Opened 3 years ago

Closed 3 years ago

#7184 closed defect (can't reproduce)

Crash in Qt event loop running AlphaFold prediction

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 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 0x00000002022fe600 (most recent call first):
  File "/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
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  "procLaunch" : "2022-06-27 12:36:15.6353 -0400",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "procStartAbsTime" : 3648137356504,
  "coalitionID" : 636,
  "osVersion" : {
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    "build" : "21D62",
    "releaseType" : "User"
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  "captureTime" : "2022-06-27 20:06:23.4675 -0400",
  "incident" : "76B6E684-EE22-4181-8FCA-89C4D7EF305C",
  "bug_type" : "309",
  "pid" : 29117,
  "procExitAbsTime" : 3855316403268,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Users\/USER\/Desktop\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
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  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BB068531-94FF-ADC7-F615-F37A4279D59B",
  "wakeTime" : 4688,
  "sleepWakeUUID" : "5BA98B79-D0D6-4FC8-90CA-F4620EA71BAC",
  "sip" : "enabled",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x65722e62616c6fcb","rawCodes":[1,7309956145251905483],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x65722e62616c6fcb -> 0x00002e62616c6fcb (possible pointer authentication failure)"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed 'SEQCROW==1.4.4'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting SEQCROW==1.4.4  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/seqcrow/releases/1.4.4/SEQCROW-1.4.4-py3-none-
any.whl (5.4 MB)  
Requirement already satisfied: psutil in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (5.8.0)  
Requirement already satisfied: ChimeraX-Core=1.2 in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (1.3)  
Requirement already satisfied: jinja2 in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (3.0.1)  
Requirement already satisfied: Send2Trash in
/Users/jaredford/Library/Application Support/ChimeraX/1.3/site-packages (from
SEQCROW==1.4.4) (1.8.0)  
Requirement already satisfied: scipy in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.4.4) (1.7.1)  
Requirement already satisfied: MarkupSafe>=2.0 in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jinja2->SEQCROW==1.4.4) (2.0.1)  
Requirement already satisfied: numpy=1.16.5 in
./ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from scipy->SEQCROW==1.4.4) (1.21.2)  
Installing collected packages: SEQCROW  
Attempting uninstall: SEQCROW  
Found existing installation: SEQCROW 1.3.2  
Uninstalling SEQCROW-1.3.2:  
Successfully uninstalled SEQCROW-1.3.2  
Successfully installed SEQCROW-1.4.4  
  

WARNING: Value for scheme.platlib does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/jaredford/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application Support/ChimeraX/1.3/site-
packages  
sysconfig: /Users/jaredford/Library/Python/3.9/lib/python/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application
Support/ChimeraX/include/python3.9/SEQCROW  
sysconfig: /Users/jaredford/Library/Python/3.9/include/SEQCROW  
WARNING: Value for scheme.scripts does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application Support/ChimeraX/bin  
sysconfig: /Users/jaredford/Library/Python/3.9/bin  
WARNING: Value for scheme.data does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application Support/ChimeraX  
sysconfig: /Users/jaredford/Library/Python/3.9  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
  
distutils: /Users/jaredford/Library/Application
Support/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /Users/jaredford/Library/Python/3.9/include/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 22.1.2 is
available.  
You should consider upgrading via the
'/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/MacOS/ChimeraX -m pip
install --upgrade pip' command.  
  

> open 1DNP

1dnp title:  
Structure of deoxyribodipyrimidine photolyase [more info...]  
  
Chain information for 1dnp #1  
---  
Chain | Description | UniProt  
A B | DNA photolyase | PHR_ECOLI  
  
Non-standard residues in 1dnp #1  
---  
FAD — flavin-adenine dinucleotide  
MHF — 5,10-methenyl-6,7,8-trihydrofolic acid  
  
1dnp mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show AlphaFold

> alphafold predict #1/A

Running AlphaFold prediction  

> open "/Users/jaredford/Desktop/Chimera runs/Photolyase with alphafold
> predict and R344K.cxs"

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 629, in changeEvent  
self.hide_floating_tools = self.isMinimized()  
File
"/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 734, in hide_floating_tools  
tw._mw_set_shown(True)  
File
"/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2187, in _mw_set_shown  
self.__toolkit.shown = shown  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
AttributeError: 'NoneType' object has no attribute 'shown'  
  
File
"/Users/jaredford/Desktop/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 2187, in _mw_set_shown  
self.__toolkit.shown = shown  
  
See log for complete Python traceback.  
  

> hide #3 models

> close #3

> close #2

> alphafold predict
> TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARKGK

Using the same data path for profile, may corrupt the data.  

Running AlphaFold prediction  

> ui tool show AlphaFold

> alphafold predict #1/A

Using the same data path for profile, may corrupt the data.  

Running AlphaFold prediction  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7ff5e31f1860>
contents scale of 2 - updating layer to match.  

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7ff5e31f1860>
contents scale of 1 - updating layer to match.  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 8 GB

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 21 days 11:25

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        HISENSE:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 3840 x 2160 @ 30.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Television: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    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: 1.3
    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-DistUI: 1.0
    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-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    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: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    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: 1.0.1
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    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
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    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: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    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: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    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
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    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: 3.0.23
    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: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    Send2Trash: 1.8.0
    SEQCROW: 1.4.4
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash running AlphaFold prediction

Was using 8.5GB at the time.

comment:2 by Tom Goddard, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
Summary: Crash running AlphaFold prediction → Crash in Qt event loop running AlphaFold prediction

Probable crash related to Qt html widget used by AlphaFold. There are 53 threads (search for "frames") and some are related to Chrome_*, some related to GPU rendering of chrome. The main thread that crashed has a useless stack trace which is in _sigtramp. The second thread is com.apple.rosetta.exceptionserver. Maybe we'd get more useful info from a native Mac M1 ChimeraX build on this M1 computer.

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