Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5972 closed defect (can't reproduce)

Crash setting window size during session restore

Reported by: kelvin.lau@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
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.
Fatal Python error: Segmentation fault

Current thread 0x000000011729b600 (most recent call first):
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/windowsize.py", line 38 in window_size
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/gsession.py", line 115 in set_state_from_snapshot
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/gsession.py", line 67 in restore_snapshot
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 725 in restore
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 995 in open
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py", line 26 in open
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 403 in remember_data_format
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 433 in collated_open
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 181 in provider_open
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118 in cmd_open
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36 in run
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 155 in _qt_safe
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.3.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" : 170000,
  "procLaunch" : "2022-01-20 13:14:25.2362 +0100",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "procStartAbsTime" : 171220308409404,
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    "build" : "21A559",
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  "captureTime" : "2022-01-20 13:15:29.2820 +0100",
  "incident" : "2BC0B2A1-2700-4B4A-8543-0CBB4828D242",
  "bug_type" : "309",
  "pid" : 99112,
  "procExitAbsTime" : 171284341078961,
  "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":"10596464-2B5D-54DA-9D5F-AF7DE20D5475","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F3393346-4E79-1CE3-B49B-B5954C451C84",
  "wakeTime" : 3850,
  "bridgeVersion" : {"build":"19P549","train":"6.0"},
  "sleepWakeUUID" : "4E563F9D-5817-4E51-A39A-228C0D758742",
  "sip" : "enabled",
  "vmRegionInfo" : "0x20 is not in any region.  Bytes before following region: 4428840928\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      107fac000-107fad000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000020","rawCodes":[1,32],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000020"},
  "vmregioninfo" : "0x20 is not in any region.  Bytes before following region: 4428840928\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      107fac000-107fad000    [    4K] r-x\/r-x SM=COW  ...acOS\/ChimeraX",
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    "uuid" : "dd0028a3-78e3-3a8a-a51b-ddd68123adef",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4428840960,
    "CFBundleShortVersionString" : "1.3.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 4096,
    "uuid" : "9596eff5-d2be-396c-9c4e-6177235c3dae",
    "path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.3.0.0"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4683083776,
    "size" : 442368,
    "uuid" : "1a6ae033-9438-33c0-8077-988fd885250a",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4513038336,
    "size" : 62603264,
    "uuid" : "9112000d-375c-34f0-9a66-9d68f91a12cd",
    "path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas.0.dylib",
    "name" : "libopenblas.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4936085504,
    "size" : 131002368,
    "uuid" : "86651daf-3bff-3a6f-b313-e84d303e55eb",
    "path" : "\/Applications\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWebEngineCore.framework\/Versions\/5\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  }
],
  "sharedCache" : {
  "base" : 140703409987584,
  "size" : 15213641728,
  "uuid" : "3d05845f-3f65-358f-9ebf-2236e772ac01"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=5.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.0G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 2880K        8 \nCG image                            84K       13 \nColorSync                          232K       26 \nCoreAnimation                      116K       19 \nCoreGraphics                        16K        3 \nCoreUI image data                 2568K       32 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             4.4G      788 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        24K        4 \nOpenGL GLSL                        384K        5 \nSTACK GUARD                        104K       26 \nStack                            156.2M       27 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      103.1M       82 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__DATA                            41.6M      658 \n__DATA_CONST                      31.2M      334 \n__DATA_DIRTY                      1620K      213 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       727.9M      139 \n__OBJC_RO                         81.5M        1 \n__OBJC_RW                         3120K        2 \n__TEXT                           740.6M      655 \n__UNICODE                          588K        1 \ndyld private memory               1024K        1 \nmapped file                      427.0M       52 \nshared memory                     2976K       24 \n===========                     =======  ======= \nTOTAL                              7.1G     3132 \nTOTAL, minus reserved VM space     6.7G     3132 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "607844aa04477260f58a8077",
      "factorPackIds" : {
        "SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
      },
      "deploymentId" : 240000066
    },
    {
      "rolloutId" : "602ad4dac86151000cf27e46",
      "factorPackIds" : {
        "SIRI_DICTATION_ASSETS" : "614a34c5eae97a2111628dc5"
      },
      "deploymentId" : 240000290
    },
    {
      "rolloutId" : "60da5e84ab0ca017dace9abf",
      "factorPackIds" : {

      },
      "deploymentId" : 240000008
    },
    {
      "rolloutId" : "601d9415f79519000ccd4b69",
      "factorPackIds" : {
        "SIRI_TEXT_TO_SPEECH" : "61c0d3122be4e338e11ae9e1"
      },
      "deploymentId" : 240000362
    },
    {
      "rolloutId" : "5fc94383418129005b4e9ae0",
      "factorPackIds" : {

      },
      "deploymentId" : 240000207
    },
    {
      "rolloutId" : "5ffde50ce2aacd000d47a95f",
      "factorPackIds" : {

      },
      "deploymentId" : 240000094
    }
  ],
  "experiments" : [

  ]
}
}
===== Log before crash start =====
> graphics silhouettes true

> lighting soft

> windowsize 800 800

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kelvinlau/Downloads/stick_on_full1.cxs

Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc as #4, grid size
300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #7.2, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #7.3, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 3 as #7.4, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened j479.mrc as #13, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 1 as #14.2, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 2 as #14.3, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 3 as #14.4, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 0 as #15.1, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #15.2, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #5.1.2, grid size
300,300,300, pixel 1.38, shown at level 0.213, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #5.2.2, grid size
300,300,300, pixel 1.38, shown at level 0.237, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #6.1.2, grid size
300,300,300, pixel 1.38, shown at level 0.24, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #6.2.2, grid size
300,300,300, pixel 1.38, shown at level 0.24, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #8.1.2, grid
size 300,300,300, pixel 1.38, shown at level 0.08, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #8.1.3, grid
size 300,300,300, pixel 1.38, shown at level 0.08, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #8.2.2, grid
size 300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #8.2.3, grid
size 300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
opened ChimeraX session  

> open "/Volumes/GoogleDrive/Shared drives/2-Fab-Omicron/from-
> Dong/Full-j497/full.cxs"

Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc as #4, grid size
300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc as #3, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #5.2, grid size
300,300,300, pixel 1.38, shown at level 0.213, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #6.2, grid size
300,300,300, pixel 1.38, shown at level 0.237, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #8.2, grid size
300,300,300, pixel 1.38, shown at level 0.24, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #9.2, grid size
300,300,300, pixel 1.38, shown at level 0.24, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #7.2, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #7.3, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 3 as #7.4, grid size
300,300,300, pixel 1.38, shown at level 0.19, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #10.2, grid
size 300,300,300, pixel 1.38, shown at level 0.08, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #10.3, grid
size 300,300,300, pixel 1.38, shown at level 0.08, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 1 as #11.2, grid
size 300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
Opened cryosparc_P42_J497_004_volume_map_sharp_localz.mrc 2 as #11.3, grid
size 300,300,300, pixel 1.38, shown at level 0.06, step 1, values float32  
Opened j479.mrc as #13, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 1 as #14.2, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 2 as #14.3, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened j479.mrc 3 as #14.4, grid size 300,300,300, pixel 1.38, shown at level
0.233, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 0 as #15.1, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  
Opened cryosparc_P42_J486_005_volume_map_sharp.mrc 1 as #15.2, grid size
300,300,300, pixel 1.38, shown at level 0.28, step 1, values float32  


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

Log:
> graphics silhouettes true

> lighting soft

> windowsize 800 800

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-18.2.10
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 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: 1715.40.15.0.0 (iBridge: 19.16.10549.0.0,0)
      OS Loader Version: 540.40.4~45

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 6 days 1:13

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        SMS24A450:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HTRC900076  
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C VGA Adapter
          Automatically Adjust Brightness: Yes
          Adapter Firmware Version: 1.91

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-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-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 (5)

comment:1 by pett, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash setting window size during session restore

comment:2 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

ChimeraX set the window size when opening a session and was then processing Qt events to let the window adjust

Current thread 0x000000011729b600 (most recent call first):

File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/windowsize.py", line 38 in window_size

Second line is the line it crashed on

ui.main_window.adjust_size(width-w, height-h)
ui.processEvents() # Make sure window resized before executing next command.

The C stack trace shows Qt was calling a Python callback due to an event (e.g. window resize) and that callback pointer seems to have been bad and it crashed.

No idea how it got the bad callback. Possibly a callback on a deleted Qt object was invoked due to some Qt bug. The computer was using two displays.

comment:3 by Tom Goddard, 4 years ago

A better theory about the cause of the crash is that the Python callback got deleted because its reference count dropped to zero or it was not reachable, but in fact it was be referenced by PyQt -- in other words a PyQt reference counting bug. We see many crashes in the event loop especially on Windows and such a reference counting bug in PyQt would explain those.

in reply to:  4 ; comment:4 by kelvin.lau@…, 4 years ago 

Hello thanks for looking in

Only thing I can think of was yes, I was using two displays, then disconnected, then reopened laptop again with main display and reloaded a session and  that’s when I got the error. However it is surprising as I reloaded a new session so I would not have thought it is linked to the using multiple displays.



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On Jan 21, 2022, at 02:58, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

#5972: Crash setting window size during session restore
--------------------------------------+-------------------------
         Reporter:  kelvin.lau@…     |      Owner:  Tom Goddard
             Type:  defect           |     Status:  closed
         Priority:  normal           |  Milestone:
        Component:  Graphics         |    Version:
       Resolution:  can't reproduce  |   Keywords:
       Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
          Project:  ChimeraX         |
--------------------------------------+-------------------------

Comment (by Tom Goddard):

A better theory about the cause of the crash is that the Python callback
got deleted because its reference count dropped to zero or it was not
reachable, but in fact it was be referenced by PyQt -- in other words a
PyQt reference counting bug.  We see many crashes in the event loop
especially on Windows and such a reference counting bug in PyQt would
explain those.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5972#comment:3>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  5 ; comment:5 by goddard@…, 4 years ago 

Thanks for the extra details.  The Qt window toolkit is pretty buggy with multiple displays on the Mac.  We've seen a number of crashes where it looks like ChimeraX was running then a display was disconnected.  Probably Qt somehow kept a no longer valid pointer to the no longer connected display.  We plan to update ChimeraX from Qt 5 to Qt 6 in coming months, and perhaps it will be better.
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