Opened 4 years ago

Closed 4 years ago

#6037 closed defect (can't reproduce)

Crash at startup, no stack info, "VM - Object is not alive"

Reported by: zhangxiaofeng@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: pett
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: Bus error

Thread 0x00007000165fa000 (most recent call first):
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007000155f7000 (most recent call first):
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013-A6F2-4929-AF89-7A8FA65766FE/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/private/var/folders/q2/swpptbzj2wd88gw8q9csf32c0000gn/T/AppTranslocation/1FD1F013

{"app_name":"ChimeraX","timestamp":"2022-01-28 20:53:24.00 +0800","app_version":"","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.1 (21C52)","incident_id":"C1A4C18F-5566-40C6-88DF-DEFD101BED26","name":"ChimeraX"}
{
  "uptime" : 5000,
  "procLaunch" : "2022-01-28 20:50:43.8084 +0800",
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro11,5",
  "procStartAbsTime" : 4932436113697,
  "coalitionID" : 2599,
  "osVersion" : {
    "train" : "macOS 12.1",
    "build" : "21C52",
    "releaseType" : "User"
  },
  "captureTime" : "2022-01-28 20:53:23.8185 +0800",
  "incident" : "C1A4C18F-5566-40C6-88DF-DEFD101BED26",
  "bug_type" : "309",
  "pid" : 3126,
  "procExitAbsTime" : 5092280794695,
  "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" : "EF911621-7548-4E93-7CAD-0E6CEC319EAC",
  "wakeTime" : 390,
  "sleepWakeUUID" : "6C1A622F-B164-4938-91A8-EB67A409FDB6",
  "sip" : "enabled",
  "vmRegionInfo" : "0x109c91623 is in 0x109b25000-0x109d8a000;  bytes after start: 1492515  bytes before end: 1018332\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 109b1c000-109b25000    [   36K] r--\/rwx SM=COW  ...t_id=a7325635\n--->  mapped file                 109b25000-109d8a000    [ 2452K] r-x\/rwx SM=COW  ...t_id=a70e1e35\n      mapped file                 109d8a000-109dc4000    [  232K] rw-\/rwx SM=COW  ...t_id=a7d6a835",
  "isCorpse" : 1,
  "exception" : {"codes":"0x000000000000000a, 0x0000000109c91623","rawCodes":[10,4459140643],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x0000000109c91623"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":3126},
  "ktriageinfo" : "VM - Object is not alive\n",
  "vmregioninfo" : "0x109c91623 is in 0x109b25000-0x109d8a000;  bytes after start: 1492515  bytes before end: 1018332\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 109b1c000-109b25000    [   36K] r--\/rwx SM=COW  ...t_id=a7325635\n--->  mapped file                 109b25000-109d8a000    [ 2452K] r-x\/rwx SM=COW  ...t_id=a70e1e35\n      mapped file                 109d8a000-109dc4000    [  232K] rw-\/rwx SM=COW  ...t_id=a7d6a835",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
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}
===== 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  


===== 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 ATI-4.7.101
OpenGL renderer: AMD Radeon R9 M370X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,5
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.5 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 428.60.3.0.0
      OS Loader Version: 540.60.2~89
      SMC Version (system): 2.30f2

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 2:38

Graphics/Displays:

    AMD Radeon R9 M370X:

      Chipset Model: AMD Radeon R9 M370X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6821
      Revision ID: 0x0083
      ROM Revision: 113-C5670E-945
      VBIOS Version: 113-C567A1-006
      EFI Driver Version: 01.00.945
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.20 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.20 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 1

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 (2)

comment:1 by Tom Goddard, 4 years ago

Cc: pett added
Component: Unassigned → Window Toolkit
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash at startup, no stack info, "VM - Object is not alive"

It looks like ChimeraX crashed just after startup since the Log does not show any commands. The crash Python stack trace does not show it in any ChimeraX code which makes me think this is a bug in the Qt window toolkit used by ChimeraX.

If you can tell us anything more about what you did in ChimeraX before it crashed, for example, did it just crash after staring the program before you did anything? That info would help us better judge the cause.

If it is in the Qt window toolkit, we plan to have a ChimeraX tech preview daily build next week that updates the Qt toolkit from version 5 to 6 which may fix such crashes.

comment:2 by Tom Goddard, 4 years ago

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