Mac display configuration crash unplugging external monitor

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.8.dev202404300104 (2024-04-30 01:04:30 UTC)
Description
Last time you used ChimeraX it crashed.

Had external 4k display connected (usbc to hdmi cable) and laptop screen open, mirroring off, started ChimeraX April 30 daily build on laptop (primary) display, opened PDB 8j0s, dragged ChimeraX to external display, and pulled out usbc display cable and ChimeraX immediately crashed.
Fatal Python error: Segmentation fault

Thread 0x000070001ee06000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001de03000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001ce00000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001bdfd000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000070001adfa000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700019df7000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700018df4000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700017df1000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700016dee000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700015deb000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700014de8000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700013de5000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700012de2000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700011ddf000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000700010ddc000 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007ff849392100 (most recent call first):
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/Users/goddard/Desktop/ChimeraX April 30 2024.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath (total: 55)


{"app_name":"ChimeraX","timestamp":"2024-05-22 11:35:09.00 -0700","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"65F6A445-5A74-4E38-89AA-D551B8EAD7FF"}
{
  "uptime" : 610,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 503,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,1",
  "coalitionID" : 938,
  "osVersion" : {
    "train" : "macOS 14.4.1",
    "build" : "23E224",
    "releaseType" : "User"
  },
  "captureTime" : "2024-05-22 11:35:06.7739 -0700",
  "codeSigningMonitor" : 0,
  "incident" : "65F6A445-5A74-4E38-89AA-D551B8EAD7FF",
  "pid" : 744,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-05-22 11:27:49.3106 -0700",
  "procStartAbsTime" : 180055530559,
  "procExitAbsTime" : 617517430172,
  "procName" : "ChimeraX",
  "procPath" : "\/Users\/USER\/Desktop\/ChimeraX April 30 2024.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"49BE9650-B1E3-50F9-9004-12B1A5562D22","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "CB271660-942B-10C8-0F10-6B527246D68B",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bridgeVersion" : {"build":"21P4222","train":"8.4"},
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4491563008\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10bb7d000-10bb81000    [   16K] r-x\/r-x SM=COW  \/Users\/USER\/Desktop\/ChimeraX April 30 2024.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":744},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4491563008\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10bb7d000-10bb81000    [   16K] r-x\/r-x SM=COW  \/Users\/USER\/Desktop\/ChimeraX April 30 2024.app\/Contents\/MacOS\/ChimeraX",
  "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" : 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    "name" : "libsystem_pthread.dylib"
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    "arch" : "x86_64",
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    "size" : 557048,
    "uuid" : "6d02e870-f215-36ed-bf7d-435f66996bfe",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703227756544,
    "size" : 45048,
    "uuid" : "56a3704c-42f6-3fb2-b45c-5371848c9400",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703318614016,
    "CFBundleShortVersionString" : "1.600.0",
    "CFBundleIdentifier" : "com.apple.SkyLight",
    "size" : 4591609,
    "uuid" : "d0094308-9053-3411-906d-4a914a79a432",
    "path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
    "name" : "SkyLight"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703225860096,
    "size" : 290802,
    "uuid" : "85907582-b9ae-3a02-baca-2da374c6fbac",
    "path" : "\/usr\/lib\/system\/libdispatch.dylib",
    "name" : "libdispatch.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64h",
    "base" : 140703227977728,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4829165,
    "uuid" : "2780e326-c5fd-3a12-b906-b9449288005c",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "2420"
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    "arch" : "x86_64",
    "base" : 140703406616576,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 2732028,
    "uuid" : "5d06c99c-ac78-3bc4-8908-45a394e8180b",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703285268480,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 21159926,
    "uuid" : "4905ef83-f061-3c82-bc30-70a4def63eee",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2487.50.124"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703223836672,
    "size" : 592736,
    "uuid" : "899f1e34-b624-3162-8003-04daa6829461",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703226720256,
    "size" : 503796,
    "uuid" : "1ada3159-e0b9-3850-9d06-ed79891009e8",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
  }
],
  "sharedCache" : {
  "base" : 140703223140352,
  "size" : 25769803776,
  "uuid" : "59b61d18-2d12-3a06-a536-f0b08e953ca2"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG image                           168K       10 \nColorSync                          248K       30 \nCoreAnimation                      404K       50 \nCoreGraphics                        16K        3 \nCoreUI image data                 3600K       27 \nFoundation                          32K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.7G      107 \nMALLOC guard page                   96K       24 \nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        240K       60 \nStack                            413.5M       61 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      195.0M      166 \nVM_ALLOCATE (reserved)            64.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            45.4M      790 \n__DATA_CONST                      65.3M      460 \n__DATA_DIRTY                      1842K      230 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       211.7M      153 \n__OBJC_RO                         71.7M        1 \n__OBJC_RW                         2196K        2 \n__TEXT                             1.0G      797 \ndyld private memory                292K        3 \nmapped file                      204.6M       56 \nshared memory                     2992K       29 \n===========                     =======  ======= \nTOTAL                              5.1G     3081 \nTOTAL, minus reserved VM space     5.0G     3081 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "0d55d7cc7e1201a304b3671cd1b34d5984140fec",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "652eff3d1bce5442b8d753c9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000009
    },
    {
      "rolloutId" : "648a2601f74c42732876cb5b",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "663189ed2a3d926e3b50f166"
      },
      "deploymentId" : 240000171
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "2dffbe18-a39a-4f33-ada9-2cce30af39ca",
      "experimentId" : "6384d56b96e8d228551ec182",
      "deploymentId" : 400000032
    }
  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202404300104 (2024-04-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

