Opened 4 years ago

Last modified 4 years ago

#6038 assigned defect

ChimeraX Log panel broken on Fedora

Reported by: paulaj@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Dear ChimeraX developers,
Since I switched to Fedora, I've been getting an error that does not allow the log and some other tools (such as the start view with the previous structures) to open. I tried to use the bug reporter tool, but when I click submit, nothing happens. The error happens with both the rpm and the tarball version, but the tarball allows me to see the log in the terminal. I appended it here along with the information the bug reporter detects.
Thank you in advance!
Paula

____________ log ___________

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
NOTE: Traceback (most recent call last):
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool
    ti = api._api_caller.start_tool(api, session, self, tool_info)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool
    return cls._get_func(api, "start_tool")(session, ti.name)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/__init__.py", line 39, in start_tool
    return cmd.get_singleton(session, create=True)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/cmd.py", line 19, in get_singleton
    return tools.get_singleton(session, Log, 'Log', create=create)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton
    tinst = tool_class(session, tool_name, **kw)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py", line 161, in __init__
    from chimerax.ui.widgets import ChimeraXHtmlView
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/ui/widgets/ChimeraXHtmlView.py", line 20, in <module>
    from Qt.QtWebEngineWidgets import QWebEngineView, QWebEnginePage,
QWebEngineProfile
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/Qt/QtWebEngineWidgets.py", line 4, in <module>
    from PyQt5.QtWebEngineWidgets import *
ImportError: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/tools.py", line 379, in start_tools
    bi.start_tool(session, tool_name)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
    raise ToolshedError(
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b


BUG: Tool "Log" failed to start:
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in
bundle ChimeraX-Log:
/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version
OPENSSL_1_1_1b

File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool
raise ToolshedError(

 _See log for complete Python traceback._


NOTE: UCSF ChimeraX version: 1.3 (2021-12-08)
NOTE: © 2016-2021 Regents of the University of California.  All rights reserved.
NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html)

NOTE: Traceback (most recent call last):
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
    return self._func(self._name, data)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py", line 110, in
_delayed_register_log_recorder
    _register_log_recorder(session)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/bug_reporter/crash_report.py", line 144, in
_register_log_recorder
    log.record_to_file(log_file)
  File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py", line 396, in record_to_file
    self._log_to_file(self.page_source)
AttributeError: 'Log' object has no attribute 'page_source'


BUG: Error processing trigger "new frame":
AttributeError: 'Log' object has no attribute 'page_source'

File "/home/paula/Apps/install/ChimeraX-1.3/chimerax-1.3/lib/python3.9/site-
packages/chimerax/log/tool.py", line 396, in record_to_file
self._log_to_file(self.page_source)

 _See log for complete Python traceback._

____________ system info ___________

Platform: Linux-5.15.14-200.fc35.x86_64-x86_64-with-glibc2.34
ChimeraX version: 1.3 (2021-12-08 23:08:33 UTC)

Gathered information:

OpenGL version: 4.6 (Core Profile) Mesa 21.3.4

OpenGL renderer: Mesa Intel(R) HD Graphics 520 (SKL GT2)

OpenGL vendor: Intel

Manufacturer: LENOVO

Model: 80UK

OS: Fedora Linux 35

Architecture: 64bit ELF

Virutal Machine: none

CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz

Cache Size: 3072 KB

Memory:

              total        used        free      shared  buff/cache   available

Mem:           7.6Gi       3.8Gi       391Mi       872Mi       3.4Gi       2.7Gi

Swap:          7.6Gi        42Mi       7.6Gi


Graphics:

00:02.0 VGA compatible controller [0300]: Intel Corporation Skylake GT2 [HD Graphics 520] [8086:1916] (rev 07)

Subsystem: Lenovo Device [17aa:381d]

Kernel driver in use: i915

Locale: ('en_GB', 'UTF-8')

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: 2021.10.8

    cftime: 1.5.1.1

    charset-normalizer: 2.0.9

    ChimeraX-AddCharge: 1.2.2

    ChimeraX-AddH: 2.1.11

    ChimeraX-AlignmentAlgorithms: 2.0

    ChimeraX-AlignmentHdrs: 3.2

    ChimeraX-AlignmentMatrices: 2.0

    ChimeraX-Alignments: 2.2.3

    ChimeraX-AlphaFold: 1.0

    ChimeraX-AltlocExplorer: 1.0.1

    ChimeraX-AmberInfo: 1.0

    ChimeraX-Arrays: 1.0

    ChimeraX-Atomic: 1.31

    ChimeraX-AtomicLibrary: 4.2

    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: 2.6.1

    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

    ChimeraX-CommandLine: 1.1.5

    ChimeraX-ConnectStructure: 2.0

    ChimeraX-Contacts: 1.0

    ChimeraX-Core: 1.3

    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-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: 2.1.2

