Opened 3 years ago

Closed 3 years ago

#8361 closed defect (can't reproduce)

QOpenGLFramebufferObject: Framebuffer incomplete attachment

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit 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: 1.4.dev202203190100 (2022-03-19 01:00:21 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Illegal instruction

Current thread 0x00000002026fe2c0 (most recent call first):
  File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/78EF130C-AC1B-4E7A-BDC2-21DCAA71974F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
  File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/78EF130C-AC1B-4E7A-BDC2-21DCAA71974F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/78EF130C-AC1B-4E7A-BDC2-21DCAA71974F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/78EF130C-AC1B-4E7A-BDC2-21DCAA71974F/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/78EF130C-AC1B-4E7A-BDC2-21DCAA71974F/d/ChimeraX_Daily.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" : 430000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro17,1",
  "coalitionID" : 14822,
  "osVersion" : {
    "train" : "macOS 13.0.1",
    "build" : "22A400",
    "releaseType" : "User"
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  "captureTime" : "2023-01-23 11:56:03.4132 -0800",
  "incident" : "44AA8502-795F-4190-8A1C-8514E97C714E",
  "pid" : 91333,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-01-17 13:46:12.3421 -0800",
  "procStartAbsTime" : 6566959387868,
  "procExitAbsTime" : 10490401428687,
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2A554CB2-D81E-5AB0-8057-FC287B0A43CC","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1588EBE2-4379-A243-BF8B-E4CFCCEE94E9",
  "wakeTime" : 1,
  "sleepWakeUUID" : "391C75DB-83C2-4D77-8063-D8210C61A7D0",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_INSTRUCTION","signal":"SIGILL"},
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  "faultingThread" : 0,
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  "trialInfo" : {
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]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/data
> analysis/cryosparc_P2_J29_class_00_final_volume.mrc" format mrc

Opened cryosparc_P2_J29_class_00_final_volume.mrc as #1, grid size 64,64,64,
pixel 1.9, shown at level 0.105, step 1, values float32  

> open 6no7

6no7 title:  
Crystal Structure of the full-length wild-type PKA RIa Holoenzyme [more
info...]  
  
Chain information for 6no7 #2  
---  
Chain | Description | UniProt  
A C E G | cAMP-dependent protein kinase catalytic subunit α | KAPCA_HUMAN  
B D F H | cAMP-dependent protein kinase type I-alpha regulatory subunit |
KAP0_BOVIN  
  
Non-standard residues in 6no7 #2  
---  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
  
6no7 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> show atoms

> hide atoms

> show cartoons

> scalebar bar

Expected a number or a keyword  

> scalebar

> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/data
> analysis/cryosparc_P2_J29_class_01_final_volume.mrc"

Opened cryosparc_P2_J29_class_01_final_volume.mrc as #4, grid size 64,64,64,
pixel 1.9, shown at level 0.0848, step 1, values float32  

> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/data
> analysis/cryosparc_P2_J35_class_00_final_volume.mrc"

Opened cryosparc_P2_J35_class_00_final_volume.mrc as #5, grid size 64,64,64,
pixel 1.9, shown at level 0.111, step 1, values float32  

> molmap #1 15

No atoms specified  

> hide #!1 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> molmap #2 15

Opened 6no7 map 15 as #6, grid size 43,46,44, pixel 5, shown at level 0.0525,
step 1, values float32  
No map chosen to save  

> save #2

Cannot determine format for '#2'  

> save "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/6no7.png" width 864 height 615 supersample 3
> transparentBackground true

> save "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/6no7.mrc" models #6

> hide #!2 models

> scalebar

> scalebar 100

> hide #!6 models

> show #!5 models

> volume #5 level -0.0007704

> show #!6 models

> select add #6

2 models selected  

> ui mousemode right translate

> volume #5 level 0.0004234

Drag select of 6 6no7.mrc  

> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/data
> analysis/cryosparc_P2_J35_class_00_final_volume.mrc"

Opened cryosparc_P2_J35_class_00_final_volume.mrc as #7, grid size 64,64,64,
pixel 1.9, shown at level 0.111, step 1, values float32  

> hide #!5 models

> hide #!6 models

> volume #7 level -0.001964

> volume #7 level 0.0004234

> show #!6 models

> show #!5 models

> hide #!5 models

> volume #7 level 0.006392

> volume #7 level 0.003408

> hide #!7 models

> scalebar 100

> hide #!6 models

> select subtract #6

Nothing selected  

> show #!2 models

> scalebar 100

> color bg white

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color bg whitebgcolor white

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> bgcolor white

Unknown command: bgcolor white  

> set bgColor white

> set bgColor #ffffff00

> ui mousemode right zoom

> ui mousemode right translate

> select /a

2746 atoms, 2818 bonds, 336 residues, 1 model selected  

> hide /a

> cartoon hide sel

> select /b

2259 atoms, 2299 bonds, 285 residues, 1 model selected  

> cartoonhide /b

Unknown command: cartoonhide /b  

> cartoon hide /b

> select /c

2775 atoms, 2847 bonds, 340 residues, 1 model selected  

> cartoon hide /c

> select /d

2268 atoms, 2308 bonds, 286 residues, 1 model selected  

> cartoon hide /d

> ui mousemode right zoom

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right "translate selected models"

> select /e

2799 atoms, 2871 bonds, 8 pseudobonds, 342 residues, 2 models selected  

> select /f

2248 atoms, 2288 bonds, 284 residues, 1 model selected  

> select /B

2259 atoms, 2299 bonds, 285 residues, 1 model selected  

> select /D

2268 atoms, 2308 bonds, 286 residues, 1 model selected  

> select /F

2248 atoms, 2288 bonds, 284 residues, 1 model selected  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  

QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
QOpenGLFramebufferObject: Framebuffer incomplete, missing attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  

Failed to lock QIOSurfaceGraphicsBuffer(0x600000c95560, surface=0x0,
size=QSize(-2147483648, -2147483648), isLocked=false, isInUse=false)
-536870206  


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

Log:
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MJ123LL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 40 days, 1 hour, 32 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      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


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.5.30
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.36.2
    ChimeraX-AtomicLibrary: 6.1.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    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: 1.5.1
    ChimeraX-CommandLine: 1.2.2
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202203190100
    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-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: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.8
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 2.5
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.31.1
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.2
    kiwisolver: 1.4.0
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.28
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt6-commercial: 6.2.3
    PyQt6-sip: 13.2.0
    PyQt6-WebEngine-commercial: 6.2.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Cc: pett added
Component: UnassignedWindow Toolkit
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionQOpenGLFramebufferObject: Framebuffer incomplete attachment

comment:2 by pett, 3 years ago

Resolution: can't reproduce
Status: assignedclosed
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