Changes between Initial Version and Version 1 of Ticket #7580


Ignore:
Timestamp:
Sep 12, 2022, 11:45:16 AM (3 years ago)
Author:
Eric Pettersen
Comment:

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #7580

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

  • Ticket #7580 – Description

    initial v1  
    66Last time you used ChimeraX it crashed.
    77Please describe steps that led to the crash here.
     8
     9
     10{"app_name":"ChimeraX","timestamp":"2022-09-10 00:41:02.00 -0500","app_version":"","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"","platform":1,"share_with_app_devs":1,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.5.1 (21G83)","incident_id":"FE42EC72-6C17-40CA-9149-49B567102052","name":"ChimeraX"}
     11{
     12  "uptime" : 74000,
     13  "procLaunch" : "2022-09-09 16:12:34.8492 -0500",
     14  "procRole" : "Background",
     15  "version" : 2,
     16  "userID" : 501,
     17  "deployVersion" : 210,
     18  "modelCode" : "Mac14,7",
     19  "procStartAbsTime" : 1731831176546,
     20  "coalitionID" : 10852,
     21  "osVersion" : {
     22    "train" : "macOS 12.5.1",
     23    "build" : "21G83",
     24    "releaseType" : "User"
     25  },
     26  "captureTime" : "2022-09-10 00:41:01.4323 -0500",
     27  "incident" : "FE42EC72-6C17-40CA-9149-49B567102052",
     28  "bug_type" : "309",
     29  "pid" : 30238,
     30  "procExitAbsTime" : 1787678151908,
     31  "translated" : true,
     32  "cpuType" : "X86-64",
     33  "procName" : "ChimeraX",
     34  "procPath" : "\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
     35  "parentProc" : "launchd",
     36  "parentPid" : 1,
     37  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
     38  "crashReporterKey" : "BF073A52-2EA5-8CDC-A433-2403CAD974F2",
     39  "wakeTime" : 141,
     40  "sleepWakeUUID" : "308E59AB-ADF8-4E01-BA96-468CC0C62A90",
     41  "sip" : "enabled",
     42  "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",
     43  "isCorpse" : 1,
     44  "exception" : {"codes":"0x000000000000000a, 0x000000010d2dd1d0","rawCodes":[10,4516073936],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010d2dd1d0"},
     45  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":30238},
     46  "ktriageinfo" : "VM - Object is not alive\nVM - Object is not alive\nVM - Object is not alive\n",
     47  "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",
     48  "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},
     49  "faultingThread" : 0,
     50  "threads" : 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     69    "arch" : "x86_64",
     70    "base" : 140703378259968,
     71    "CFBundleShortVersionString" : "6.9",
     72    "CFBundleIdentifier" : "com.apple.CoreFoundation",
     73    "size" : 5246976,
     74    "uuid" : "32d2d187-4e52-376e-bc07-245a48c37e2b",
     75    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
     76    "name" : "CoreFoundation",
     77    "CFBundleVersion" : "1866"
     78  },
     79  {
     80    "source" : "P",
     81    "arch" : "x86_64",
     82    "base" : 8666054656,
     83    "size" : 442368,
     84    "uuid" : "f71fb3ca-5fcc-3577-9457-b047888a46d1",
     85    "path" : "\/usr\/lib\/dyld",