> open 8j0s

Summary of feedback from opening 8j0s fetched from pdb  
---  
notes | Fetching compressed mmCIF 8j0s from http://files.rcsb.org/download/8j0s.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
8j0s title:  
Cryo-EM structure of Mycobacterium tuberculosis ATP synthase in complex with
bedaquiline(BDQ) [more info...]  
  
Chain information for 8j0s #1  
---  
Chain | Description | UniProt  
1 2 3 4 5 6 7 8 9 | ATP synthase subunit c | A0A045H4W8_MYCTX 1-81  
A B C | ATP synthase subunit alpha | ATPA_MYCTU 1-549  
D E F | ATP synthase subunit beta | ATPB_MYCTU 1-486  
G | ATP synthase gamma chain | ATPG_MYCTU 1-305  
H | ATP synthase epsilon chain | ATPE_MYCTU 1-121  
a | ATP synthase subunit a | A0A045J1C5_MYCTX 1-250  
b | ATP synthase subunit b | A0A045H294_MYCTX 1-171  
d | Multifunctional fusion protein | A0A045JVE3_MYCTX 1-446  
  
Non-standard residues in 8j0s #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
BQ1 — Bedaquiline  
MG — magnesium ion  
  


===== Log before crash end =====

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8.dev202404300104 (2024-04-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: MacBookPro15,1
      Processor Name: 6-Core Intel Core i9
      Processor Speed: 2.9 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
      OS Loader Version: 580~1678

Software:

    System Software Overview:

      System Version: macOS 14.4.1 (23E224)
      Kernel Version: Darwin 23.4.0
      Time since boot: 11 minutes, 37 seconds

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      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


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    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: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.4
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    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: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202404300104
    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
    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: 1.1.9
    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
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    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: 1.0.3
    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: 1.16.3
    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: 1.38
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.1.3
    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: 4.51.0
    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: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    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: 4.2.1
    prompt-toolkit: 3.0.43
    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: 26.0.2
    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
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

[Tom Goddard]

The same crash happens when plugging in the external display, ticket #15278.

[Tom Goddard]

Surprisingly the crash does not happen if no model is opened and only the file history thumbnails are shown.

[Tom Goddard]

If no model is open but the graphics pane is shown instead of the file history then it does crash. So the crash is possibly related to redrawing the graphics on the new screen.

[Tom Goddard]

If I comment out the view.draw() in the update loop so the graphics is never drawn then it does not crash.

If I leave drawing enabled but set the maximum frame rate to 1 frame/second then it does not crash.

It seems like the crash may be caused by attempting to draw the graphics too soon when either the Qt window or screen has not been properly updated.

[Tom Goddard]

ChimeraX 1.7.1 does not crash when drawing at full frame rate and unplugging display while ChimeraX is on external display.

My guess is this is a Qt bug where ChimeraX tries to draw but the Qt window or screen is in an inconsistent state.

[Tom Goddard]

Same crash happens in May 21, 2024 ChimeraX 1.8 release candidate.

