Opened 3 years ago

Closed 3 years ago

#8671 closed defect (can't reproduce)

Crash in ctypes calling change_tracker_changed

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x00007ff859a0b680 (most recent call first):
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py", line 2128 in changed
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/changes.py", line 20 in check_for_changes
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 58 in draw_new_frame
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/6c/bnq9f2r17696s6077t1w4fzr0000gn/T/AppTranslocation/54105E0A-885C-41C8-B28C-8C2B4350E238/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2023-03-18 17:37:45.00 -0400","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 13.2.1 (22D68)","roots_installed":0,"incident_id":"23F79AEA-934F-4DE2-9603-A48298741AA1","name":"ChimeraX"}
{
  "uptime" : 3700,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro14,3",
  "coalitionID" : 1852,
  "osVersion" : {
    "train" : "macOS 13.2.1",
    "build" : "22D68",
    "releaseType" : "User"
  },
  "captureTime" : "2023-03-18 17:37:44.5735 -0400",
  "incident" : "23F79AEA-934F-4DE2-9603-A48298741AA1",
  "pid" : 5289,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-03-18 17:37:08.4055 -0400",
  "procStartAbsTime" : 3707635092575,
  "procExitAbsTime" : 3743781527713,
  "procName" : "ChimeraX",
  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3F956437-33EF-145B-5828-80A116D73BE4",
  "throttleTimeout" : 2147483647,
  "wakeTime" : 1519,
  "bridgeVersion" : {"build":"14Y910","train":"3.0"},
  "sleepWakeUUID" : "8CE0D3EA-3A03-4336-ABAB-E54CD68F6C69",
  "sip" : "enabled",
  "vmRegionInfo" : "0x119f677c0 is in 0x119f52000-0x119f86000;  bytes after start: 88000  bytes before end: 124991\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 119f0e000-119f52000    [  272K] r--\/rwx SM=COW  ...t_id=b09cd68f\n--->  mapped file                 119f52000-119f86000    [  208K] r-x\/rwx SM=COW  ...t_id=af4fa78f\n      mapped file                 119f86000-119f88000    [    8K] rw-\/rwx SM=COW  ...t_id=b0707c8f",
  "exception" : {"codes":"0x000000000000000a, 0x0000000119f677c0","rawCodes":[10,4730550208],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x0000000119f677c0"},
  "ktriageinfo" : "VM - Object has no pager\n",
  "vmregioninfo" : "0x119f677c0 is in 0x119f52000-0x119f86000;  bytes after start: 88000  bytes before end: 124991\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      mapped file                 119f0e000-119f52000    [  272K] r--\/rwx SM=COW  ...t_id=b09cd68f\n--->  mapped file                 119f52000-119f86000    [  208K] r-x\/rwx SM=COW  ...t_id=af4fa78f\n      mapped file                 119f86000-119f88000    [    8K] rw-\/rwx SM=COW  ...t_id=b0707c8f",
  "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":81499,"name":"CrBrowserMain","threadState":{"r13":{"value":140701961622928},"rax":{"value":0},"rflags":{"value":582},"cpu":{"value":0},"r14":{"value":10},"rsi":{"value":10},"r8":{"value":140320972300104},"cr2":{"value":140320972300104},"rdx":{"value":0},"r10":{"value":140704632321664,"symbolLocation":0,"symbol":"_main_thread"},"r9":{"value":11586699228194179465},"r15":{"value":22},"rbx":{"value":140704632321664,"symbolLocation":0,"symbol":"_main_thread"},"trap":{"value":133},"err":{"value":33554760},"r11":{"value":582},"rip":{"value":140703498330666,"matchesCrashFrame":1},"rbp":{"value":140320972298880},"rsp":{"value":140320972298840},"r12":{"value":259},"rcx":{"value":140320972298840},"flavor":"x86_THREAD_STATE","rdi":{"value":259}},"frames":[{"imageOffset":140703498330666,"imageIndex":0},{"imageOffset":140703497561216,"imageIndex":0},{"imageOffset":140703498734621,"imageIndex":0},{"imageOffset":0,"imageIndex":0},{"imageOffset":140701961622944,"imageIndex":0}]},{"id":81555,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4507558463,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81556,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4507558463,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81557,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4507558463,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81721,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4856895247,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81722,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4856895247,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81723,"frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4856895247,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81941,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":140703498341998,"imageIndex":0},{"imageOffset":5082999079,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082501805,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81942,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553965,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81943,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553821,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81944,"name":"Chrome_IOThread","frames":[{"imageOffset":140703498341998,"imageIndex":0},{"imageOffset":5082999079,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5064930210,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81945,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81946,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553965,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81947,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553965,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81948,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553965,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81949,"name":"CompositorTileWorker1","frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":5082762523,"imageIndex":0},{"imageOffset":5117159725,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81950,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81951,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":140703498341998,"imageIndex":0},{"imageOffset":5082999079,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81952,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81953,"name":"VizCompositorThread","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81966,"name":"NetworkService","frames":[{"imageOffset":140703498341998,"imageIndex":0},{"imageOffset":5082999079,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81967,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":81968,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082554061,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82061,"frames":[{"imageOffset":140703498542168,"imageIndex":0}]},{"id":82065,"name":"Thread (pooled)","frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4486642678,"imageIndex":0},{"imageOffset":4486641934,"imageIndex":0},{"imageOffset":4486641758,"imageIndex":0},{"imageOffset":4486618439,"imageIndex":0},{"imageOffset":4486600291,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82066,"name":"Thread (pooled)","frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4486642678,"imageIndex":0},{"imageOffset":4486641934,"imageIndex":0},{"imageOffset":4486641758,"imageIndex":0},{"imageOffset":4486618439,"imageIndex":0},{"imageOffset":4486600291,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82067,"name":"Thread (pooled)","frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4486642678,"imageIndex":0},{"imageOffset":4486641934,"imageIndex":0},{"imageOffset":4486641758,"imageIndex":0},{"imageOffset":4486618439,"imageIndex":0},{"imageOffset":4486600291,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82068,"name":"Thread (pooled)","frames":[{"imageOffset":140703498314010,"imageIndex":0},{"imageOffset":4486642678,"imageIndex":0},{"imageOffset":4486641934,"imageIndex":0},{"imageOffset":4486641758,"imageIndex":0},{"imageOffset":4486618439,"imageIndex":0},{"imageOffset":4486600291,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82085,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82091,"frames":[{"imageOffset":140703498542168,"imageIndex":0}]},{"id":82092,"frames":[{"imageOffset":140703498542168,"imageIndex":0}]},{"id":82097,"name":"com.apple.NSEventThread","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":140703499459774,"imageIndex":0},{"imageOffset":140703499454250,"imageIndex":0},{"imageOffset":140703499451232,"imageIndex":0},{"imageOffset":140703552606585,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82098,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554988,"imageIndex":0},{"imageOffset":5082553821,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82104,"name":"MemoryInfra","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082794991,"imageIndex":0},{"imageOffset":5081965001,"imageIndex":0},{"imageOffset":5082462812,"imageIndex":0},{"imageOffset":5082167704,"imageIndex":0},{"imageOffset":5082603192,"imageIndex":0},{"imageOffset":5082603594,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]},{"id":82105,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":140703498302914,"imageIndex":0},{"imageOffset":140703498360324,"imageIndex":0},{"imageOffset":140703498331701,"imageIndex":0},{"imageOffset":140703498303656,"imageIndex":0},{"imageOffset":5082795558,"imageIndex":0},{"imageOffset":5082552255,"imageIndex":0},{"imageOffset":5082554266,"imageIndex":0},{"imageOffset":5082553869,"imageIndex":0},{"imageOffset":5082765576,"imageIndex":0},{"imageOffset":140703498560089,"imageIndex":0},{"imageOffset":140703498542203,"imageIndex":0}]}],
  "usedImages" : [
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=182.4M resident=0K(0%) swapped_out_or_unallocated=182.4M(100%)\nWritable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG backing stores                 2528K        4 \nCG image                           104K        7 \nColorSync                          236K       27 \nCoreAnimation                       72K       10 \nCoreGraphics                        12K        2 \nCoreUI image data                 2640K       18 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                           563.9M      768 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            256K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        136K       34 \nStack                            175.3M       35 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      117.9M      112 \nVM_ALLOCATE (reserved)           128.0M        5         reserved VM address space (unallocated)\n__DATA                              11K        1 \n__DATA_CONST                        20K        1 \n__DATA_DIRTY                         7K        1 \n__LINKEDIT                       181.8M        1 \n__TEXT                             596K        1 \ndyld private memory                512K        3 \nmapped file                      537.4M      622 \nshared memory                     8664K       46 \n===========                     =======  ======= \nTOTAL                              2.0G     1720 \nTOTAL, minus reserved VM space     1.6G     1720 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "62b4513af75dc926494899c6",
      "factorPackIds" : {
        "COREOS_ICD" : "62fbe3cfa9a700130f60b3ea"
      },
      "deploymentId" : 240000019
    },
    {
      "rolloutId" : "60f8ddccefea4203d95cbeef",
      "factorPackIds" : {

