Error contacting toolshed for updates

[mchow1@…]

The following bug report has been submitted:
Platform:        Linux-5.10.0-23-amd64-x86_64-with-glibc2.31
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007feb32ffd700 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 954 in getaddrinfo
  File "/usr/lib/ucsf-chimerax/lib/python3.9/socket.py", line 823 in create_connection
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 946 in connect
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1447 in connect
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 980 in send
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1040 in _send_output
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1280 in endheaders
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1331 in _send_request
  File "/usr/lib/ucsf-chimerax/lib/python3.9/http/client.py", line 1285 in request
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1346 in do_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 1389 in https_open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 494 in _call_chain
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 534 in _open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 517 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.9/urllib/request.py", line 214 in urlopen
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/available.py", line 49 in load
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 456 in reload_available
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007feb87f7f740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.182.03
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=KDE
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:0
Manufacturer: System manufacturer
Model: System Product Name
OS: Debian GNU/Linux 11 bullseye
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
Cache Size: 16384 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.4Gi        27Gi        86Mi       1.6Gi        28Gi
	Swap:           15Gi          0B        15Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117 [GeForce GTX 1650] [10de:1f82] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. TU117 [GeForce GTX 1650] [1043:8773]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Reported by Martin Chow

[Greg Couch]

This appears to be dying in Python's network code. Let's start with: does this happen every time? And are you on a VPN? And if so, does ChimeraX work if you're not on the VPN?

[mchow1@…]

Chimerax/chimerax-daily won't start since day one, complaining something about OpenGL.
However, after installing the libgl1-mesa-dev package, both programs started working.
Thank you.
Martin Chow
ps OS = Debian 11 (bullseye).

________________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, June 9, 2023 8:57 PM
To: gregc@cgl.ucsf.edu; Chow, Martin
Subject: Re: [ChimeraX] #9160: Error contacting toolshed for updates

CAUTION: External Sender


#9160: Error contacting toolshed for updates
--------------------------------+------------------------
          Reporter:  mchow1@…   |      Owner:  Greg Couch
              Type:  defect     |     Status:  assigned
          Priority:  normal     |  Milestone:
         Component:  Tool Shed  |    Version:
        Resolution:             |   Keywords:
        Blocked By:             |   Blocking:
Notify when closed:             |   Platform:  all
           Project:  ChimeraX   |
--------------------------------+------------------------
Comment (by Greg Couch):

 This appears to be dying in Python's network code.  Let's start with: does
 this happen every time?  And are you on a VPN?  And if so, does ChimeraX
 work if you're not on the VPN?
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9160#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Greg Couch]

Sounds like you installed the generic Linux ChimeraX tarball. If so, you are responsible for installing any dependencies.

So it was probably not libgl1-mesa-dev that fixed things, but one of its dependencies. The dev packages are not be needed. If you haven't installed libglu1-mesa, you should do so.

If you can use the package for Ubuntu 20.04, which is based on Debian Bulleye, and use apt to install it, you'll automatically get all of the dependencies. I'm planning to provide a flatpak alternative to the generic Linux version in the next few weeks. And, depending on feedback, getting rid of the tarball.

[Greg Couch]

That still doesn't explain the crash in the Python networking code.

[mchow1@…]

A little backstory first: I have built two Debian 11 systems with different CPUs and GPUs. One of them initially had issues with OpenGL, while the other one worked fine, including Chimerax/Chimerax-daily. The problematic system continued to work normally but not Chimerax. I didn't follow up on this issue simply because I have an alternative for using Chimerax.

You are absolutely right about the libgl1-mesa-dev package, as I only needed runtime. Usually, I check the Debian wiki for package information, but I didn't this time.
I suppose I was too eager to proceed. However, I did install the bulleye *chimerax.deb package on both systems.

I believe we can conclude this thread because it seems the issue was not with the software itself, but rather a problem with the computer from the beginning.

Finally, I have no knowledge about Python networking code. In fact, I wasn't even aware that the dialog box appeared after libgl1-mesa-dev was installed and
after Chimerax started to work. The only thing I can think of is that I didn't restart the terminal, similar to rebooting MS-DOS. However, I doubt this would be related.

I hope this clarifies the situation.
Thanks,
Martin