Opened 3 years ago

Last modified 3 years ago

#7580 feedback defect

Unknown crash

Reported by: gomezamy0@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard, Zach Pearson
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-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.5.dev202209082348 (2022-09-08 23:48:00 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.


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{
  "uptime" : 74000,
  "procLaunch" : "2022-09-09 16:12:34.8492 -0500",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "procStartAbsTime" : 1731831176546,
  "coalitionID" : 10852,
  "osVersion" : {
    "train" : "macOS 12.5.1",
    "build" : "21G83",
    "releaseType" : "User"
  },
  "captureTime" : "2022-09-10 00:41:01.4323 -0500",
  "incident" : "FE42EC72-6C17-40CA-9149-49B567102052",
  "bug_type" : "309",
  "pid" : 30238,
  "procExitAbsTime" : 1787678151908,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BF073A52-2EA5-8CDC-A433-2403CAD974F2",
  "wakeTime" : 141,
  "sleepWakeUUID" : "308E59AB-ADF8-4E01-BA96-468CC0C62A90",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10d2dd1d0 is in 0x10d0de000-0x10d347000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             10d0dd000-10d0de000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 10d0de000-10d347000    [ 2468K] r-x\/rwx SM=COW  ...t_id=8e130d19\n      mapped file                 10d347000-10d381000    [  232K] rw-\/rwx SM=COW  ...t_id=8b8c6119",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x000000010d2dd1d0","rawCodes":[10,4516073936],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010d2dd1d0"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":30238},
  "ktriageinfo" : "VM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",
  "vmregioninfo" : "0x10d2dd1d0 is in 0x10d0de000-0x10d347000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             10d0dd000-10d0de000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 10d0de000-10d347000    [ 2468K] r-x\/rwx SM=COW  ...t_id=8e130d19\n      mapped file                 10d347000-10d381000    [  232K] rw-\/rwx SM=COW  ...t_id=8b8c6119",
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    "size" : 196608,
    "uuid" : "ef33add1-6b70-3cc9-8bbc-c8544b609d2b",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703377715200,
    "size" : 229376,
    "uuid" : "792406fe-2224-3c14-ba9f-f076fd7839d2",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703377944576,
    "size" : 49152,
    "uuid" : "f32b6d06-b156-3da0-b086-a31cf011362b",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703374688256,
  "size" : 19331678208,
  "uuid" : "f3387257-f96f-3907-b94c-1d7f0ebef98b"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=205.2M resident=0K(0%) swapped_out_or_unallocated=205.2M(100%)\nWritable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                            84K        7 \nColorSync                          224K       26 \nCoreAnimation                      116K       10 \nCoreGraphics                        12K        2 \nCoreUI image data                 1228K        9 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           380.6M       75 \nMALLOC guard page                  192K        8 \nMALLOC_MEDIUM (reserved)         888.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1392K      345 \nRosetta IndirectBranch            1024K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               680K       68 \nRosetta Thread Context             680K       68 \nSTACK GUARD                         36K        9 \nStack                            144.6M       34 \nStack Guard                       56.1M       25 \nVM_ALLOCATE                      103.3M      164 \nVM_ALLOCATE (reserved)           160.1M       14         reserved VM address space (unallocated)\n__DATA                             355K       45 \n__DATA_CONST                      3030K       39 \n__DATA_DIRTY                        79K       24 \n__LINKEDIT                       192.2M        7 \n__OBJC_RO                         82.8M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                            13.0M       50 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        6.6G      933 \nshared memory                     4332K       34 \nunshared pmap                     11.4M        7 \n===========                     =======  ======= \nTOTAL                              9.1G     2035 \nTOTAL, minus reserved VM space     7.7G     2035 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000454
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000198
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5.dev202209082348 (2022-09-08)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  


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

Log:
UCSF ChimeraX version: 1.5.dev202209082348 (2022-09-08)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2 days 9:44

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.1
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.2
    ChimeraX-AtomicLibrary: 7.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.1
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209082348
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.6
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.9
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
    fonttools: 4.37.1
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

Change History (3)

comment:1 by Eric Pettersen, 3 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

comment:2 by Eric Pettersen, 3 years ago

Cc: Zach Pearson added

Hi Amy,

Thanks for reporting this problem. Do you remember what you were doing when this crash occurred? Did ChimeraX crash at startup?
Also, I would recommend not running ChimeraX directly from the .dmg folder. Instead, drag/copy it somewhere else (e.g. your desktop or your Applications folder) and run it from there. It will start up faster and possibly be more reliable.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 3 years ago

Status: accepted → feedback
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