ChimeraX hangs at startup

[p.drougkas@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19043
ChimeraX Version: 1.3.dev202109240602 (2021-09-24 06:02:51 UTC)
Description
ChimeraX not responded after launching. Also running a daily build didnt help. Renaming the AppData preference folder and running ChimeraX with default setting did the trick. I am attaching a zip-file (ChimeraX_Renamed) with the faulty setting so you can review and possibly figure out what went wrong. 

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3.dev202109240602 (2021-09-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 462.31
OpenGL renderer: GeForce GTX 1660 Ti with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: G3 3590
OS: Microsoft Windows 10 Home (Build 19043)
Memory: 16,980,701,184
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    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
    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: 2.1
    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.dev202109240602
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    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: 2.1.1
    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
    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: 2.0.1
    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
    ChimeraX-ModelPanel: 1.2
    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: 1.7
    ChimeraX-PDB: 2.6.2
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    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: 2.4.4
    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
    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
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distlib: 0.3.2
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    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: 4.8.1
    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: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    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: 2.1.0
    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
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1
File attachment: ChimeraX_Renamed.rar

ChimeraX_Renamed.rar​

[p.drougkas@…]

Added by email2trac

[pett]

Reported by Panagiotis Drougkas

[Greg Couch]

Can you make a similar rar file of your configuration that works and submit that? That would help us look for differences. Eric is the expert, but my scan didn't see any obvious bug, so being able to make a comparison will be very helpful.

[p.drougkas@…]

Dear Greg Couch,
Please find attached both configurations. The default is contained within
the folder ChimeraX and the problematic one within the ChimeraX_renamed.
I hope it helps.
Best
Panagiotis

On Fri, Sep 24, 2021 at 11:50 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

ChimeraX.rar​

ChimeraX_Renamed-1.rar​

[p.drougkas@…]

Added by email2trac

[p.drougkas@…]

Added by email2trac

[pett]

Using the provided config file worked fine on my Mac at home, as well as on a Windows box at work (snow). I'm a wee bit at a loss as to how to make any progress here since those both worked.

--Eric

[p.drougkas@…]

Hi Eric,
I am also a bit confused because it happened again with the default file
and after going through the renaming procedure again the issue was
resolved. No worries though. The program is still working fine now that I
ve found the fix. I will let you know if anything changes. Thanks for your
time!

Best
Panagiotis

On Mon, Sep 27, 2021 at 10:06 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[p.drougkas@…]

Dear Eric,

Sorry to bother you yet again. It seems likely that the crash is related to
how many projects I have stored in the ChimeraX homepage. For now I manage
to reproduce this by starting with default details and opening mrc maps and
closing the session. After 3-4 sessions were stored in the homepage the app
crashes.
I believe the freezing I reported in my previous messages is related to
that cause I must have had at least 10-15 sessions resting on the homepage
screen.
Please find the logs of the 2 crashes I mentioned, below.
Hope this helps.
Thank you for your time!

Best regards
Panagiotis


On Tue, Sep 28, 2021 at 10:06 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

Description_2.txt​

Description.txt​

Gathered Information.txt​

Gathered Information_2.txt​

[p.drougkas@…]

Added by email2trac

[p.drougkas@…]

Added by email2trac

[p.drougkas@…]

Added by email2trac

[p.drougkas@…]

Added by email2trac

[pett]

Opening/closing a few maps and one structure.

[Tom Goddard]

This ticket started out reporting ChimeraX not starting correctly.

Now 4 attachments are about crashes when closing a session when ChimeraX runs Python garbage collection. That is an entirely separate error and would best be reported in a separate ticket. That garbage collection crash is one we have seen dozens of times but have never been able to reproduce, debug or fix.

I am retitling this ticket to match the original reported problem. If the crashes you saw in the attachments are reproducible, please report them separately. ChimeraX daily builds on Windows should ask you to report a crash the next time you run it.

[Tom Goddard]

Eric was not able to reproduce the hang at startup. For the separate crashing problems please make a separate bug report.

[p.drougkas@…]

Dear ChimeraX team,

I managed to find what was the cause of this issue. I am using a laptop and
I connect it to a secondary display both at work and at home. The cause of
the issue is that ChimeraX is set to start up on my main display which was
different at my home ( secondary display) and my office (laptop build-in
display). As soon as the display setting were re-adjusted the issue was
resolved. I just wanted to let you know both for closure and in case this
info is useful to you in the future.

Best
Panagiotis


On Tue, Sep 28, 2021 at 9:48 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

Thanks! That will help us when others encounter the problem.

Do I understand your explanation correctly? You told Windows to start ChimeraX on the external display which you have at home. But then if there was no external display connected (at the office) then ChimeraX would hang at startup? And the solution was to just not tell Windows to start on that external display?

[p.drougkas@…]

Hi Tom,

No in both cases an external display was connected. At home the external
display serves as the main display, so any program starts is launched
there.
Now at the office the main display was my build in display so each time I
tried to launch ChimeraX it froze.
The fix was to go to the display settings and select my external display as
my main display.

Hope it is more clear now
Let me know if you need more details.

Best
Panagiotis

On Tue, 5 Oct 2021, 18:33 ChimeraX, <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[goddard@…]

Thanks for the clarification.

It is puzzling.  At the office the main display is the laptop display and there is an external display and ChimeraX hangs on startup?  That sounds like a pretty standard configuration, so I am surprised that can cause a hang.

I vaguely recall a ChimeraX problem where it tries to start with a window size bigger than the screen and fails somehow.  ChimeraX remembers the last window size and uses that the next time you start it.  So maybe you ran ChimeraX at home on the external display with a large window size.  Then next tried to start it at the office and the large window size (in pixels) would not fit on the laptop display causing the hang.  I can test this.

In any case it seems like a bug in the Qt window toolkit.

[p.drougkas@…]

Yes it sounds exactly like what happened!

On Tue, 5 Oct 2021, 19:03 ChimeraX, <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

[Tom Goddard]

I tried with ChimeraX 1.2.5 and daily build on Windows 10 with two displays to get it to hang on startup by making the window two big to fit on the smaller display then restarting ChimeraX on that smaller display. Nothing I did hung ChimeraX at startup. Every time it either made ChimeraX smaller or allowed it to extend beyond the edge of the screen. I tried making the external display the primary display, or the laptop display the primary display. Neither of my displays are 4K (I think both UHD). Qt treats high-DPI displays (e.g. 4K) in special ways so maybe that is needed to get the hang.

At any rate I was unable to reproduce the problem.