Opened 2 years ago

Closed 2 years ago

#9844 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        macOS-12.5-arm64-arm-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: Segmentation fault

Thread 0x00000002e58e7000 (most recent call first):
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x0000000104d14580 (most recent call first):
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 341 in _cleanup
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 381 in cb
  File "/Applications/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 "/Applications/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 "/Applications/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 "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


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{
  "uptime" : 130000,
  "procLaunch" : "2023-09-25 12:53:55.7269 -0700",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "procStartAbsTime" : 3243497251154,
  "coalitionID" : 12745,
  "osVersion" : {
    "train" : "macOS 12.5",
    "build" : "21G72",
    "releaseType" : "User"
  },
  "captureTime" : "2023-09-25 13:43:34.2941 -0700",
  "incident" : "B2FED511-8CC0-4942-B811-CDBA536EB7D6",
  "bug_type" : "309",
  "pid" : 17057,
  "procExitAbsTime" : 3313802627007,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2083DA98-3244-52A2-96E9-64A3B05BDEAA","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "979DD0B0-4B58-EA7F-8E71-70D415EE4751",
  "wakeTime" : 899,
  "sleepWakeUUID" : "F44973DC-2727-4286-9CF2-338C5F21E073",
  "sip" : "enabled",
  "vmRegionInfo" : "0x16e63f0d0 is not in any region.  Bytes after previous region: 258257  Bytes before following region: 3888\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_TINY                 16e500000-16e600000    [ 1024K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x40000 BYTES\n      CoreUI image data           16e640000-16e650000    [   64K] r--\/r-- SM=PRV  ",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x000000016e63f0d0","rawCodes":[1,6147010768],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000016e63f0d0"},
  "ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
  "vmregioninfo" : "0x16e63f0d0 is not in any region.  Bytes after previous region: 258257  Bytes before following region: 3888\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_TINY                 16e500000-16e600000    [ 1024K] rw-\/rwx SM=PRV  \n--->  GAP OF 0x40000 BYTES\n      CoreUI image data           16e640000-16e650000    [   64K] r--\/r-- SM=PRV  ",
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  "faultingThread" : 0,
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    "arch" : "arm64",
    "base" : 5370527744,
    "size" : 622592,
    "uuid" : "a07d6b8c-b467-339b-8483-3ba6dc00495e",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7470940160,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5533696,
    "uuid" : "1643f3d9-7049-37e4-b844-c0c0a42bde3b",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1866"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7618330624,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "7112f6f2-a77e-39db-83c8-f627b8a49df8",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7516721152,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15437824,
    "uuid" : "07bc3607-552a-3eb9-a941-4911c589dbc5",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4372856832,
    "CFBundleShortVersionString" : "1.5.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "a5992708-d5b4-36ec-ac0a-e525f6105b56",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.5.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 4375298048,
    "size" : 393216,
    "uuid" : "75627683-a780-32ad-ae34-cf86dd23a26b",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 4401610752,
    "size" : 20709376,
    "uuid" : "6b8373ed-7142-34ea-9b4b-9f502e8a6f33",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 10737418240,
    "size" : 144654336,
    "uuid" : "21c8f378-4426-330a-89d1-26ab67c6fa56",
    "path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  }
],
  "sharedCache" : {
  "base" : 7467319296,
  "size" : 3144695808,
  "uuid" : "ffede77c-d90b-366b-96f2-665c2f50ee59"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=26.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=26.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               768K        6 \nActivity Tracing                   256K        1 \nCG backing stores                 2944K        8 \nCG image                           864K       35 \nColorSync                          640K       28 \nCoreAnimation                      800K       26 \nCoreGraphics                        48K        3 \nCoreUI image data                 5488K       54 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            24.8G      614 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         776.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        96K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        560K       35 \nStack                            176.8M       36 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      249.7M      452 \nVM_ALLOCATE (reserved)           160.0M        3         reserved VM address space (unallocated)\n__AUTH                            2624K      311 \n__AUTH_CONST                      20.6M      510 \n__CTF                               756        1 \n__DATA                            24.2M      670 \n__DATA_CONST                      27.9M      676 \n__DATA_DIRTY                      1804K      216 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       611.9M      166 \n__OBJC_CONST                      3665K      282 \n__OBJC_RO                         83.0M        1 \n__OBJC_RW                         3168K        1 \n__TEXT                           734.1M      695 \n__UNICODE                          592K        1 \ndyld private memory               1216K        3 \nmapped file                      719.4M       70 \nshared memory                     3424K       32 \n===========                     =======  ======= \nTOTAL                             28.5G     4968 \nTOTAL, minus reserved VM space    27.5G     4968 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "5f72dc58705eff005a46b3a9",
      "factorPackIds" : {