     86    "name" : "dyld"
     87  },
     88  {
     89    "source" : "P",
     90    "arch" : "arm64",
     91    "base" : 140703125880832,
     92    "size" : 196608,
     93    "uuid" : "ef33add1-6b70-3cc9-8bbc-c8544b609d2b",
     94    "path" : "\/usr\/libexec\/rosetta\/runtime",
     95    "name" : "runtime"
     96  },
     97  {
     98    "source" : "P",
     99    "arch" : "x86_64",
     100    "base" : 140703377715200,
     101    "size" : 229376,
     102    "uuid" : "792406fe-2224-3c14-ba9f-f076fd7839d2",
     103    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
     104    "name" : "libsystem_kernel.dylib"
     105  },
     106  {
     107    "source" : "P",
     108    "arch" : "x86_64",
     109    "base" : 140703377944576,
     110    "size" : 49152,
     111    "uuid" : "f32b6d06-b156-3da0-b086-a31cf011362b",
     112    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
     113    "name" : "libsystem_pthread.dylib"
     114  }
     115],
     116  "sharedCache" : {
     117  "base" : 140703374688256,
     118  "size" : 19331678208,
     119  "uuid" : "f3387257-f96f-3907-b94c-1d7f0ebef98b"
     120},
     121  "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",
     122  "legacyInfo" : {
     123  "threadTriggered" : {
     124    "name" : "CrBrowserMain",
     125    "queue" : "com.apple.main-thread"
     126  }
     127},
     128  "trialInfo" : {
     129  "rollouts" : [
     130    {
     131      "rolloutId" : "5fc94383418129005b4e9ae0",
     132      "factorPackIds" : {
     133
     134      },
     135      "deploymentId" : 240000454
     136    },
     137    {
     138      "rolloutId" : "5ffde50ce2aacd000d47a95f",
     139      "factorPackIds" : {
     140
     141      },
     142      "deploymentId" : 240000198
     143    }
     144  ],
     145  "experiments" : [
     146
     147  ]
     148}
     149}
     150===== Log before crash start =====
     151UCSF ChimeraX version: 1.5.dev202209082348 (2022-09-08) 
     152© 2016-2022 Regents of the University of California. All rights reserved. 
     153How to cite UCSF ChimeraX 
     154
     155
     156===== Log before crash end =====
     157
     158Log:
     159UCSF ChimeraX version: 1.5.dev202209082348 (2022-09-08) 
     160© 2016-2022 Regents of the University of California. All rights reserved. 
     161How to cite UCSF ChimeraX 
     162
     163
     164
     165
     166OpenGL version: 4.1 Metal - 76.3
     167OpenGL renderer: Apple M2
     168OpenGL vendor: Apple
     169
     170Python: 3.9.11
     171Locale: UTF-8
     172Qt version: PyQt6 6.3.1, Qt 6.3.1
     173Qt runtime version: 6.3.1
     174Qt platform: cocoa
     175Hardware:
     176
     177    Hardware Overview:
     178
     179      Model Name: MacBook Pro
     180      Model Identifier: Mac14,7
     181      Chip: Apple M2
     182      Total Number of Cores: 8 (4 performance and 4 efficiency)
     183      Memory: 8 GB
     184      System Firmware Version: 7459.141.1
     185      OS Loader Version: 7459.141.1
     186
     187Software:
     188
     189    System Software Overview:
     190
     191      System Version: macOS 12.5.1 (21G83)
     192      Kernel Version: Darwin 21.6.0