[Tom Goddard]

Qt bug 84741 seems related, although it says it was fixed a few years ago.

​https://bugreports.qt.io/browse/QTBUG-84741

Here's another bug report that seems to be the same crash, claimed fixed in Qt 5.14

​https://github.com/keepassxreboot/keepassxc/issues/3810

I found these and other similar crash reports googling for Qt displayConfigFinalizedProc

[Tom Goddard]

Qt bug 84741 has a better traceback that shows displayConfigFinalizedProc() is from the Mac Skylight package and that it ends up calling Qt QCocoaScreen::updateScreens(). That might be allowing a timer event to go off and our rendering then crashes.

[Tom Goddard]

I tried adding to the ChimeraX QApplication screenAdded and screenRemoved signal handlers and in those handlers block redrawing. That prevents the crash. Restarting the blocked drawing after a second avoided the crash in 5 out of 6 tries, but did crash once. Blocking for 2 seconds avoided the crash in about 5 out of 5 tries.

[Tom Goddard]

Fixed in daily build and ChimeraX 1.8 release candidate.

Worked around Qt 6.6 bug where graphics rendering timer gets called when a screen is added or removed on Mac causing a crash probably because of inconsistent Qt QScreen state.

I was only able to reproduce this bug on an old Intel MacBook Pro laptop with AMD graphics. When we switch to Qt 6.7 might be worth testing again to see if the work-around can be removed.

[Tom Goddard]

Unfortunately the work-around does not fix it in all cases, for example #15639.

Testing the 1.8 release candidate and 1.9 daily build from June 3, 2024, on the Intel iMac on my office desk it crashes when ChimeraX is simply started on the iMac display and the external display is unplugged. Surprisingly it does not crash if I first move ChimeraX to the external display and unplug and replug and unplug and replug. Maybe if it is on the main display ChimeraX is not getting the add/remove screen Qt notifications.

If I open ChimeraX 1.9 daily with no external display, hide file history so black graphics pane shown, the plug in external monitor, wait for it to connect, no crash, then unplug external monitor and ChimeraX crashes immediately. If I do not hide the file history then these steps do not cause a crash. So it seems the cause is still that the ChimeraX is drawing the graphics. Putting in a print statement shows it is still getting the add and remove screen callbacks with file history shown, and gets the add screen when file history is hidden. It seems to crash before when history is hidden before the remove screen message is logged.

If I hide file history but block redraw in the shell (session.update_loop.block_redraw()) then no crash unplugging display. Now my guess is that the screen removed callback is too late and a redraw happening before the screen remove is issued causes the crash. If I block for 100 seconds it still crashes. So it does seem that the crash happens before the remove screen callback is received.

Surprisingly logging the screen remove to a file shows that ChimeraX does get the screen remove callback before the crash. So why does it not crash if I block redraw before unplugging but it does crash if only the remove screen callback blocks redraw? It must be that a redraw occurs before the screen removed callback but it doesn't crash until later after the screen removed callback. In other words the crash is set up before the callback but happens after the callback.

It appears that the crash is caused by running the graphics update loop before the screen remove callback. It still crashed even if it never drew the graphics as long as it ran the update loop (new frame callback, ...). That is why blocking update avoids the crash because the update loop is not run. Writing log messages to a file shows that the update loop is not called after the remove screen callback when it crashes. So somehow the update loop just before the screen removed callback causes the crash. I included the number of screens in the logged update loop output and the last log entry before the screen remove log entry shows it still thinks it has two screens. So even if I determine what Qt calls in the update loop are leading to the crash it doesn't look like I will have any way of knowing that the screen remove is in process and will cause a crash.

This theory is wrong. If I just comment out view.draw() in the update loop then there is no crash.

Need to investigate more.

[Tom Goddard]

The exact same steps in the previous comment do not crash ChimeraX on a Mac M1 laptop and Samsung external display. I suspect this crash is almost always with Intel Macs and AMD graphics and is caused by the flaky Apple Intel and AMD OpenGL drivers.

[Tom Goddard]

Further testing shows that if after the screen is added any graphics draw is done at any time before the screen is removed then it crashes. Blocking redraw only fixes the crash if it is done early enough so that no graphics is drawn after the screen is added.

