Opened 10 months ago

Closed 10 months ago

#16728 closed defect (limitation)

SBGrid install of 1.9 fails to launch; 1.8 works

Reported by: pedro.alzari@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
After installing Chimerax 1.9 with SBGrid, it crashed. I had to reinstall Chimerax 1.8, which works Ok.
{"app_name":"ChimeraX","timestamp":"2025-01-29 16:49:28.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3 (24D60)","roots_installed":0,"name":"ChimeraX","incident_id":"1F198894-B5C3-46CB-AC60-838A5DF6FA69"}
{
  "uptime" : 40000,
  "procRole" : "Unspecified",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac15,9",
  "coalitionID" : 853,
  "osVersion" : {
    "train" : "macOS 15.3",
    "build" : "24D60",
    "releaseType" : "User"
  },
  "captureTime" : "2025-01-29 16:49:28.2742 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "1F198894-B5C3-46CB-AC60-838A5DF6FA69",
  "pid" : 4029,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-01-29 16:49:28.2412 +0100",
  "procStartAbsTime" : 975610403715,
  "procExitAbsTime" : 975611190736,
  "procName" : "ChimeraX",
  "procPath" : "\/opt\/sbgrid\/*\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"B5D3EA71-1BF4-543F-A8DF-43650E59F04F","thirdParty":true},
  "parentProc" : "Exited process",
  "parentPid" : 4028,
  "coalitionName" : "com.apple.Terminal",
  "crashReporterKey" : "CD75C76C-CA43-32B2-00A3-F7E1FD59513C",
  "responsiblePid" : 1026,
  "responsibleProc" : "Terminal",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"5AAAACABAAAoAQAAMAEAADgBAABAAQAASAEAAGQBAAAwQYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkeBj\/pe\/AwCR\/XvBqP8PX9bAA1\/WEC2A0g=="},
  "bootSessionUUID" : "57A22221-7781-4F97-B9DC-6E09F132A646",
  "wakeTime" : 28706,
  "sleepWakeUUID" : "97AF5D47-9842-4366-8D57-BEB390D7BBBE",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "termination" : {"code":1,"flags":518,"namespace":"DYLD","indicator":"Library missing","details":["(terminated at launch; ignore backtrace)"],"reasons":["Library not loaded: @rpath\/Versions\/3.11\/Python","Referenced from:  \/opt\/sbgrid\/*\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX","Reason: tried: '\/opt\/sbgrid\/i386-mac\/chimerax\/1.9\/ChimeraX-1.9.app\/Contents\/lib\/Versions\/3.11\/Python' (no such file), '\/opt\/sbgrid\/i386-mac\/chimerax\/1.9\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python' (no such file), '\/opt\/sbgrid\/i386-mac\/chimerax\/1.9\/ChimeraX-1.9.app\/Contents\/lib\/Versions\/3.11\/Python' (no such file), '\/opt\/sbgrid\/i386-mac\/chimerax\/1.9\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python' (no such file), '\/usr\/lib\/Python' (no such file, not in dyld cache)"]},
  "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,
  "threads" : [{"triggered":true,"id":820153,"threadState":{"x":[{"value":6},{"value":1},{"value":6094508624},{"value":123},{"value":6094507600},{"value":0},{"value":0},{"value":1536},{"value":32},{"value":6094507470},{"value":10},{"value":0},{"value":52},{"value":0},{"value":11267230065},{"value":6094514082},{"value":521},{"value":6978900820,"symbolLocation":420,"symbol":"__simple_bprintf"},{"value":0},{"value":0},{"value":6094507600},{"value":123},{"value":6094508624},{"value":1},{"value":6},{"value":257},{"value":6978887680},{"value":6094511296},{"value":6094511448}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6979351028},"cpsr":{"value":2147487744},"fp":{"value":6094507552},"sp":{"value":6094507488},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6979321552,"matchesCrashFrame":1},"far":{"value":0}},"frames":[{"imageOffset":433872,"symbol":"__abort_with_payload","symbolLocation":8,"imageIndex":1},{"imageOffset":463348,"symbol":"abort_with_payload_wrapper_internal","symbolLocation":104,"imageIndex":1},{"imageOffset":463400,"symbol":"abort_with_payload","symbolLocation":16,"imageIndex":1},{"imageOffset":45524,"symbol":"dyld4::halt(char const*, dyld4::StructuredError const*)","symbolLocation":300,"imageIndex":1},{"imageOffset":31648,"symbol":"dyld4::prepare(dyld4::APIs&, dyld3::MachOAnalyzer const*)","symbolLocation":3996,"imageIndex":1},{"imageOffset":27584,"symbol":"dyld4::start(dyld4::KernelArgs*, void*, void*)::$_0::operator()() const","symbolLocation":544,"imageIndex":1},{"imageOffset":24668,"symbol":"start","symbolLocation":2304,"imageIndex":1}]}],
  "usedImages" : [
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4372299776,
    "CFBundleShortVersionString" : "1.9.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "17982d98-65bc-3327-8526-577ec996453c",
    "path" : "\/opt\/sbgrid\/*\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.9.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6978887680,
    "size" : 532288,
    "uuid" : "398a133c-9bcb-317f-a064-a40d3cea3c0f",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 6978076672,
  "size" : 4865835008,
  "uuid" : "d326f1a9-b205-3526-879c-7b2105224601"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=606.7M resident=0K(0%) swapped_out_or_unallocated=606.7M(100%)\nWritable regions: Total=8288K written=96K(1%) resident=96K(1%) swapped_out=0K(0%) unallocated=8192K(99%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nSTACK GUARD                       56.0M        1 \nStack                             8176K        1 \nVM_ALLOCATE                         16K        1 \n__DATA                              27K        2 \n__DATA_CONST                        40K        2 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       606.2M        2 \n__TEXT                             536K        2 \n__TPRO_CONST                       272K        1 \npage table in kernel                96K        1 \n===========                     =======  ======= \nTOTAL                            671.2M       14 \n",
  "legacyInfo" : {
  "threadTriggered" : {

  }
},
  "logWritingSignature" : "cdf65dbfaa164fe0a8c5c658dae1c3e1da73ec7e",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6761d0c9df60af01adb250fb",
      "factorPackIds" : {

      },
      "deploymentId" : 240000001
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    }
  ],
  "experiments" : [

  ]
}
}


OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,9
      Model Number: Z1AH001Q3FN/A
      Chip: Apple M3 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 128 GB
      System Firmware Version: 11881.81.2
      OS Loader Version: 11881.81.2

Software:

    System Software Overview:

      System Version: macOS 15.3 (24D60)
      Kernel Version: Darwin 24.3.0
      Time since boot: 1 day, 1 hour, 11 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Thunderbolt Display:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 10 months ago

Cc: chimera-programmers added
Component: Unassigned → Third Party
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SBGrid install of 1.9 fails to launch; 1.8 works

Looks like 1.9 could not find Python

comment:2 by Greg Couch, 10 months ago

Resolution: → limitation
Status: assigned → closed

Please file a bug with sbgrid. We don't control how they install ChimeraX. And we don't have sbgrid for macOS, so we can't debug it.

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