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Opened 8 months ago
Closed 8 months ago
#16850 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405150316 (2024-05-15 03:16:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
I connected to a monitor via HDMI
Fatal Python error: Segmentation fault
Thread 0x00000002a0fd7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029ffcb000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029efbf000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029dfb3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029cfa7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029bf9b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029af8f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000299f83000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000298f77000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000297f6b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000296f5f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001fbabe100 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
File "/Applications/ChimeraX_Daily.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, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.graphics._graphics (total: 54)
{"app_name":"ChimeraX","timestamp":"2025-02-13 10:21:01.00 +0000","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.7.1 (22H221)","roots_installed":0,"name":"ChimeraX","incident_id":"99375DBB-EC61-470B-B9AD-76EBF395EF42"}
{
"uptime" : 1500000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 29421,
"osVersion" : {
"train" : "macOS 13.7.1",
"build" : "22H221",
"releaseType" : "User"
},
"captureTime" : "2025-02-13 10:20:55.8639 +0000",
"incident" : "99375DBB-EC61-470B-B9AD-76EBF395EF42",
"pid" : 49407,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-13 09:57:58.0006 +0000",
"procStartAbsTime" : 38245588971524,
"procExitAbsTime" : 38278639670861,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5FCA6CCB-C7C6-55AA-BEE5-FD6D1213EF9E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "180EB434-0C60-593C-0A31-80FDEEC5BE98",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3824,
"sleepWakeUUID" : "E92D91E2-862B-44D7-BE91-2E1BF6957ED2",
"sip" : "enabled",
"vmRegionInfo" : "0x6199d48fcb08 is not in any region. Bytes after previous region: 1759670946569 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00006199d48fcb08","rawCodes":[1,107313324083976],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00006199d48fcb08"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":49407},
"vmregioninfo" : "0x6199d48fcb08 is not in any region. Bytes after previous region: 1759670946569 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600018000000-600020000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"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":21109919,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4966349464},{"value":99},{"value":95},{"value":5744082800},{"value":1},{"value":13097637025759372360},{"value":13097637025380549960},{"value":14757395258967641293},{"value":4294967286},{"value":4966349394},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8595846728},{"value":0},{"value":11},{"value":8517312768,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8517312992,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4388685360,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8475066368,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":8475066368,"symbolLocation":0,"symbol":"OBJC_IVAR_$__NSSliderCellDataDrivenMetrics._state"},{"value":5},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":7022492712},"cpsr":{"value":1073745920},"fp":{"value":4966349536},"sp":{"value":4966349504},"esr":{"value":1442840704,"description":" 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"uuid" : "5738cf33-a520-3e9e-86f4-ff53217708a6",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7022465024,
"size" : 53248,
"uuid" : "e74e3db0-f8cb-34ab-831e-db30cbec154f",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7021015040,
"size" : 520184,
"uuid" : "d76df494-de63-350c-9d1b-25581159a9b1",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7022669824,
"size" : 28668,
"uuid" : "26b1286a-70dc-3e34-99d0-73d26257de71",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7075762176,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15798272,
"uuid" : "1a4ffce3-6623-3c15-9d96-dcb94ea59e23",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.77.138"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7103160320,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4378624,
"uuid" : "306893bd-1e88-3e5e-aca7-3f9af305992d",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7020707840,
"size" : 294912,
"uuid" : "d9d62056-1af0-3d72-b951-f1ff84abecca",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7022882816,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5087232,
"uuid" : "4a35b66a-3b0e-34fd-811d-c44fb389ce8f",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979.104.901"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7182946304,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "c8970896-b9d1-3fd0-aa1e-99bc8ff4e84d",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7018962944,
