Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6012 closed defect (duplicate)

Crash in rapid_access_shown at startup on Linux

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.1.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.4.dev202201082018 (2022-01-08 20:18:28 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007f142af1c740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 819 in rapid_access_shown
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 839 in showEvent
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 532 in __init__
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 220 in build
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 688 in init
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show AlphaFold

> open
> /data/fremont/ydai/Fremont_Dai_NS1-p2-F96-grid2_TitanF4_121421/relion/InitialModel/job020/run_it300_class001.mrc

Opened run_it300_class001.mrc as #1, grid size 360,360,360, pixel 0.7, shown
at level 0.00533, step 2, values float32  

> close #1

> alphafold predict
> ELCNKQQQQGPFTFADYQESPLNVSRLQIKVTKTTVQDRGKNFVIGYRAYWRSYCYNGGSLDGNTGCYNSLNPKPPTKDELKTWGQEEVCYTGPEVQDAWSGDSSICFVDWKMDNKHRAKELEKRSNNNHFAHHTCNLSWRCGVTNTHLEVRLVASGTQPQAVIVMPNGTTRAVSMVAETFWTDGEFSYLYSPKVFGTRAETKFIPCFKEHVKTRLDQGGSDYLIHDLTTEKFHCKDGDNFFEFPSSGFICLPDACYKNEKQKNNLLHPGMWNISEKLHAASVYDVNNVIHSLVYETESLRLSLAQLDHRFSVLTKLMNKMVSSLAKIDDRLIGALLEKPMASKFISPTKFMVSPCVAVLEEESNCHKDSIYRDGRWVYNNDPTKCFILNSSQTIDLFNFKTLWLPQLVAAKVEGVVSDEDGWTFVANSKQALLDTMTYTKNGGRGTSMEDVLNYPSGWLSGKLNG,ELCNKQQQQGPFTFADYQESPLNVSRLQIKVTKTTVQDRGKNFVIGYRAYWRSYCYNGGSLDGNTGCYNSLNPKPPTKDELKTWGQEEVCYTGPEVQDAWSGDSSICFVDWKMDNKHRAKELEKRSNNNHFAHHTCNLSWRCGVTNTHLEVRLVASGTQPQAVIVMPNGTTRAVSMVAETFWTDGEFSYLYSPKVFGTRAETKFIPCFKEHVKTRLDQGGSDYLIHDLTTEKFHCKDGDNFFEFPSSGFICLPDACYKNEKQKNNLLHPGMWNISEKLHAASVYDVNNVIHSLVYETESLRLSLAQLDHRFSVLTKLMNKMVSSLAKIDDRLIGALLEKPMASKFISPTKFMVSPCVAVLEEESNCHKDSIYRDGRWVYNNDPTKCFILNSSQTIDLFNFKTLWLPQLVAAKVEGVVSDEDGWTFVANSKQALLDTMTYTKNGGRGTSMEDVLNYPSGWLSGKLNG,ELCNKQQQQGPFTFADYQESPLNVSRLQIKVTKTTVQDRGKNFVIGYRAYWRSYCYNGGSLDGNTGCYNSLNPKPPTKDELKTWGQEEVCYTGPEVQDAWSGDSSICFVDWKMDNKHRAKELEKRSNNNHFAHHTCNLSWRCGVTNTHLEVRLVASGTQPQAVIVMPNGTTRAVSMVAETFWTDGEFSYLYSPKVFGTRAETKFIPCFKEHVKTRLDQGGSDYLIHDLTTEKFHCKDGDNFFEFPSSGFICLPDACYKNEKQKNNLLHPGMWNISEKLHAASVYDVNNVIHSLVYETESLRLSLAQLDHRFSVLTKLMNKMVSSLAKIDDRLIGALLEKPMASKFISPTKFMVSPCVAVLEEESNCHKDSIYRDGRWVYNNDPTKCFILNSSQTIDLFNFKTLWLPQLVAAKVEGVVSDEDGWTFVANSKQALLDTMTYTKNGGRGTSMEDVLNYPSGWLSGKLNG
> prokaryote true

Running AlphaFold prediction  

Downloaded prediction file not found:
/home/ydai/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb  

AlphaFold prediction finished  
Results in /home/ydai/Downloads/ChimeraX/AlphaFold/prediction_1  

> alphafold predict
> ELCNKQQQQGPFTFADYQESPLNVSRLQIKVTKTTVQDRGKNFVIGYRAYWRSYCYNGGSLDGNTGCYNSLNPKPPTKDELKTWGQEEVCYTGPEVQDAWSGDSSICFVDWKMDNKHRAKELEKRSNNNHFAHHTCNLSWRCGVTNTHLEVRLVASGTQPQAVIVMPNGTTRAVSMVAETFWTDGEFSYLYSPKVFGTRAETKFIPCFKEHVKTRLDQGGSDYLIHDLTTEKFHCKDGDNFFEFPSSGFICLPDACYKNEKQKNNLLHPGMWNISEKLHAASVYDVNNVIHSLVYETESLRLSLAQLDHRFSVLTKLMNKMVSSLAKIDDRLIGALLEKPMASKFISPTKFMVSPCVAVLEEESNCHKDSIYRDGRWVYNNDPTKCFILNSSQTIDLFNFKTLWLPQLVAAKVEGVVSDEDGWTFVANSKQALLDTMTYTKNGGRGTSMEDVLNYPSGWLSGKLNG

Running AlphaFold prediction  
Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in /home/ydai/Downloads/ChimeraX/AlphaFold/prediction_2  

> hide #1 models

> show #1 models

> color bfactor #1 palette alphafold

7296 atoms, 466 residues, atom bfactor range 26.4 to 97.2  

> hide #1 models

> show #1 models


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

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.4.dev202201082018 (2022-01-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Locale: en_US.UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:0
Manufacturer: GIGABYTE
Model: G481-HA0-00
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 80 Intel(R) Xeon(R) Gold 6230 CPU @ 2.10GHz
Cache Size: 28160 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           503G        286G        194G        219M         21G        215G
	Swap:           31G          0B         31G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:1000]	
	Kernel driver in use: ast

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.10
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.32.2
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    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
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202201082018
    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: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    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: 2.6.5
    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: 2.4.6
    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: 1.7.4
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.15.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.5.1
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.3
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 6.6.0
    ipython: 7.30.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.1
    jupyter-client: 7.1.0
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    nest-asyncio: 1.5.4
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.24
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.0
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.7.0
    tifffile: 2021.4.8
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by pett, 4 years ago

Cc: pett added
Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Unknown crash

The Python stack trace and log contents seem to be in conflict. According to the stack trace, the crash occurred when initially showing Rapid Access. According to the log, the crash occurred after doing some AlphaFold prediction and other work.

Not sure why they're "out of sync" and which one is actually the applicable one.

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

The crash is the usual rapid_access_shown on Linux at startup. ChimeraX has not even been fully initialized yet so the log panel has not been created so almost all reports of this bug contain no log. But in this case probably the user was running another copy of ChimeraX to run an AlphaFold job and so it wrote the log file. Then the crash report combined the Python faulthandler stack trace with the log from the other ChimeraX. The problem is each ChimeraX tries to write the same log file so these mix ups will happen when multiple copies of ChimeraX are running. I don't think that is worth fixing right now.

I hope we can get Qt 6 ChimeraX tested so we can get it in the hands of users to see if it fixes this (and many other) Qt bugs.

comment:3 by Tom Goddard, 4 years ago

Summary: Unknown crash → Crash in rapid_access_shown at startup on Linux
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