Opened 3 years ago

Closed 3 years ago

#8743 closed defect (can't reproduce)

glDrawBuffer: invalid operation

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-5.15.0-40-generic-x86_64-with-debian-bookworm-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/jeyasankar/Documents/Data/Maps/VRA002/cryosparc_P39_J154_005_volume_map.mrc
> /home/jeyasankar/Documents/Data/Maps/VRA002/cryosparc_P39_J153_005_volume_map.mrc

Opened cryosparc_P39_J154_005_volume_map.mrc, grid size 256,256,256, pixel
0.914, shown at level 0.0516, step 1, values float32  

> volume #1.1 level 0.175

> volume #1.2 level 0.1048

> volume #1.1 level 0.209

> close #1

> open
> /home/jeyasankar/Documents/Data/Maps/VRA002/cryosparc_P39_J170_004_volume_map_sharp.mrc
> /home/jeyasankar/Documents/Data/Maps/VRA002/cryosparc_P39_J169_005_volume_map_sharp.mrc

Opened cryosparc_P39_J170_004_volume_map_sharp.mrc, grid size 300,300,300,
pixel 0.914, shown at level 0.0989, step 2, values float32  

> volume #1.1 step 1

> volume #1.2 step 1

> volume #1.1 color #62a0ea

> volume #1.2 color #ed333b

> volume #1.2 color #c061cb

> open /home/jeyasankar/Documents/Data/PDB/3GIZ_fit.pdb

3GIZ_fit.pdb title:  
Crystal structure of the fab fragment of ANTI-CD20 antibody ofatumumab [more
info...]  
  
Chain information for 3GIZ_fit.pdb #2  
---  
Chain | Description  
H | fab fragment of ANTI-CD20 antibody ofatumumab, heavy chain  
L | fab fragment of ANTI-CD20 antibody ofatumumab, light chain  
  
Non-standard residues in 3GIZ_fit.pdb #2  
---  
ZN — zinc ion  
  

> volume #1.1 level 0.182

> select #2

3485 atoms, 3341 bonds, 8 pseudobonds, 651 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui tool show "Fit in Map"

Average map value = 0.1573 for 3485 atoms, 2037 outside contour  
Average map value = 0.1573 for 3485 atoms, 2037 outside contour  
Correlation = 0.6549, Correlation about mean = 0.09725, Overlap = 440.2  
  
Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J170_004_volume_map_sharp.mrc
using 8572 points  
correlation = 0.6858, correlation about mean = 0.1647, overlap = 477.4  
steps = 120, shift = 4.57, angle = 15.1 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J170_004_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.05846765 0.93781425 0.34217828 -60.30368924  
-0.99744498 -0.04078495 -0.05865233 266.07885891  
-0.04104927 -0.34473327 0.93780271 72.69798904  
Axis -0.14350882 0.19224117 -0.97079789  
Axis point 91.84945435 169.61664145 0.00000000  
Rotation angle (degrees) 94.63023685  
Shift along axis -10.76963266  
  
Average map value = 0.1725 for 3485 atoms, 1891 outside contour  

> transparency #1.1.1 50

> set bgColor white

> ui mousemode right "rotate selected models"

Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J170_004_volume_map_sharp.mrc
using 8572 points  
correlation = 0.7077, correlation about mean = 0.1607, overlap = 506.1  
steps = 108, shift = 2.36, angle = 13.3 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J170_004_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.04382855 -0.88285041 -0.46760476 359.35874463  
0.96991872 0.07458157 -0.23172241 58.17743322  
0.23945092 -0.46369466 0.85302434 74.14920809  
Axis -0.11618246 -0.35412627 0.92795270  
Axis point 153.58385206 226.30485270 0.00000000  
Rotation angle (degrees) 93.33141012  
Shift along axis 6.45361675  
  
Average map value = 0.1819 for 3485 atoms, 1862 outside contour  

> save /home/jeyasankar/Desktop/image1.png supersample 3

> save /home/jeyasankar/Desktop/image2.png supersample 3

> volume #1.2 level 0.2724

> transparency #1.2.1 50

> volume #1.2 level 0.2839

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J169_005_volume_map_sharp.mrc
using 8572 points  
correlation = 0.6733, correlation about mean = 0.0993, overlap = 587  
steps = 80, shift = 4.07, angle = 3.76 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J169_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.03532016 -0.91068725 -0.41158380 353.82324137  
0.96514899 0.07577632 -0.25049029 57.46576470  
0.25930661 -0.40608704 0.87627245 35.09165712  
Axis -0.07786590 -0.33573633 0.93873213  
Axis point 151.39241803 215.22327551 0.00000000  
Rotation angle (degrees) 92.38623957  
Shift along axis -13.90244332  
  