    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-LinuxSupport: 1.0

    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: 2.0.4

    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: 1.2.6

    ChimeraX-ModelPanel: 1.2.1

    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: 2.6.5

    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: 1.0.1

    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: 2.4.6

    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: 1.6.1

    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: 1.13.7

    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

    cxservices: 1.1

    cycler: 0.11.0

    Cython: 0.29.24

    decorator: 5.1.0

    distro: 1.6.0

    docutils: 0.17.1

    filelock: 3.0.12

    funcparserlib: 0.3.6

    grako: 3.16.5

    h5py: 3.6.0

    html2text: 2020.1.16

    idna: 3.3

    ihm: 0.21

    imagecodecs: 2021.4.28

    imagesize: 1.3.0

    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: 4.9.1

    kiwisolver: 1.3.2

    line-profiler: 3.3.0

    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: 2.8.0

    numpy: 1.21.2

    openvr: 1.16.801

    packaging: 21.3

    ParmEd: 3.2.0

    parso: 0.8.3

    pexpect: 4.8.0

    pickleshare: 0.7.5

    Pillow: 8.3.2

    pip: 21.2.4

    pkginfo: 1.7.1

    prompt-toolkit: 3.0.23

    psutil: 5.8.0

    ptyprocess: 0.7.0

    pycollada: 0.7.1

    pydicom: 2.1.2

    Pygments: 2.10.0

    PyOpenGL: 3.1.5

    PyOpenGL-accelerate: 3.1.5

    pyparsing: 3.0.6

    PyQt5-commercial: 5.15.2

    PyQt5-sip: 12.8.1

    PyQtWebEngine-commercial: 5.15.2

    python-dateutil: 2.8.2

    pytz: 2021.3

    pyzmq: 22.3.0

    qtconsole: 5.1.1

    QtPy: 1.11.3

    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: 2.2.0

    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: 5.1.1

    urllib3: 1.26.7

    wcwidth: 0.2.5

    webcolors: 1.11.1

    wheel: 0.37.0

    wheel-filename: 1.3.0

Change History (3)

comment:1 by Tom Goddard, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Platform
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: Log start error → ChimeraX Log panel broken on Fedora

Thanks for the bug report! That log traceback is very useful info. We have seen ChimeraX Log panel and other things not work in recent versions of Fedora and your info may help us understand why it doesn't work, looks like an openssl problem related to the Qt window toolkit support for html panels like the Log.

ImportError: /lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b

What we have found is that a new tech preview daily build of ChimeraX that uses Qt 6 instead of the Qt 5 we have been using in ChimeraX works on newer Fedora. We expect this working ChimeraX to be on our download page as a "tech preview" (at the bottom) early next week.

Maybe with the traceback you provide we will be able to figure out how to make Qt 5 ChimeraX work too. It may require some additional OpenSSL package on your system.

comment:2 by Tom Goddard, 4 years ago

What version of Fedora are you using?

in reply to:  3 ; comment:3 by paulaj@…, 4 years ago 

Awesome, I will definitely keep an eye out for Qt 6 ChimeraX too.
I am on fedora 35.
Thank you for the feedback!
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, January 28, 2022 23:05
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; Paula Jofily <paulaj@uwaterloo.ca>
Subject: Re: [ChimeraX] #6038: ChimeraX Log panel broken on Fedora

#6038: ChimeraX Log panel broken on Fedora
-------------------------------+------------------------
          Reporter:  paulaj@…  |      Owner:  Greg Couch
              Type:  defect    |     Status:  assigned
          Priority:  normal    |  Milestone:
         Component:  Platform  |    Version:
        Resolution:            |   Keywords:
        Blocked By:            |   Blocking:
Notify when closed:            |   Platform:  all
           Project:  ChimeraX  |
-------------------------------+------------------------

Comment (by Tom Goddard):

 What version of Fedora are you using?

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6038#comment:2>
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