Opened 3 years ago

Closed 3 years ago

#8870 closed defect (nonchimerax)

Crash in fork during "devel install"

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Platform 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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  "procLaunch" : "2023-04-19 13:38:17.5896 +0200",
  "procRole" : "Foreground",
  "version" : 2,
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  "captureTime" : "2023-04-19 13:38:33.3453 +0200",
  "incident" : "F2F3EF47-4873-4F3D-92E1-417FB4ECC5BD",
  "bug_type" : "309",
  "pid" : 12562,
  "procExitAbsTime" : 5736022639322,
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  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
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  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "CACF4A9F-26D6-5320-3217-094D718C9A8D",
  "wakeTime" : 3986,
  "sleepWakeUUID" : "6EE7B4BF-7BF5-4041-A65A-78CA9B787A2C",
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  "isCorpse" : 1,
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    "size" : 1589248,
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    "name" : "QtWidgets"
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    "name" : "libqcocoa.dylib"
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    "arch" : "x86_64",
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    "arch" : "x86_64",
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    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3096576,
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    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
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    "arch" : "x86_64",
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    "CFBundleShortVersionString" : "1.4.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG backing stores                 3520K        4 \nCG image                            52K        5 \nColorSync                          228K       26 \nCoreAnimation                      116K        8 \nCoreGraphics                        12K        2 \nCoreUI image data                 2180K       13 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.0G       89 \nMALLOC guard page                  192K       10 \nMALLOC_MEDIUM (reserved)         872.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     6144K        3 \nRosetta Generic                   1420K      352 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               920K       92 \nRosetta Thread Context             920K       92 \nSTACK GUARD                         44K       11 \nStack                            192.1M       38 \nStack Guard                       56.1M       27 \nVM_ALLOCATE                      109.4M      202 \nVM_ALLOCATE (reserved)           224.1M       13         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            44.4M      664 \n__DATA_CONST                      31.0M      341 \n__DATA_DIRTY                      1644K      214 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       737.0M      143 \n__OBJC_RO                         82.7M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           796.9M      664 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        5.2G     1130 \nshared memory                     3128K       20 \nunshared pmap                     10.1M        8 \n===========                     =======  ======= \nTOTAL                              9.7G     4205 \nTOTAL, minus reserved VM space     8.4G     4205 \n",
  "legacyInfo" : {
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},
  "trialInfo" : {
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      "factorPackIds" : {
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  "experiments" : [
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      "experimentId" : "6317d2003d24842ff850182a",
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7jjo format mmcif fromDatabase pdb

7jjo title:  
Structural Basis of the Activation of Heterotrimeric Gs-protein by
Isoproterenol-bound Beta1-Adrenergic Receptor [more info...]  
  
Chain information for 7jjo #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short |
GNAS2_BOVIN  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_BOVIN  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_BOVIN  
N | Nanobody 35 |  
R | Beta1-Adrenergic Receptor |  
  
Non-standard residues in 7jjo #1  
---  
5FW — isoprenaline  
  

> devel build /Users/aaron.sweeney/Documents/ChimeraX_exts/ProPLID

running build  
running build_py  
copying src/Interactions.py -> build/lib/chimerax/ProPLID  
copying src/data_classes.py -> build/lib/chimerax/ProPLID  
running bdist_wheel  
/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning:
setup.py install is deprecated. Use build and pip and other standards-based
tools.  
warnings.warn(  
installing to build/bdist.macosx-10.9-x86_64/wheel  
running install  
running install_lib  
creating build/bdist.macosx-10.9-x86_64/wheel  
creating build/bdist.macosx-10.9-x86_64/wheel/chimerax  
creating build/bdist.macosx-10.9-x86_64/wheel/chimerax/ProPLID  
copying build/lib/chimerax/ProPLID/ProPLID.py ->
build/bdist.macosx-10.9-x86_64/wheel/chimerax/ProPLID  
copying build/lib/chimerax/ProPLID/__init__.py ->
build/bdist.macosx-10.9-x86_64/wheel/chimerax/ProPLID  
copying build/lib/chimerax/ProPLID/Interactions.py ->
build/bdist.macosx-10.9-x86_64/wheel/chimerax/ProPLID  
copying build/lib/chimerax/ProPLID/data_classes.py ->
build/bdist.macosx-10.9-x86_64/wheel/chimerax/ProPLID  
running install_egg_info  
running egg_info  
writing ChimeraX_ProPLID.egg-info/PKG-INFO  
writing dependency_links to ChimeraX_ProPLID.egg-info/dependency_links.txt  
writing requirements to ChimeraX_ProPLID.egg-info/requires.txt  
writing top-level names to ChimeraX_ProPLID.egg-info/top_level.txt  
reading manifest file 'ChimeraX_ProPLID.egg-info/SOURCES.txt'  
writing manifest file 'ChimeraX_ProPLID.egg-info/SOURCES.txt'  
Copying ChimeraX_ProPLID.egg-info to
build/bdist.macosx-10.9-x86_64/wheel/ChimeraX_ProPLID-0.1-py3.9.egg-info  
running install_scripts  
creating build/bdist.macosx-10.9-x86_64/wheel/ChimeraX_ProPLID-0.1.dist-
info/WHEEL  
creating 'dist/ChimeraX_ProPLID-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-x86_64/wheel' to it  
adding 'chimerax/ProPLID/Interactions.py'  
adding 'chimerax/ProPLID/ProPLID.py'  
adding 'chimerax/ProPLID/__init__.py'  
adding 'chimerax/ProPLID/data_classes.py'  
adding 'ChimeraX_ProPLID-0.1.dist-info/METADATA'  
adding 'ChimeraX_ProPLID-0.1.dist-info/WHEEL'  
adding 'ChimeraX_ProPLID-0.1.dist-info/top_level.txt'  
adding 'ChimeraX_ProPLID-0.1.dist-info/RECORD'  
removing build/bdist.macosx-10.9-x86_64/wheel  
Distribution is in
/Users/aaron.sweeney/Documents/ChimeraX_exts/ProPLID/dist/ChimeraX_ProPLID-0.1-py3-none-
any.whl  
  

> devel install /Users/aaron.sweeney/Documents/ChimeraX_exts/ProPLID


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

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7jjo format mmcif fromDatabase pdb

7jjo title:  
Structural Basis of the Activation of Heterotrimeric Gs-protein by
Isoproterenol-bound Beta1-Adrenergic Receptor [more info...]  
  
Chain information for 7jjo #1  
---  
Chain | Description | UniProt  
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short |
GNAS2_BOVIN  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_BOVIN  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_BOVIN  
N | Nanobody 35 |  
R | Beta1-Adrenergic Receptor |  
  
Non-standard residues in 7jjo #1  
---  
5FW — isoprenaline  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 32 GB

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 5 days 20:14

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 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: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    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: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-HelloWorld: 0.1
    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: 1.1.1
    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: 1.9
    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-ProPLID: 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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-TutorialSelector: 0.1
    ChimeraX-UI: 1.18.3
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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: 4.10.0
    kiwisolver: 1.4.2
    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: 1.5.5
    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: 3.0.29
    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: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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

Component: Unassigned → Platform
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in fork during "devel install"

comment:2 by pett, 3 years ago

Resolution: → nonchimerax
Status: accepted → closed
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