Average map value = 0.2137 for 3485 atoms, 2308 outside contour  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J169_005_volume_map_sharp.mrc
using 8572 points  
correlation = 0.5105, correlation about mean = 0.1224, overlap = 426.9  
steps = 120, shift = 4.44, angle = 21.7 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J169_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.14945131 0.19139666 0.97006785 -51.27407092  
-0.02103145 0.98147972 -0.19040808 -14.59994116  
-0.98854539 0.00805481 0.15070878 183.41284035  
Axis 0.10023022 0.98916340 -0.10728310  
Axis point 79.48069329 0.00000000 118.48803054  
Rotation angle (degrees) 81.90470636  
Shift along axis -39.25803732  
  
Average map value = 0.1519 for 3485 atoms, 2533 outside contour  

> ui mousemode right "translate selected models"

Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J169_005_volume_map_sharp.mrc
using 8572 points  
correlation = 0.4936, correlation about mean = 0.11, overlap = 422.1  
steps = 88, shift = 3.04, angle = 6.84 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J169_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.03152377 0.19116062 0.98105243 -59.19031555  
-0.03615555 0.98111595 -0.19001123 36.41681226  
-0.99884885 -0.02948062 0.03783999 210.26090917  
Axis 0.08029088 0.99026612 -0.11369431  
Axis point 78.24251504 0.00000000 138.17899568  
Rotation angle (degrees) 88.55370919  
Shift along axis 7.40442417  
  
Average map value = 0.1532 for 3485 atoms, 2526 outside contour  
Fit map 3GIZ_fit.pdb map 6 in map cryosparc_P39_J169_005_volume_map_sharp.mrc
using 8572 points  
correlation = 0.4821, correlation about mean = 0.08207, overlap = 425.5  
steps = 164, shift = 3.44, angle = 16.1 degrees  
  
Position of 3GIZ_fit.pdb map 6 (#3) relative to
cryosparc_P39_J169_005_volume_map_sharp.mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.18921160 0.26077073 0.94667714 -26.07405149  
-0.18146554 0.93819999 -0.29470500 45.31118107  
-0.96502292 -0.22755088 -0.13019742 330.71091001  
Axis 0.03420413 0.97370097 -0.22524762  
Axis point 123.20537182 0.00000000 181.18315040  
Rotation angle (degrees) 100.98806487  
Shift along axis -31.26414465  
  
Average map value = 0.1541 for 3485 atoms, 2465 outside contour  

> hide #!2 models

> ~select #2

Nothing selected  

> save /home/jeyasankar/Desktop/image3.png supersample 3

> save /home/jeyasankar/Desktop/image4.png supersample 3

> show #!2 models

> select #2

3485 atoms, 3341 bonds, 8 pseudobonds, 651 residues, 3 models selected  
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.  
  
Traceback (most recent call last):  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/core/updateloop.py", line 73, in
draw_new_frame  
view.draw(check_for_changes = False)  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/view.py", line 165, in
draw  
self._draw_scene(camera, drawings)  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/view.py", line 248, in
_draw_scene  
pixel_width = self._highlight_width)  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/drawing.py", line 1556,
in draw_highlight_outline  
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 1796,
in finish_rendering_outline  
r.pop_framebuffer()  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 654,
in pop_framebuffer  
fb.activate()  
File "/cryoem_software/applications/chimerax_1.1/usr/lib/ucsf-
chimerax/lib/python3.7/site-packages/chimerax/graphics/opengl.py", line 2182,
in activate  
GL.glDrawBuffer(self._draw_buffer)  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDrawBuffer,  
cArguments = (GL_BACK,)  
)  
  




OpenGL version: 3.3.0 NVIDIA 510.73.05
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: FUJITSU
Model: CELSIUS W580power
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
CPU: 16 Intel(R) Xeon(R) E-2288G CPU @ 3.70GHz
Cache Size: 16384 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       4.0Gi       8.1Gi       166Mi        19Gi        26Gi
	Swap:          2.0Gi       734Mi       1.3Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:12a0]	
	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 pett, 3 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → glDrawBuffer: invalid operation

comment:2 by Tom Goddard, 3 years ago

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

Possible graphics driver bug. Selecting a PDB model. Very old ChimeraX version 1.1.

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