Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5901 closed defect (can't reproduce)

Unknown crash with unformatted stack trace

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 (last modified by Eric Pettersen) 

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.


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{
  "uptime" : 29000,
  "procLaunch" : "2022-01-11 14:34:19.1995 +0100",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "procStartAbsTime" : 369270759689,
  "coalitionID" : 2485,
  "osVersion" : {
    "train" : "macOS 12.1",
    "build" : "21C52",
    "releaseType" : "User"
  },
  "captureTime" : "2022-01-11 18:29:05.9470 +0100",
  "incident" : "A1486F10-2BAF-4E0F-AE32-53446BD6A603",
  "bug_type" : "309",
  "pid" : 2554,
  "procExitAbsTime" : 706848799009,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "622E5DB9-E767-AF7C-74C7-74FD2919A297",
  "wakeTime" : 10388,
  "sleepWakeUUID" : "9BAC81B1-A565-442A-B904-544455BE975B",
  "sip" : "enabled",
  "vmRegionInfo" : "0x1090a3320 is in 0x108ea8000-0x10910d000;  bytes after start: 2077472  bytes before end: 433375\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             108ea7000-108ea8000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 108ea8000-10910d000    [ 2452K] r-x\/rwx SM=COW  ...t_id=b3af96b7\n      mapped file                 10910d000-109147000    [  232K] rw-\/rwx SM=COW  ...t_id=b386a9b7",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x00000001090a3320","rawCodes":[10,4446630688],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x00000001090a3320"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":2554},
  "ktriageinfo" : "VM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",
  "vmregioninfo" : "0x1090a3320 is in 0x108ea8000-0x10910d000;  bytes after start: 2077472  bytes before end: 433375\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             108ea7000-108ea8000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 108ea8000-10910d000    [ 2452K] r-x\/rwx SM=COW  ...t_id=b3af96b7\n      mapped file                 10910d000-109147000    [  232K] rw-\/rwx SM=COW  ...t_id=b386a9b7",
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      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "61a80a438feb033580c2778b"
      },
      "deploymentId" : 240000290
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000196
    },
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "61c11dcd2cb6041dc630dc63"
      },
      "deploymentId" : 240000357
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000090
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open /Users/dramalhassan/Downloads/robetta_models_180015.pdb

Summary of feedback from opening
/Users/dramalhassan/Downloads/robetta_models_180015.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK ID 180015 MODEL 1 ADAM12  
  
Ignored bad PDB record found on line 2  
PFRMAT TS  
  
Ignored bad PDB record found on line 3  
TARGET ADAM12  
  
Ignored bad PDB record found on line 5  
METHOD ROSETTA provides both ab initio and  
  
Ignored bad PDB record found on line 6  
METHOD comparative models of protein domains.  
  
75 messages similar to the above omitted  
  
Chain information for robetta_models_180015.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A | No description available  
  

> hide #1.1 models

> hide #1.2 models

> show #1.1 models

> show #1.2 models

> hide #1.1 models

> hide #1.2 models

> hide #1.3 models

> hide #1.4 models

> hide #1.5 models

> hide #!1 models

> show #1.1 models

> show #1.2 models

> show #1.3 models

> show #1.4 models

> show #1.5 models

> hide #1.4 models

> hide #1.3 models

> hide #1.2 models

> hide #1.5 models

> color #1.1 bychain

> color #1.1 bypolymer

> rainbow #1.1

> mlp #1.1

Map values for surface "robetta_models_180015.pdb_A SES surface": minimum
-27.31, mean -3.341, maximum 28.2  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!1.1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for robetta_models_180015.pdb_A SES surface #1.1.1: minimum,
-20.65, mean 1.21, maximum 23.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!1.1

Coulombic values for robetta_models_180015.pdb_A SES surface #1.1.1: minimum,
-20.65, mean 1.21, maximum 23.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color bfactor #!1.1

13828 atoms, 909 residues, 1 surfaces, atom bfactor range 0.62 to 24.6  

> color bfactor #!1.1

13828 atoms, 909 residues, 1 surfaces, atom bfactor range 0.62 to 24.6  

> color #!1.1 byhetero

> select #1.5

13828 atoms, 13989 bonds, 909 residues, 1 model selected  

> style #!1.1 stick

Changed 13828 atom styles  

> style #!1.1 stick

Changed 13828 atom styles  

> rainbow #!1.1

> color #!1.1 bypolymer

> rainbow #!1.1

> color bfactor #!1.1

13828 atoms, 909 residues, 1 surfaces, atom bfactor range 0.62 to 24.6  

> show #!1.1 atoms

> hide #!1.1 atoms

> show #!1.1 atoms

> style #!1.1 stick

Changed 13828 atom styles  

> style #!1.1 ball

Changed 13828 atom styles  

> style #!1.1 sphere

Changed 13828 atom styles  

> color #!1.1 bychain

> color #!1.1 byhetero

> color #!1.1 bypolymer

> rainbow #!1.1

> coulombic #!1.1

Coulombic values for robetta_models_180015.pdb_A SES surface #1.1.1: minimum,
-20.65, mean 1.21, maximum 23.36  
To also show corresponding color key, enter the above coulombic command and
add key true  

> nucleotides #!1.1 atoms

> style nucleic & #!1.1 stick

Changed 0 atom styles  

> nucleotides #!1.1 atoms

> style nucleic & #!1.1 stick

Changed 0 atom styles  

> nucleotides #!1.1 atoms

> style nucleic & #!1.1 stick

Changed 0 atom styles  

> show #!1.1 surfaces

> hide #!1.1 surfaces

> style #!1.1 sphere

Changed 13828 atom styles  

> interfaces #!1.1 & ~solvent

0 buried areas:  

> ui tool show AlphaFold

> alphafold search #1.1

> alphafold predict #1.1

ChimeraX REST job id: job_5e6fidd8  
Running AlphaFold prediction  
BlastProtein finished.  
Parsing BLAST results.  
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  




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 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 19:29

Graphics/Displays:

    Apple G13G:

      Chipset Model: Apple G13G
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        DELL S2721HS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: Off
          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
    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 (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Core
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Unknown crash with unformatted stack trace

comment:2 by Eric Pettersen, 4 years ago

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

Even more uninformative than usual.

comment:3 by Tom Goddard, 4 years ago

It is screaming for help

"ktriageinfo" : "VM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",

Also log shows the last command run was alphafold predict. We see a hefty number of crashes in alphafold predict which is somewhat surprising because ChimeraX is not doing much since it is all run on Google Colab. But ChimeraX is creating a Qt html widget -- and I think that is the source of all these crashes. Maybe a drag and drop or other unusual action on that Qt web widget which starts out undocked is the source of all these alphafold predict crashes.

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