Opened 4 years ago

Closed 4 years ago

#6427 closed defect (nonchimerax)

[ChimeraX] OpenGL.error.GLError: GLError with VirtualGL 3.0 and TurboVNC 2.2.7

Reported by: Chung-Han.Tsai@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Hi UCSF ChimeraX,

I would like to submit a bug/issue report as the following.

This issue happens after VirtualGL 3.0 is activated with the EGL backend and TurboVNC 2.2.7 is used to create a monitor with GPU acceleration. When ChimeraX is opened by running "vglrun -d /dev/dri/card7 chimerax", ChimeraX can be opened successfully; however, when just clicked a mrc model, this OpenGL issue pops up. I can also see that Chimerax runs with GPU from nvidia-smi.(Describe the actions that caused this problem to occur here)
This issue happens after VirtualGL 3.0 is activated with the EGL backend and TurboVNC 2.2.7 is used to create a monitor with GPU acceleration. When ChimeraX is opened by running "vglrun -d /dev/dri/card7 chimerax", ChimeraX can be opened successfully; however, when just clicked a mrc model, this OpenGL issue pops up. I can also see that Chimerax runs with GPU from nvidia-smi.


---------------------------------------------
Opened NCI_cryosparc_P7_J19_008_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1, shown at level 0.298, step 1, values float32
Traceback (most recent call last):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest
    self._callback(info)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept
    return interceptor(request_info, *args)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 366, in intercept
    chimerax_intercept(*args, view=view, session=session)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept
    session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 382, in thread_safe
    func(*args, **kw)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 459, in defer
    cxcmd(session, topic)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd
    run(session, cmd)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856, in run
    result = ci.function(session, **kw_args)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 118, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2856, in run
    result = ci.function(session, **kw_args)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 238, in provider_open
    session.logger.status(status, log=status)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/logger.py", line 456, in status
    StatusLogger.status(self, msg, **kw)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/logger.py", line 199, in status
    if l.status(msg, color, secondary) and getattr(l, "excludes_other_logs", True):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 889, in status
    sbar.status(msg, color, secondary)
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/statusbar.py", line 150, in status
    r.draw_background()
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1166, in draw_background
    GL.glClear(flags)
  File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
 err = 1282,
 description = b'invalid operation',
 baseOperation = glClear,
 cArguments = (16640,)
)

OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glClear,
cArguments = (16640,)
)

File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError

See log for complete Python traceback.

An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error.

GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glGetString,
cArguments = (GL_VERSION,),
result = b'3.3.0 NVIDIA 510.47.03'
)

Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 139, in draw
if not self._use_opengl():
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 106, in _use_opengl
self._initialize_opengl()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 117, in _initialize_opengl
r.check_opengl_version()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1052, in check_opengl_version
vmajor, vminor = self.opengl_version_number()
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1038, in opengl_version_number
vs = self.opengl_version().split()[0].split('.')[:2]
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1034, in opengl_version
return GL.glGetString(GL.GL_VERSION).decode('utf-8')
File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glGetString,
cArguments = (GL_VERSION,),
result = b'3.3.0 NVIDIA 510.47.03'
)

---------------------------------------------

OpenGL version: 3.3.0 NVIDIA 510.47.03
OpenGL renderer: NVIDIA A40/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: DSS8440
OS: Red Hat Enterprise Linux 8.5 Ootpa
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 5218 CPU @ 2.30GHz
Cache Size: 22528 KB
Memory:
             total        used        free      shared  buff/cache   available
Mem:          754Gi       3.5Gi       748Gi        53Mi       1.6Gi       747Gi
Swap:         299Gi          0B       299Gi

Graphics:
03:00.0 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. Integrated Matrox G200eW3 Graphics Controller [102b:0536] (rev 04)
DeviceName: Embedded Video
Subsystem: Dell Device [1028:088d]
Locale: ('en_US', '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 (2)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Graphics
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned

comment:2 by Greg Couch, 4 years ago

Resolution: → nonchimerax
Status: assigned → closed

That appears to be a VirtualGL bug. Please file a bug at ​https://github.com/VirtualGL/virtualgl/issues.

In the meantime, you should consider switching to VirtualGL 2.6.5 with the OpenGL backend.

An aside, and possibly related, is that ChimeraX does not work with the Qt6 Wayland EGL platform.

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