"make install" hangs, possibly contacting RBVI servers

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.dev202303240108 (2023-03-24 01:08:46 UTC)
Description
"make install" on a pure Python bundle is taking 20-30 seconds instead of 2 seconds about half the time.  It just freezes after the make install command for 20 seconds, then completes normally.  I fear it is ChimeraX contacting our servers and they are slow to respond.  I see crick has a load average of 30 right now.  Of course ChimeraX should not be contacting our servers on "make install".

Here is an example, on vive.cgl.ucsf.edu (Windows 10) from a cygwin shell

cd chimerax/src/bundles/model_panel
$ time make install
PYTHONNOUSERSITE=1 ../../../ChimeraX.app/bin/python.exe -I -m chimerax.core --nogui --exit --safemode --cmd "devel install . user false exit true  "
Executing: devel install . user false exit true
running build
running build_py
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\model_panel
copying build\lib\chimerax\model_panel\tool.py -> build\bdist.win-amd64\wheel\.\
chimerax\model_panel
copying build\lib\chimerax\model_panel\__init__.py -> build\bdist.win-amd64\whee
l\.\chimerax\model_panel
running install_egg_info
running egg_info
writing ChimeraX_ModelPanel.egg-info\PKG-INFO
writing dependency_links to ChimeraX_ModelPanel.egg-info\dependency_links.txt
writing requirements to ChimeraX_ModelPanel.egg-info\requires.txt
writing top-level names to ChimeraX_ModelPanel.egg-info\top_level.txt
reading manifest file 'ChimeraX_ModelPanel.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_ModelPanel.egg-info\SOURCES.txt'
Copying ChimeraX_ModelPanel.egg-info to build\bdist.win-amd64\wheel\.\ChimeraX_M
odelPanel-1.3.7-py3.9.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_ModelPanel-1.3.7.dist-info\WHEEL
creating 'dist\ChimeraX_ModelPanel-1.3.7-py3-none-any.whl' and adding 'build\bdi
st.win-amd64\wheel' to it
adding 'chimerax/model_panel/__init__.py'
adding 'chimerax/model_panel/tool.py'
adding 'ChimeraX_ModelPanel-1.3.7.dist-info/METADATA'
adding 'ChimeraX_ModelPanel-1.3.7.dist-info/WHEEL'
adding 'ChimeraX_ModelPanel-1.3.7.dist-info/top_level.txt'
adding 'ChimeraX_ModelPanel-1.3.7.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in .\dist\ChimeraX_ModelPanel-1.3.7-py3-none-any.whl
Installing bundle
Executing: toolshed install .\dist\ChimeraX_ModelPanel-1.3.7-py3-none-any.whl us
erOnly false reinstall true
Errors may have occurred when running pip:
pip standard error:
---

[notice] A new release of pip is available: 23.0 -> 23.0.1
[notice] To update, run: C:\cygwin64\home\goddard\ucsf\chimerax\ChimeraX.app\bin
\python.exe -m pip install --upgrade pip
---
pip standard output:
---
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/py
pi/
Processing c:\cygwin64\home\goddard\ucsf\chimerax\src\bundles\model_panel\dist\c
himerax_modelpanel-1.3.7-py3-none-any.whl
Installing collected packages: ChimeraX-ModelPanel
  Attempting uninstall: ChimeraX-ModelPanel
    Found existing installation: ChimeraX-ModelPanel 1.3.7
    Uninstalling ChimeraX-ModelPanel-1.3.7:
      Successfully uninstalled ChimeraX-ModelPanel-1.3.7
Successfully installed ChimeraX-ModelPanel-1.3.7
---
Successfully installed ChimeraX-ModelPanel-1.3.7
Installed ChimeraX-ModelPanel (1.3.7)


real    0m24.255s
user    0m0.015s
sys     0m0.123s

I checked the load average on plato nodes right after this test:

$ ssh plato.cgl.ucsf.edu
Last login: Mon Dec 19 16:43:35 2022 from 169.230.21.34
[goddard@watson ~]$ w
 14:55:45 up 14 days, 17:57,  1 user,  load average: 0.10, 0.09, 0.13
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
goddard  pts/2    169.230.21.232   14:55    1.00s  0.15s  0.06s w

[goddard@watson ~]$ ssh franklin
Last login: Thu Jan 26 15:09:24 2023 from 169.230.21.34
[goddard@franklin ~]$ w
 14:56:04 up 14 days, 17:35,  1 user,  load average: 0.14, 0.07, 0.09
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
goddard  pts/5    169.230.27.32    14:56    1.00s  0.14s  0.06s w

[goddard@franklin ~]$ ssh crick
Last login: Fri Mar 24 13:37:04 2023 from 169.230.21.34
[goddard@crick ~]$ w
 14:56:12 up 14 days, 17:50,  2 users,  load average: 31.54, 31.32, 31.40
USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT
goddard  pts/0    169.230.27.22    14:56    1.00s  0.07s  0.03s w
murashka pts/2    169.230.79.31    13:46    1:01m  0.24s  0.06s kadmin



Log:
Startup Messages  
---  
warnings | QWindowsWindow::setDarkBorderToWindow: Unable to set dark window
border.  
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.  
  
Could not find tool "Tabbed Toolbar"  
UCSF ChimeraX version: 1.6.dev202303240108 (2023-03-24)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 528.24
OpenGL renderer: Quadro P6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.1, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: To be filled by O.E.M.
OS: Microsoft Windows 10 Home (Build 19044)
Memory: 66,135,482,368
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.0.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.7
    ChimeraX-AtomicLibrary: 10.0.3
    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: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.1
    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-Clipper: 0.20.0
    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.dev202303240108
    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: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 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-ISOLDE: 1.6.dev1
    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: 1.1.4
    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: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    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-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.13
    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: 1.0
    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: 2.8.1
    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: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    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-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-TugLigands: 1.1
    ChimeraX-UI: 1.26.1
    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: 0.1.2
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.2.0
    jupyterlab-widgets: 3.0.5
    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
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.0
    pandas: 1.5.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6: 6.4.1
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pywin32: 305
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 65.1.1
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    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: 1.0.2
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5
    WMI: 1.5.1
    zipp: 3.12.0