"size" : 584980,
"uuid" : "668a9a3c-85c0-3a58-8691-565e6db4c3ca",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7021535232,
"size" : 577528,
"uuid" : "a1240ffc-a95a-3824-b47d-fb1ef6e55b9b",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
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"arch" : "arm64e",
"base" : 7020527616,
"size" : 180220,
"uuid" : "01961bbc-5ba4-31c2-b07c-79360aab0a8d",
"path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
"name" : "libsystem_malloc.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7018676224,
"size" : 286432,
"uuid" : "89f215e2-0cbd-3a9b-9e0c-9218f7f434a6",
"path" : "\/usr\/lib\/libobjc.A.dylib",
"name" : "libobjc.A.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7039246336,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 10248192,
"uuid" : "85439347-8d4e-3c37-a41a-ae79b0bffd8b",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1979.104.901"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7019569152,
"size" : 278528,
"uuid" : "5489c8a5-3452-349f-8ece-56d0f6c0df3e",
"path" : "\/usr\/lib\/system\/libxpc.dylib",
"name" : "libxpc.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"sharedCache" : {
"base" : 7018299392,
"size" : 3586146304,
"uuid" : "c23c8eaf-0e55-380f-8553-41916c29d775"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=3.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 1872K 46 \nColorSync 608K 30 \nCoreAnimation 2208K 69 \nCoreGraphics 48K 3 \nCoreUI image data 5392K 42 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 1.9G 1046 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 584.0M 7 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 96K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 800K 50 \nStack 332.3M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 341.7M 159 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 1886K 380 \n__AUTH_CONST 29.2M 616 \n__CTF 824 1 \n__DATA 20.7M 762 \n__DATA_CONST 40.0M 768 \n__DATA_DIRTY 2021K 238 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 832.3M 151 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 878.1M 788 \ndyld private memory 320K 3 \nmapped file 218.6M 61 \nshared memory 3344K 27 \n=========== ======= ======= \nTOTAL 5.6G 5341 \nTOTAL, minus reserved VM space 4.7G 5341 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "48eab75848ac88f352d9bbb0b427852ec03c759e",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6410af69ed1e1e7ab93ed169",
"factorPackIds" : {
},
"deploymentId" : 240000011
},
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
}
],
"experiments" : [
]
}
}
===== 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'
UCSF ChimeraX version: 1.9.dev202405150316 (2024-05-15)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/danny/Desktop/ChimeraX/Division fork Pal-KO-6.5.cxs" format
> session
Opened TS04_filtered.mrc scaled scaled copy as #3, grid size 512,720,165,
pixel 8.85,8.85,8.85, shown at level 455, step 1, values int16
Opened TS04_filtered.mrc scaled scaled copy scaled copy as #4, grid size
512,720,165, pixel 8.85,8.85,8.85, shown at level 440, step 1, values int16
opened ChimeraX session
> volume #3 level 468.2
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #3 level 475.3
> hide #!4 models
> show #!4 models
> ui tool show "Side View"
> volume #4 level 450
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select ~sel & ##selected
Nothing selected
> ui tool show "Side View"
> hide #!3 models
> show #!3 models
> ui tool show "Map Filter"
> volume gaussian #3 sDev 5
Opened TS04_filtered.mrc scaled scaled copy gaussian as #1, grid size
512,720,165, pixel 8.85,8.85,8.85, shown at step 1, values int16
> show #!3 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> volume gaussian #3 sDev 15 modelId #1
Opened TS04_filtered.mrc scaled scaled copy gaussian as #1, grid size
512,720,165, pixel 8.85,8.85,8.85, shown at step 1, values int16
> volume #1 level 436.4
> show #!3 models
> show #!4 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> volume #1 step 2
> volume #1 level 431.7
> color #1 #2fbf21ff models
> color #1 #bf82a2ff models
> color #1 #bf9abbff models
> color #1 #b79abfff models
> color #1 #dbb7e4ff models
> color #1 #e1b0e4ff models
> color #1 #e3aee4ff models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 429
> volume #4 level 440
> hide #!4 models
> volume #1 step 1
> volume #1 level 421.5
> show #!4 models
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> hide #!4 models
> volume erase #1 center 2290.6,704.21,521.63 radius 89.188
> volume erase #1 center 2285.8,774.41,402.18 radius 89.188
> volume erase #1 center 2263.1,826.19,303.93 radius 89.188
> volume erase #1 center 2232,882.51,241.36 radius 89.188
> show #!4 models
Can only have one displayed volume when erasing
> hide #!4 models
> volume erase #1 center 1077.8,1131.4,-663 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 1284.8,1135.3,-564.34 radius 222.97
> volume erase #1 center 1542.7,1146.5,-607.74 radius 222.97
> volume erase #1 center 1766.7,1204.6,-684.02 radius 222.97
> volume erase #1 center 2013,1329.3,-668.19 radius 222.97
> volume erase #1 center 1817.4,1196.4,-502.43 radius 222.97