      },
      "deploymentId" : 240000015
    },
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    }
  ],
  "experiments" : [
    {
      "treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
      "experimentId" : "64406ba83deb637ac8a04419",
      "deploymentId" : 900000017
    }
  ]
}
}
===== Log before crash start =====
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/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/TVMT_maps/48nm_to_be_improved/cryosparc_P9_J475_map_sharp.mrc
> format mrc

Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel
1.1, shown at level 0.106, step 4, values float32  

> volume #1 level 0.08861

> volume #1 level 0.04711

> volume #1 step 1

> ui tool show "Hide Dust"

> surface dust #1 size 6.6

> lighting full

> close session

> open "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 - TVMT/TVMT Modeling (my
> reference)/B_tubule_ID_08182023.cxs" format session

Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel
1.1, shown at level 0.0456, step 4, values float32  
opened ChimeraX session  

> lighting soft

> lighting simple

> lighting full

> select /HZ:45@OE2

1 atom, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /HD

Alignment identifier is 2/HD  

> select /HD

1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> select /HD:195-232

300 atoms, 300 bonds, 38 residues, 1 model selected  

> select /HD

1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> select /HD

1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> select /HD

1563 atoms, 1603 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> close session

> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/My Drive/3. Extracurricular/1. Research/Project #4 -
> TVMT/TVMT Modeling (my reference)/FAP52_fit_09052023.cxs" format session

Opened cryosparc_P9_J475_map_sharp.mrc as #1.1.1.1, grid size 640,640,640,
pixel 1.1, shown at level 0.0801, step 1, values float32  
Opened cryosparc_P9_J475_map_sharp.mrc as #2, grid size 640,640,640, pixel
1.1, shown at level 0.0829, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> volume #2 level 0.06766

> volume #2 level 0.05895

> ui mousemode right "crop volume"

> volume #2 region 337,187,403,427,276,549

> volume #2 region 337,187,403,435,276,549

> volume #2 level 0.05024

> volume #2 level 0.04661

> volume #2 level 0.0408

> close session

> open "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 - TVMT/TVMT Modeling (my
> reference)/B_tubule_ID_08182023.cxs" format session

Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel
1.1, shown at level 0.0456, step 4, values float32  
opened ChimeraX session  

> volume #1 level 0.03378

> volume #1 step 1

> volume #1 step 2

> volume #1 level 0.02892

> hide #!2 models

> volume #1 step 1

> volume #1 step 2

> show #!2 models

> close session

> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/My Drive/3. Extracurricular/1. Research/Project #4 -
> TVMT/TVMT Modeling (my reference)/FAP52_fit_09052023.cxs" format session

Opened cryosparc_P9_J475_map_sharp.mrc as #1.1.1.1, grid size 640,640,640,
pixel 1.1, shown at level 0.0801, step 1, values float32  
Opened cryosparc_P9_J475_map_sharp.mrc as #2, grid size 640,640,640, pixel
1.1, shown at level 0.0829, step 1, values float32  
opened ChimeraX session  

> volume #2 level 0.07275

> volume #2 level 0.06912

> volume #2 level 0.07638

> volume #2 level 0.08219

> volume #2 level 0.06185

> volume #2 level 0.06694

> select clear

> volume #2 level 0.06403

> close session

> open "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 - TVMT/TVMT Modeling (my
> reference)/B_tubule_ID_08182023.cxs" format session

Opened cryosparc_P9_J475_map_sharp.mrc as #1, grid size 640,640,640, pixel
1.1, shown at level 0.0456, step 4, values float32  
opened ChimeraX session  

> view orient

> select /Go:247@CB

1 atom, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> close session


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

Log:
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 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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 Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5 (21G72)
      Kernel Version: Darwin 21.6.0
      Time since boot: 16 days 20:26

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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
        DELL P2714H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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: 2.2.1
    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-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-DataFormats: 1.2.2
    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-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-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    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-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-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    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-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-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
    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
    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 Eric Pettersen, 2 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 2 years ago

Resolution: → duplicate
Status: accepted → closed

_cleanup was removed for just this reason

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