     193      Time since boot: 2 days 9:44
     194
     195Graphics/Displays:
     196
     197    Apple M2:
     198
     199      Chipset Model: Apple M2
     200      Type: GPU
     201      Bus: Built-In
     202      Total Number of Cores: 10
     203      Vendor: Apple (0x106b)
     204      Metal Family: Supported, Metal GPUFamily Apple 7
     205      Displays:
     206        Color LCD:
     207          Display Type: Built-In Retina LCD
     208          Resolution: 2560 x 1600 Retina
     209          Main Display: Yes
     210          Mirror: Off
     211          Online: Yes
     212          Automatically Adjust Brightness: Yes
     213          Connection Type: Internal
     214
     215
     216Installed Packages:
     217    alabaster: 0.7.12
     218    appdirs: 1.4.4
     219    appnope: 0.1.3
     220    asttokens: 2.0.8
     221    Babel: 2.10.3
     222    backcall: 0.2.0
     223    blockdiag: 3.0.0
     224    build: 0.8.0
     225    certifi: 2021.10.8
     226    cftime: 1.6.1
     227    charset-normalizer: 2.1.1
     228    ChimeraX-AddCharge: 1.4
     229    ChimeraX-AddH: 2.2
     230    ChimeraX-AlignmentAlgorithms: 2.0
     231    ChimeraX-AlignmentHdrs: 3.2.1
     232    ChimeraX-AlignmentMatrices: 2.0
     233    ChimeraX-Alignments: 2.6
     234    ChimeraX-AlphaFold: 1.0
     235    ChimeraX-AltlocExplorer: 1.0.3
     236    ChimeraX-AmberInfo: 1.0
     237    ChimeraX-Arrays: 1.0
     238    ChimeraX-Atomic: 1.41.2
     239    ChimeraX-AtomicLibrary: 7.0.3
     240    ChimeraX-AtomSearch: 2.0.1
     241    ChimeraX-AxesPlanes: 2.3
     242    ChimeraX-BasicActions: 1.1.2
     243    ChimeraX-BILD: 1.0
     244    ChimeraX-BlastProtein: 2.1.2
     245    ChimeraX-BondRot: 2.0.1
     246    ChimeraX-BugReporter: 1.0.1
     247    ChimeraX-BuildStructure: 2.7.1
     248    ChimeraX-Bumps: 1.0
     249    ChimeraX-BundleBuilder: 1.2
     250    ChimeraX-ButtonPanel: 1.0.1
     251    ChimeraX-CageBuilder: 1.0.1
     252    ChimeraX-CellPack: 1.0
     253    ChimeraX-Centroids: 1.3.1
     254    ChimeraX-ChangeChains: 1.0
     255    ChimeraX-CheckWaters: 1.1.1
     256    ChimeraX-ChemGroup: 2.0
     257    ChimeraX-Clashes: 2.2.4
     258    ChimeraX-ColorActions: 1.0.1
     259    ChimeraX-ColorGlobe: 1.0
     260    ChimeraX-ColorKey: 1.5.2
     261    ChimeraX-CommandLine: 1.2.4
     262    ChimeraX-ConnectStructure: 2.0.1
     263    ChimeraX-Contacts: 1.0.1
     264    ChimeraX-Core: 1.5.dev202209082348
     265    ChimeraX-CoreFormats: 1.1
     266    ChimeraX-coulombic: 1.3.2
     267    ChimeraX-Crosslinks: 1.0
     268    ChimeraX-Crystal: 1.0
     269    ChimeraX-CrystalContacts: 1.0.1
     270    ChimeraX-DataFormats: 1.2.2
     271    ChimeraX-Dicom: 1.1
     272    ChimeraX-DistMonitor: 1.3
     273    ChimeraX-DockPrep: 1.0
     274    ChimeraX-Dssp: 2.0
     275    ChimeraX-EMDB-SFF: 1.0
     276    ChimeraX-ExperimentalCommands: 1.0
     277    ChimeraX-FileHistory: 1.0.1
     278    ChimeraX-FunctionKey: 1.0.1
     279    ChimeraX-Geometry: 1.2
     280    ChimeraX-gltf: 1.0
     281    ChimeraX-Graphics: 1.1
     282    ChimeraX-Hbonds: 2.4
     283    ChimeraX-Help: 1.2.1
     284    ChimeraX-HKCage: 1.3
     285    ChimeraX-IHM: 1.1
