Opened 5 years ago

Closed 5 years ago

#3786 closed defect (can't reproduce)

graphics hung?

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.18.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        5.8G         94G        4.2G         25G        114G
	Swap:          255G          0B        255G

Graphics:
	08:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1e81] (rev a1)	
	Subsystem: PNY Device [196e:133f]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → graphics hung?

comment:2 by Tom Goddard, 5 years ago

Resolution: → can't reproduce
Status: assigned → closed

The user pressed ctrl-C a bunch of times in the shell where they started ChimeraX on Linux (CentOS 7). There is nothing else in the log so they had not opened any files. But the user interface was working since they sent this bug via the Report a Bug tool. The log says "available bundle cache has not been initialized yet" which worries me, maybe ChimeraX was hung at startup making a toolshed internet connection.

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