Opened 2 years ago

Closed 2 years ago

#9902 closed defect (can't reproduce)

Unknown crash

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 

The following bug report has been submitted:
Platform:        macOS-13.2-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
  "uptime" : 8600000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,3",
  "coalitionID" : 378675,
  "osVersion" : {
    "train" : "macOS 13.2",
    "build" : "22D49",
    "releaseType" : "User"
  },
  "captureTime" : "2023-10-04 12:20:19.2996 -0500",
  "incident" : "5ED0D82C-B987-4C7B-BAEF-566335DA4444",
  "pid" : 55571,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-08-30 16:52:37.5268 -0500",
  "procStartAbsTime" : 149468194212244,
  "procExitAbsTime" : 207220005858596,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "172CE817-4B3F-A7F1-02D0-BFA078DC51A7",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 3127,
  "sleepWakeUUID" : "98C5912B-546F-400D-8A13-92453E8C1D2D",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10165c2b4 is in 0x101490000-0x101700000;  bytes after start: 1884852  bytes before end: 671051\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      shared memory               101488000-10148c000    [   16K] rw-\/rw- SM=SHM  \n      GAP OF 0x4000 BYTES\n--->  mapped file                 101490000-101700000    [ 2496K] r-x\/rwx SM=COW  ...t_id=9a4a7427\n      mapped file                 101700000-101708000    [   32K] r--\/rwx SM=COW  ...t_id=982db427",
  "exception" : {"codes":"0x000000000000000a, 0x000000010165c2b4","rawCodes":[10,4318413492],"type":"EXC_BAD_ACCESS","signal":"SIGILL","subtype":"KERN_MEMORY_ERROR at 0x000000010165c2b4"},
  "termination" : {"flags":0,"code":4,"namespace":"SIGNAL","indicator":"Illegal instruction: 4","byProc":"ChimeraX","byPid":55571},
  "ktriageinfo" : "VM - Object has no pager\nVM - Object has no pager\nVM - Object has no pager\nVM - Object has no pager\nVM - Object has no pager\n",
  "vmregioninfo" : "0x10165c2b4 is in 0x101490000-0x101700000;  bytes after start: 1884852  bytes before end: 671051\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      shared memory               101488000-10148c000    [   16K] rw-\/rw- SM=SHM  \n      GAP OF 0x4000 BYTES\n--->  mapped file                 101490000-101700000    [ 2496K] r-x\/rwx SM=COW  ...t_id=9a4a7427\n      mapped file                 101700000-101708000    [   32K] r--\/rwx SM=COW  ...t_id=982db427",
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    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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],
  "vmSummary" : "ReadOnly portion of Libraries: Total=768.3M resident=0K(0%) swapped_out_or_unallocated=768.3M(100%)\nWritable regions: Total=5.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nActivity Tracing                   256K        1 \nCG backing stores                  832K        8 \nCG image                           128K        8 \nColorSync                          576K       28 \nCoreAnimation                      224K       14 \nCoreGraphics                       240K       15 \nCoreUI image data                   80K        1 \nFoundation                          16K        1 \nKernel Alloc Once                   32K        1 \nMALLOC                             3.9G      188 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         624.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        656K       41 \nStack                            320.0M       42 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      237.5M      323 \nVM_ALLOCATE (reserved)           128.0M        3         reserved VM address space (unallocated)\n__DATA                              11K        1 \n__DATA_CONST                        22K        1 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       767.8M        1 \n__TEXT                             556K        1 \ndyld private memory                416K        3 \nmapped file                      472.2M      611 \nshared memory                     5616K       36 \n===========                     =======  ======= \nTOTAL                              6.7G     1357 \nTOTAL, minus reserved VM space     5.7G     1357 \n",
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  "threadTriggered" : {
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},
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  "rollouts" : [
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      "rolloutId" : "6297d96be2c9387df974efa4",
      "factorPackIds" : {

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      "deploymentId" : 240000014
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      "factorPackIds" : {
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    {
      "treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
      "experimentId" : "64406ba83deb637ac8a04419",
      "deploymentId" : 900000017
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},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
> herc5_home/ribosome.cxs" format session

No such file/path: /Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
herc5_home/ribosome.cxs  

> open "/Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
> herc5_home/ribosome.cxs" format session

No such file/path: /Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
herc5_home/ribosome.cxs  

> open "/Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
> herc5_home/ribosome.cxs" format session

No such file/path: /Users/uthscsaadmin/Desktop/EM analysis/march2023- 80S
herc5_home/ribosome.cxs  

> open "/Users/uthscsaadmin/Desktop/ribosome project/ribosome session.cxs"

Opened cryosparc_P10_J108_class_00_00033_volume.mrc as #4, grid size
144,144,144, pixel 2.66, shown at level 0.0271, step 1, values float32  
Opened cryosparc_P10_J108_class_01_00033_volume.mrc as #5, grid size
144,144,144, pixel 2.66, shown at level 0.0131, step 1, values float32  
Opened cryosparc_P10_J108_class_02_00033_volume.mrc as #6, grid size
144,144,144, pixel 8, shown at level 0.026, step 1, values float32  
Opened cryosparc_P10_J108_class_02_00033_volume.mrc z flip as #2, grid size
144,144,144, pixel 6.5, shown at level 0.0287, step 1, values float32  

> set bgColor #ffffff00

opened ChimeraX session  

> open "/Users/uthscsaadmin/Desktop/ribosome project/EM analysis/march2023-
> 80S herc5_home/intial model and 3D class.cxs"

Opened cryosparc_P10_J108_class_00_00033_volume.mrc as #4, grid size
144,144,144, pixel 2.66, shown at level 0.0271, step 1, values float32  
Opened cryosparc_P10_J108_class_01_00033_volume.mrc as #5, grid size
144,144,144, pixel 2.66, shown at level 0.0131, step 1, values float32  
Opened cryosparc_P10_J108_class_02_00033_volume.mrc as #6, grid size
144,144,144, pixel 8, shown at level 0.026, step 1, values float32  
Opened cryosparc_P10_J108_class_02_00033_volume.mrc z flip as #2, grid size
144,144,144, pixel 6.5, shown at level 0.0287, step 1, values float32  
Opened cryosparc_P10_J102_class_00_final_volume.mrc as #3, grid size
128,128,128, pixel 2.99, shown at level 0.0361, step 1, values float32  
Opened cryosparc_P10_J102_class_01_final_volume.mrc as #7, grid size
128,128,128, pixel 2.99, shown at level 0.0413, step 1, values float32  
Opened cryosparc_P10_J102_class_02_final_volume.mrc as #8, grid size
128,128,128, pixel 2.99, shown at level 0.0374, step 1, values float32  
Opened cryosparc_P10_J102_class_03_final_volume.mrc as #9, grid size
128,128,128, pixel 2.99, shown at level 0.0366, step 1, values float32  
opened ChimeraX session  

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!2 models

> show #!1 models

> 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: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
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: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac14,3
      Model Number: MMFK3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 152 days, 1 hour, 10 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        VG259:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 144.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    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: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    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
    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: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    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: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    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: 1.0.1
    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: 2.6.8
    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: 1.10
    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: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    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: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    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: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    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
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    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: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

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

comment:2 by Eric Pettersen, 2 years ago

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