     286    ChimeraX-ImageFormats: 1.2
     287    ChimeraX-IMOD: 1.0
     288    ChimeraX-IO: 1.0.1
     289    ChimeraX-ItemsInspection: 1.0.1
     290    ChimeraX-Label: 1.1.6
     291    ChimeraX-ListInfo: 1.1.1
     292    ChimeraX-Log: 1.1.5
     293    ChimeraX-LookingGlass: 1.1
     294    ChimeraX-Maestro: 1.8.1
     295    ChimeraX-Map: 1.1.1
     296    ChimeraX-MapData: 2.0
     297    ChimeraX-MapEraser: 1.0.1
     298    ChimeraX-MapFilter: 2.0
     299    ChimeraX-MapFit: 2.0
     300    ChimeraX-MapSeries: 2.1.1
     301    ChimeraX-Markers: 1.0.1
     302    ChimeraX-Mask: 1.0.1
     303    ChimeraX-MatchMaker: 2.0.6
     304    ChimeraX-MDcrds: 2.6
     305    ChimeraX-MedicalToolbar: 1.0.2
     306    ChimeraX-Meeting: 1.0.1
     307    ChimeraX-MLP: 1.1
     308    ChimeraX-mmCIF: 2.7
     309    ChimeraX-MMTF: 2.1
     310    ChimeraX-Modeller: 1.5.6
     311    ChimeraX-ModelPanel: 1.3.6
     312    ChimeraX-ModelSeries: 1.0.1
     313    ChimeraX-Mol2: 2.0
     314    ChimeraX-Mole: 1.0
     315    ChimeraX-Morph: 1.0
     316    ChimeraX-MouseModes: 1.1.1
     317    ChimeraX-Movie: 1.0
     318    ChimeraX-Neuron: 1.0
     319    ChimeraX-Nucleotides: 2.0.3
     320    ChimeraX-OpenCommand: 1.9.1
     321    ChimeraX-PDB: 2.6.7
     322    ChimeraX-PDBBio: 1.0
     323    ChimeraX-PDBLibrary: 1.0.2
     324    ChimeraX-PDBMatrices: 1.0
     325    ChimeraX-PickBlobs: 1.0.1
     326    ChimeraX-Positions: 1.0
     327    ChimeraX-PresetMgr: 1.1
     328    ChimeraX-PubChem: 2.1
     329    ChimeraX-ReadPbonds: 1.0.1
     330    ChimeraX-Registration: 1.1.1
     331    ChimeraX-RemoteControl: 1.0
     332    ChimeraX-RenumberResidues: 1.1
     333    ChimeraX-ResidueFit: 1.0.1
     334    ChimeraX-RestServer: 1.1
     335    ChimeraX-RNALayout: 1.0
     336    ChimeraX-RotamerLibMgr: 2.0.1
     337    ChimeraX-RotamerLibsDunbrack: 2.0
     338    ChimeraX-RotamerLibsDynameomics: 2.0
     339    ChimeraX-RotamerLibsRichardson: 2.0
     340    ChimeraX-SaveCommand: 1.5.1
     341    ChimeraX-SchemeMgr: 1.0
     342    ChimeraX-SDF: 2.0
     343    ChimeraX-Segger: 1.0
     344    ChimeraX-Segment: 1.0
     345    ChimeraX-SelInspector: 1.0
     346    ChimeraX-SeqView: 2.7.2
     347    ChimeraX-Shape: 1.0.1
     348    ChimeraX-Shell: 1.0.1
     349    ChimeraX-Shortcuts: 1.1.1
     350    ChimeraX-ShowSequences: 1.0.1
     351    ChimeraX-SideView: 1.0.1
     352    ChimeraX-Smiles: 2.1
     353    ChimeraX-SmoothLines: 1.0
     354    ChimeraX-SpaceNavigator: 1.0
     355    ChimeraX-StdCommands: 1.9
     356    ChimeraX-STL: 1.0
     357    ChimeraX-Storm: 1.0
     358    ChimeraX-StructMeasure: 1.1
     359    ChimeraX-Struts: 1.0.1
     360    ChimeraX-Surface: 1.0
     361    ChimeraX-SwapAA: 2.0.1
     362    ChimeraX-SwapRes: 2.1.3
     363    ChimeraX-TapeMeasure: 1.0
     364    ChimeraX-Test: 1.0
     365    ChimeraX-Toolbar: 1.1.2
     366    ChimeraX-ToolshedUtils: 1.2.1
     367    ChimeraX-Tug: 1.0.1
     368    ChimeraX-UI: 1.24
     369    ChimeraX-uniprot: 2.2.1
     370    ChimeraX-UnitCell: 1.0.1
     371    ChimeraX-ViewDockX: 1.1.3
     372    ChimeraX-VIPERdb: 1.0
     373    ChimeraX-Vive: 1.1
     374    ChimeraX-VolumeMenu: 1.0.1