[Tom Goddard]

Curiously if the external screen is already connected and then ChimeraX is started on the iMac display, the file history is hidden, and the external screen is unplugged, then it does not crash. So maybe the key ingredients are that chimerax is running while a screen is plugged in and then a subsequent draw primes it to crash when the screen is later removed. So maybe the time to handle the problem is when the screen is added.

[Tom Goddard]

If I show file history before unplugging the display it does not crash. But then if I plug the display back in, show a molecule, then show file history and unplug then it crashes. Tried this a couple times, crashed after the second add/remove display even with file history shown. I also tried iconifying before unplugging display the first time and it crashed immediately.

My guess is that adding the display somehow corrupts Qt's QScreen data structure which then usually results in a crash when the display is removed.

[Tom Goddard]

Since the status line is also rendered with OpenGL, having it shown may also cause the crash. Should try tests where file history shown and status line is hidden. Crashed with status bar hidden (ui statusbar false) and file history shown.

[Tom Goddard]

A couple more ideas about how to work around this problem. Maybe after a display is added on Intel Mac recreate the main window opengl context. Another idea is to simply show a warning dialog when the display is added on an Intel Mac saying due to a Qt 6.6 window toolkit bug ChimeraX is likely to crash when a display is connected while it is running and then later disconnected. We suggest you finish your ChimeraX work before unplugging the external display.

[Tom Goddard]

When I deleted the opengl context after adding a new display (session.main_view.render.opengl_context.delete() in the Python shell) it crashed when the display was removed. So that does not look like a way to work around the crash.

[Tom Goddard]

It seems like the status line which uses the same opengl context and Qt code to render would cause the same crashes removing an external display after rendering to the status line. But tests show it does not. What is special about the main graphics? It uses shaders and off-screen framebuffers but I'm not sure any of those are made if no models are opened. Even if they are that is all done through PyOpenGL so I would not expect it to change Qt behavior.

[Tom Goddard]

I tested ChimeraX 1.7 (Qt 6.3) and it does not crash adding and removing a display with the exact recipe as above. So it certainly seems like a Qt 6.6 issue.

[Tom Goddard]

What if I resize the graphics window after adding the screen, maybe that will fix whatever bad data structure results from adding the screen. Still crashes.

[Tom Goddard]

None of the stack traces show where it crashes 10 stack frames below
displayConfigFinalizedProc. The bug reports mentioned in comment 8 show it in libqcocoa.dylib. And our crashes show it getting segmentation violation dereferencing a null pointer.

[Tom Goddard]

If I comment out the swap_buffers() call it still crashes. If I just return from view.draw() it does not crash, but that probably never calls make_current() and the context may never be created. If I return in view.draw() after making the context current, it still does not crash. If I just comment out the model rendering but draw background, set render size and do swap buffers it crashes. If I only draw background but no set render size or swap then it does not crash. If I just draw background and swap and done current and redraw needed false it crashes. If I draw background and swap but no done current and no redraw needed false, no crash. With background, swap and redraw needed false no crash. With just make_current() and done_current() and nothing else it crashes. And with just make_current() it does not crash.

So the QOpenGLContext.doneCurrent() call is key to making the crash happen.

If I comment out just the done current call in view.draw() then rendering works and there is no crash plugging and unplugging the external display. That call is just a safety measure to assure that Qt does not accidentally render to our ChimeraX graphics OpenGL context since it renders its widgets with its own OpenGL context. I think ChimeraX did not have that done current call for many years and I just added it for safety. So it could be disabled for Intel Mac after when an add screen is done. It is possible that this will lead to other problems though.

[Tom Goddard]

Fixed in 1.8 and daily build.

I made the add screen callback disable graphics rendering calling QOpenGLContext.doneCurrent() on Mac Intel machines to avoid the crash from connecting and disconnecting an external display.

This change is a bit risky for 1.8 which we hope to release next week, but is probably necessary to avert 50 crash reports in 1.8 during its lifetime. The OpenGL done current call is a safety measure to make sure Qt does not accidentally use our OpenGL context when rendering its widgets.

While this work-around fixed the reproducible crash described in this ticket, I have my doubts that it will fix all these Mac external display crashes. The crashes seem to be new to Qt 6.6 and hopefully the bug will be fixed in a Qt 6.7 or a later Qt release.

[Tom Goddard]

There were about 50 reports of this crash in ChimeraX 1.8 but tickets #16083 and #15982 suggest that the problem is fixed in the ChimeraX 1.9 daily builds.