> volume erase #1 center 1635.2,1120.4,-432.62 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 1534.8,1173.1,-354.84 radius 222.97
> volume erase #1 center 1714.9,1053,-113.86 radius 222.97
> volume erase #1 center 1723.9,1020.7,39.606 radius 222.97
> volume erase #1 center 1351.6,1019.2,-164.5 radius 222.97
> volume erase #1 center 1437.1,960.86,113.58 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 1076.9,972.3,-176.88 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 986.12,892.25,95.14 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 1846.5,992.49,367.66 radius 222.97
> volume erase #1 center 1870.7,1060.9,192.27 radius 222.97
> volume erase #1 center 1891.5,1137.1,10.721 radius 222.97
> volume erase #1 center 1954.9,1181.4,-214.8 radius 222.97
> volume erase #1 center 2061.8,1263,-471.41 radius 222.97
> show #!4 models
> hide #!4 models
> volume erase #1 center 1076.8,1749.1,-558.49 radius 222.97
> volume erase #1 center 1060.6,1710.8,-397.47 radius 222.97
> volume erase #1 center 1036.9,1675,-256.17 radius 222.97
> show #!4 models
> show #!3 models
> hide #2 models
> hide #!1 models
> volume #1 level 440
> hide #!3 models
> show #!1 models
> volume #1 level 430
===== 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: 1.9.dev202405150316 (2024-05-15)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16T000JCB/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.41.5
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.7.1 (22H221)
Kernel Version: Darwin 22.6.0
Time since boot: 78 days, 23 hours, 11 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VA2732 100Hz:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiobotocore: 2.19.0
aiohappyeyeballs: 2.4.4
aiohttp: 3.11.11
aioitertools: 0.12.0
aiosignal: 1.3.2
alabaster: 0.7.16
annotated-types: 0.7.0
anyio: 4.8.0
appdirs: 1.4.4
appnope: 0.1.4
asciitree: 0.3.3
asttokens: 2.4.1
asyncssh: 2.19.0
attrs: 25.1.0
Babel: 2.15.0
backoff: 2.2.1
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
boto3: 1.36.3
botocore: 1.36.3
build: 1.2.1
certifi: 2023.11.17
cffi: 1.17.1
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: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.5.0
ChimeraX-Atomic: 1.58
ChimeraX-AtomicLibrary: 14.0.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
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: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-copick: 0.5.0
ChimeraX-Core: 1.9.dev202405150316
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: 1.2.1
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
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: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OME-Zarr: 0.5.4
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: 1.3.5
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: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
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: 1.1.4
ChimeraX-Zone: 1.0.1
click: 8.1.8
cloudpickle: 3.1.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
copick: 0.8.1
cryoet-data-portal: 4.0.0
cryptography: 44.0.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
dask: 2025.1.0
debugpy: 1.8.1
decorator: 5.1.1
deepmerge: 2.0
Deprecated: 1.2.18
distinctipy: 1.3.4
distributed: 2025.1.0
docutils: 0.20.1
executing: 2.0.1
fasteners: 0.19
filelock: 3.13.4
fonttools: 4.51.0
frozenlist: 1.5.0
fsspec: 2025.2.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.7.0
gql: 3.5.0
grako: 3.16.5
graphql-core: 3.2.6
h5py: 3.11.0
hatchling: 1.27.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imageio: 2.37.0
imagesize: 1.4.1
importlib-metadata: 8.6.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jmespath: 1.0.1
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
lazy-loader: 0.4
line-profiler: 4.1.2
locket: 1.0.0
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
multidict: 6.1.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numcodecs: 0.15.0
numexpr: 2.10.0
numpy: 1.26.4
ome-zarr: 0.10.3
openvr: 1.26.701
packaging: 24.2
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
partd: 1.4.2
pathspec: 0.12.1
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
pluggy: 1.5.0
prompt-toolkit: 3.0.43
propcache: 0.2.1
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 19.0.0
pycollada: 0.8
pycparser: 2.22
pydantic: 2.10.6
pydantic-core: 2.27.2
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
pyspnego: 0.11.2
python-dateutil: 2.9.0.post0
pytz: 2024.1
PyYAML: 6.0.2
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
requests-toolbelt: 1.0.0
s3fs: 2025.2.0
s3transfer: 0.11.2
scikit-image: 0.25.1
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
smbprotocol: 1.15.0
sniffio: 1.3.1
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
sshfs: 2024.9.0
stack-data: 0.6.3
starfile: 0.5.11
strcase: 1.0.0
superqt: 0.6.3
tables: 3.8.0
tblib: 3.0.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
toolz: 1.0.0
tornado: 6.4
tqdm: 4.67.1
traitlets: 5.14.2
trimesh: 4.6.1
trove-classifiers: 2025.1.15.22
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
wrapt: 1.17.2
yarl: 1.18.3
zarr: 2.18.4
zict: 3.0.0
zipp: 3.21.0
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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