     375    ChimeraX-VTK: 1.0
     376    ChimeraX-WavefrontOBJ: 1.0
     377    ChimeraX-WebCam: 1.0.1
     378    ChimeraX-WebServices: 1.1.0
     379    ChimeraX-Zone: 1.0.1
     380    colorama: 0.4.5
     381    cxservices: 1.2
     382    cycler: 0.11.0
     383    Cython: 0.29.32
     384    debugpy: 1.6.3
     385    decorator: 5.1.1
     386    docutils: 0.19
     387    entrypoints: 0.4
     388    executing: 1.0.0
     389    filelock: 3.7.1
     390    fonttools: 4.37.1
     391    funcparserlib: 1.0.0
     392    grako: 3.16.5
     393    h5py: 3.7.0
     394    html2text: 2020.1.16
     395    idna: 3.3
     396    ihm: 0.33
     397    imagecodecs: 2022.2.22
     398    imagesize: 1.4.1
     399    importlib-metadata: 4.12.0
     400    ipykernel: 6.15.1
     401    ipython: 8.4.0
     402    ipython-genutils: 0.2.0
     403    jedi: 0.18.1
     404    Jinja2: 3.1.2
     405    jupyter-client: 7.3.4
     406    jupyter-core: 4.11.1
     407    kiwisolver: 1.4.4
     408    line-profiler: 3.5.1
     409    lxml: 4.9.1
     410    lz4: 4.0.2
     411    MarkupSafe: 2.1.1
     412    matplotlib: 3.5.2
     413    matplotlib-inline: 0.1.6
     414    msgpack: 1.0.4
     415    nest-asyncio: 1.5.5
     416    netCDF4: 1.6.0
     417    networkx: 2.8.5
     418    numexpr: 2.8.3
     419    numpy: 1.23.1
     420    openvr: 1.23.701
     421    packaging: 21.3
     422    ParmEd: 3.4.3
     423    parso: 0.8.3
     424    pep517: 0.13.0
     425    pexpect: 4.8.0
     426    pickleshare: 0.7.5
     427    Pillow: 9.2.0
     428    pip: 22.2.2
     429    pkginfo: 1.8.3
     430    prompt-toolkit: 3.0.31
     431    psutil: 5.9.1
     432    ptyprocess: 0.7.0
     433    pure-eval: 0.2.2
     434    pycollada: 0.7.2
     435    pydicom: 2.3.0
     436    Pygments: 2.12.0
     437    PyOpenGL: 3.1.5
     438    PyOpenGL-accelerate: 3.1.5
     439    pyparsing: 3.0.9
     440    PyQt6-commercial: 6.3.1
     441    PyQt6-Qt6: 6.3.1
     442    PyQt6-sip: 13.4.0
     443    PyQt6-WebEngine-commercial: 6.3.1
     444    PyQt6-WebEngine-Qt6: 6.3.1
     445    python-dateutil: 2.8.2
     446    pytz: 2022.2.1
     447    pyzmq: 23.2.1
     448    qtconsole: 5.3.1
     449    QtPy: 2.2.0
     450    RandomWords: 0.4.0
     451    requests: 2.28.1
     452    scipy: 1.9.0
     453    setuptools: 65.1.1
     454    sfftk-rw: 0.7.2
     455    six: 1.16.0
     456    snowballstemmer: 2.2.0
     457    sortedcontainers: 2.4.0
     458    Sphinx: 5.1.1
     459    sphinx-autodoc-typehints: 1.19.1
     460    sphinxcontrib-applehelp: 1.0.2
     461    sphinxcontrib-blockdiag: 3.0.0
     462    sphinxcontrib-devhelp: 1.0.2
     463    sphinxcontrib-htmlhelp: 2.0.0
     464    sphinxcontrib-jsmath: 1.0.1
     465    sphinxcontrib-qthelp: 1.0.3
     466    sphinxcontrib-serializinghtml: 1.1.5
     467    stack-data: 0.5.0
     468    tables: 3.7.0
     469    tifffile: 2022.7.31
     470    tinyarray: 1.2.4
     471    tomli: 2.0.1
     472    tornado: 6.2
     473    traitlets: 5.3.0
     474    urllib3: 1.26.12
     475    wcwidth: 0.2.5
     476    webcolors: 1.12
     477    wheel: 0.37.1
     478    wheel-filename: 1.4.1
     479    zipp: 3.8.1
     480
     481}}}