![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#6473 closed defect (can't reproduce)
Crash with suspiciously repetitive stack
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | pett | |
| 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 160000,
"procLaunch" : "2022-03-28 10:15:37.8569 +0200",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro11,4",
"procStartAbsTime" : 163585464969679,
"coalitionID" : 907,
"osVersion" : {
"train" : "macOS 12.2.1",
"build" : "21D62",
"releaseType" : "User"
},
"captureTime" : "2022-03-28 11:23:03.8188 +0200",
"incident" : "ADA469DB-A283-4608-AEA8-CC0A69A8AE5B",
"bug_type" : "309",
"pid" : 61444,
"procExitAbsTime" : 167631421241783,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.3.0","CFBundleVersion":"1.3.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"E83DAE97-A2F9-5898-A533-DC761BE11870","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E94387A5-3CA6-D3D5-989B-BC34744961E8",
"wakeTime" : 6256,
"sleepWakeUUID" : "9643E30C-7877-4F23-8715-38EEF53F4FA0",
"sip" : "enabled",
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"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x00000000000001e8","rawCodes":[1,488],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000001e8"},
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"faultingThread" : 0,
"threads" : 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"name" : "libOpenMMOpenCL.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703500406784,
"CFBundleShortVersionString" : "2.0.2",
"CFBundleIdentifier" : "com.apple.framework.IOKit",
"size" : 745472,
"uuid" : "6882364f-5963-3153-81fd-3d2444c55060",
"path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
"name" : "IOKit"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703600599040,
"CFBundleShortVersionString" : "462.4.1",
"CFBundleIdentifier" : "com.apple.IOAccelerator",
"size" : 36864,
"uuid" : "d475ccd1-62c1-31d3-a58c-f2cbf1f27d0a",
"path" : "\/System\/Library\/PrivateFrameworks\/IOAccelerator.framework\/Versions\/A\/IOAccelerator",
"name" : "IOAccelerator",
"CFBundleVersion" : "462.4.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712347791360,
"CFBundleShortVersionString" : "18.4.6",
"CFBundleIdentifier" : "com.apple.driver.AppleIntelHD5000GraphicsGLDriver",
"size" : 5324800,
"uuid" : "59a751df-047e-34ad-a873-a4cd4f8cae67",
"path" : "\/System\/Library\/Extensions\/AppleIntelHD5000GraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelHD5000GraphicsGLDriver",
"name" : "AppleIntelHD5000GraphicsGLDriver",
"CFBundleVersion" : "18.0.4"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712469188608,
"CFBundleShortVersionString" : "4.7",
"CFBundleIdentifier" : "com.apple.opencl",
"size" : 360448,
"uuid" : "5f03e88e-cb3a-3814-a535-9c984cd9f8d7",
"path" : "\/System\/Library\/Frameworks\/OpenCL.framework\/Versions\/A\/OpenCL",
"name" : "OpenCL",
"CFBundleVersion" : "4.7"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703454945280,
"size" : 290816,
"uuid" : "67d92c93-aa68-34c2-964b-23e8a8d32098",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5322174464,
"size" : 81920,
"uuid" : "722da143-5bec-3fd3-b9c5-0663a0843da2",
"path" : "\/Users\/USER\/Library\/Application Support\/ChimeraX\/*\/libopenmm.dylib",
"name" : "libopenmm.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4301668352,
"CFBundleShortVersionString" : "3.9.6, (c) 2001-2019 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2510848,
"uuid" : "7fdc4a6b-e70b-3c9e-a72e-cd15ddf0d90f",
"path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.6"
}
],
"sharedCache" : {
"base" : 140703453495296,
"size" : 15216836608,
"uuid" : "0939015d-8308-3e69-b095-bd928f835202"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 544K 74 \nColorSync 240K 28 \nCoreAnimation 576K 34 \nCoreGraphics 20K 4 \nCoreServices 164K 1 \nCoreUI image data 5328K 51 \nFoundation 44K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.8G 2068 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 24K 5 \nOpenCL 33.2M 74 \nOpenCL (reserved) 360K 9 reserved VM address space (unallocated)\nOpenGL GLSL 384K 5 \nSTACK GUARD 136K 34 \nStack 160.8M 35 \nStack Guard 56.0M 1 \nVM_ALLOCATE 157.9M 461 \n__DATA 42.8M 706 \n__DATA_CONST 30.4M 344 \n__DATA_DIRTY 1638K 217 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 740.4M 177 \n__OBJC_RO 81.8M 1 \n__OBJC_RW 3136K 2 \n__TEXT 779.5M 703 \n__UNICODE 588K 1 \ndyld private memory 1024K 1 \nmapped file 634.3M 97 \nshared memory 2988K 25 \n=========== ======= ======= \nTOTAL 4.5G 5181 \nTOTAL, minus reserved VM space 4.5G 5181 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "602ad4dac86151000cf27e46",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "6193d03f2171a2330e561dfc"
},
"deploymentId" : 240000305
},
{
"rolloutId" : "601d9415f79519000ccd4b69",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "622657ce37186c771d5404ad"
},
"deploymentId" : 240000414
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000123
},
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
"deploymentId" : 240000302
}
],
"experiments" : [
]
},
"reportNotes" : [
"thread_get_state(PAGEIN) returned 0x10000003: (ipc\/send) invalid destination port",
"thread_get_state(EXCEPTION) returned 0x10000003: (ipc\/send) invalid destination port",
"thread_get_state(FLAVOR) returned 0x10000003: (ipc\/send) invalid destination port"
]
}
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro11,4
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: 428.60.3.0.0
OS Loader Version: 540.80.2~11
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 12.2.1 (21D62)
Kernel Version: Darwin 21.3.0
Time since boot: 3 days 19:38
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal Family: Supported, Metal GPUFamily macOS 1
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: No
Connection Type: Internal
E2411:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 107NDEZ58868
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
E2411:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 107NDQA58884
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash with suspiciously repetitive stack |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Mac crash dump did not have any useful info on the crashing thread. ISOLDE was running an OpenMM energy minimization in a thread but it was the main thread that crashed.
Possibly this was a Mac graphics driver crash -- they are very common on Intel Macs.
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Reported by Barrett Davis