      },
      "deploymentId" : 240000025
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jamisonlaw/Library/CloudStorage/OneDrive-
> TheOhioStateUniversity/OSBP/Bell/Data/Synchrotron/refmac8-KZ.pdb format pdb

refmac8-KZ.pdb title:  
Salmonella typhimurium LT2 At 2.12 A Re [more info...]  
  
Chain information for refmac8-KZ.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Non-standard residues in refmac8-KZ.pdb #1  
---  
MG — (MG)  
  


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

Log:
Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 499.40.2.0.0
      OS Loader Version: 564.40.4~66
      SMC Version (system): 2.45f5

Software:

    System Software Overview:

      System Version: macOS 13.2.1 (22D68)
      Kernel Version: Darwin 22.3.0
      Time since boot: 2 hours, 8 minutes

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal Support: Metal 3

    Radeon Pro 555:

      Chipset Model: Radeon Pro 555
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c7
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AP-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      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: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-GenomeTools: 0.9
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.1.9
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-OpenCommands: 1.0
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.1.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RIBFIND: 0.2
    ChimeraX-RMF: 0.13
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.1.70
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-StrudelScore: 0.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    SEQCROW: 1.6.1
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by pett, 3 years ago

Cc: Tom Goddard added
Component: UnassignedCore
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash in ctypes calling change_tracker_changed

comment:2 by pett, 3 years ago

Resolution: can't reproduce
Status: acceptedclosed
Note: See TracTickets for help on using tickets.