       1.1Gi       695Mi        22Gi        22Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104M [Geforce RTX 3070 Ti Laptop GPU] [10de:24e0] (rev a1)	
	Subsystem: Lenovo Device [17aa:3aef]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    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: 2.12.1
    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: 1.4
    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.dev202404192135
    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: 1.4.2
    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: 1.1.9
    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: 1.2
    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
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    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: 1.0
    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: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.37.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4
    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: 0.2.2
    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: 4.51.0
    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: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    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: 24.0
    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: 4.2.0
    prompt-toolkit: 3.0.43
    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: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.2
    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
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (5)

comment:1 by Eric Pettersen, 19 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, 19 months ago

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

This is after the fix I made, so there still is a less-frequent problem. Code was accessing StructureDatas._graphics_changeds when it happened.

comment:3 by Tom Goddard, 19 months ago

The log shows the last thing they did was run a Modeller model loops job. If the results were returned would that cause any structure deletions to occur?

There were two earlier "close session" commands in the log so maybe that is where thing went bad.

comment:4 by Eric Pettersen, 19 months ago

The results processing occurs in the main thread. Some of the models might have some bonds deleted before being opened in the session.

comment:5 by Eric Pettersen, 19 months ago

Tried to reproduce the crash by mimicking the actions in this ticket, but worked fine.

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