id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16284 Crash at startup chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. {""app_name"":""ChimeraX"",""timestamp"":""2024-11-10 22:07:49.00 -0600"",""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 14.7.1 (23H222)"",""roots_installed"":0,""incident_id"":""7FCE9470-5C92-4177-BD06-3E62E4784F19"",""name"":""ChimeraX""} { ""uptime"" : 12000, ""procRole"" : ""Unspecified"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookAir8,2"", ""coalitionID"" : 3306, ""osVersion"" : { ""train"" : ""macOS 14.7.1"", ""build"" : ""23H222"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-11-10 22:07:48.6736 -0600"", ""codeSigningMonitor"" : 0, ""incident"" : ""7FCE9470-5C92-4177-BD06-3E62E4784F19"", ""pid"" : 5497, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-11-10 22:06:34.9075 -0600"", ""procStartAbsTime"" : 12260879777852, ""procExitAbsTime"" : 12334643054174, ""procName"" : ""ChimeraX"", ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""C0D7A63A-9C81-90AD-EE62-AB86FCA0D1AA"", ""responsiblePid"" : 5452, ""codeSigningID"" : """", ""codeSigningTeamID"" : """", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 0, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 958, ""bridgeVersion"" : {""build"":""22P1072"",""train"":""9.1""}, ""sleepWakeUUID"" : ""DD9AF7CF-748B-494B-AD39-CB475BF657E1"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x10b2a5f30 is in 0x10b0d2000-0x10b33b000; bytes after start: 1916720 bytes before end: 610511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 10b00b000-10b02f000 [ 144K] r--\/rwx SM=COW Object_id=9d8ea50c\n GAP OF 0xa3000 BYTES\n---> mapped file 10b0d2000-10b33b000 [ 2468K] r-x\/rwx SM=COW Object_id=8d8763dc\n mapped file 10b33b000-10b375000 [ 232K] rw-\/rwx SM=COW Object_id=1c3a7c33"", ""exception"" : {""codes"":""0x000000000000000a, 0x000000010b2a5f30"",""rawCodes"":[10,4482293552],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGILL"",""subtype"":""KERN_MEMORY_ERROR at 0x000000010b2a5f30""}, ""termination"" : {""flags"":0,""code"":4,""namespace"":""SIGNAL"",""indicator"":""Illegal instruction: 4"",""byProc"":""ChimeraX"",""byPid"":5497}, ""ktriageinfo"" : ""VM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\nVM - (arg = 0x0) Object has no pager because the backing vnode was force unmounted\n"", ""vmregioninfo"" : ""0x10b2a5f30 is in 0x10b0d2000-0x10b33b000; bytes after start: 1916720 bytes 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""usedImages"" : [ { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 140703157587968, ""size"" : 25769803776, ""uuid"" : ""a7563e1d-7a04-3ed2-9587-044987205172"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=180.7M resident=0K(0%) swapped_out_or_unallocated=180.7M(100%)\nWritable regions: Total=647.2M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=647.2M(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nKernel Alloc Once 8K 1 \nMALLOC 574.0M 118 \nMALLOC guard page 16K 4 \nMALLOC_LARGE (reserved) 128K 1 reserved VM address space (unallocated)\nSTACK GUARD 4K 1 \nStack 8712K 2 \nStack Guard 56.0M 1 \nVM_ALLOCATE 64.6M 7 \n__DATA 11K 1 \n__DATA_CONST 22K 1 \n__DATA_DIRTY 7K 1 \n__LINKEDIT 180.1M 1 \n__TEXT 580K 1 \nmapped file 82.8M 138 \nshared memory 28K 4 \n=========== ======= ======= \nTOTAL 966.7M 282 \nTOTAL, minus reserved VM space 966.6M 282 \n"", ""legacyInfo"" : { ""threadTriggered"" : { } }, ""logWritingSignature"" : ""4357a0783fa9ca30971f5770660ede2fe5c35461"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 }, { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ { ""treatmentId"" : ""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.12 OpenGL renderer: Intel(R) UHD Graphics 617 OpenGL vendor: Intel Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir8,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0) OS Loader Version: 580.140.1~51 Software: System Software Overview: System Version: macOS 14.7.1 (23H222) Kernel Version: Darwin 23.6.0 Time since boot: 2 minutes, 34 seconds Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 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: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce all ChimeraX