Opened 4 years ago

Closed 4 years ago

#6004 closed defect (nonchimerax)

Crash in graphics driver deleting ribbon graphics, possibly during simulation

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-89-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f473d7b7700 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f4888114740 (most recent call first):
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2617 in release_buffer
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2608 in delete_buffer
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1236 in _delete_geometry
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1206 in delete
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 342 in remove_drawings
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 349 in remove_all_drawings
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 581 in clear
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 34 in _make_ribbon_graphics
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/ribbon.py", line 589 in compute_ribbons
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 600 in _create_ribbon_graphics
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 337 in update_graphics_if_needed
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/nucleotides/_data.py", line 615 in _rebuild_molecule
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/atomic/changes.py", line 45 in check_for_changes
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 58 in draw_new_frame
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/programs/x86_64-linux/chimerax/1.3_c8/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> alias st isolde step $*

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/cns-obrien/dsDNA_isolde_1-21-2_6pm.pdb format pdb

Chain information for dsDNA_isolde_1-21-2_6pm.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D E F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> close

> open /home/cns-obrien/TypeIC_dsDNA_structure/dsDNA_1-22-22_8pm.pdb

Chain information for dsDNA_1-22-22_8pm.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C D E F | No description available  
G | No description available  
H | No description available  
I | No description available  
J K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> open /home/cns-
> obrien/TypeIC_dsDNA_structure/cryosparc_P16_J118_004_volume_map_sharp.mrc

Opened cryosparc_P16_J118_004_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 1.1, shown at level 0.567, step 2, values float32  

> volume #2 step 1

> volume #2 level 1.986

> transparency #2 50

> hide atoms

> show cartoons

> fitmap #1/I:350-373 inMap #2

Fit molecule dsDNA_1-22-22_8pm.pdb (#1) to map
cryosparc_P16_J118_004_volume_map_sharp.mrc (#2) using 392 atoms  
average map value = 1.16, steps = 96  
shifted from previous position = 1.42  
rotated from previous position = 6.48 degrees  
atoms outside contour = 302, contour level = 1.986  
  
Position of dsDNA_1-22-22_8pm.pdb (#1) relative to
cryosparc_P16_J118_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99382834 -0.10987391 0.01526281 24.52444409  
0.11017304 0.99370353 -0.02037621 -20.98303426  
-0.01292790 0.02193201 0.99967588 -1.39237558  
Axis 0.18733410 0.12482399 0.97433306  
Axis point 203.19971335 210.73710969 0.00000000  
Rotation angle (degrees) 6.48377390  
Shift along axis 0.61844124  
  

> select #1

49589 atoms, 50380 bonds, 20 pseudobonds, 3070 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99383,-0.10987,0.015263,26.065,0.11017,0.9937,-0.020376,-22.549,-0.012928,0.021932,0.99968,-3.3445

> ~select #1

Nothing selected  

> undo

> fitmap #1 inMap #2

Fit molecule dsDNA_1-22-22_8pm.pdb (#1) to map
cryosparc_P16_J118_004_volume_map_sharp.mrc (#2) using 49589 atoms  
average map value = 0.9349, steps = 276  
shifted from previous position = 2.1  
rotated from previous position = 6.41 degrees  
atoms outside contour = 40317, contour level = 1.986  
  
Position of dsDNA_1-22-22_8pm.pdb (#1) relative to
cryosparc_P16_J118_004_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999761 -0.00137090 -0.00170053 0.70120813  
0.00136845 0.99999803 -0.00144095 -0.01025532  
0.00170250 0.00143862 0.99999752 -1.14972929  
Axis 0.55034745 -0.65039497 0.52354949  
Axis point 611.63325144 0.00000000 479.24454454  
Rotation angle (degrees) 0.14989344  
Shift along axis -0.20936207  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for dsDNA_1-22-22_8pm.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C 1.2/D 1.2/E 1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/I | No description available  
1.2/J 1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
  
Done loading forcefield  


===== Log before crash end =====

Log:
> alias st isolde step $*

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 460.91.03
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           78Gi        33Gi       9.6Gi       203Mi        35Gi        43Gi
	Swap:          63Gi        16Gi        47Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)	
	Subsystem: PNY GP104 [GeForce GTX 1080] [196e:119e]	
	Kernel driver in use: nvidia
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-Clipper: 0.17.0
    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-ISOLDE: 1.3
    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: Tristan Croll added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash creating ribbon graphics, possibly during simulation

comment:2 by Tom Goddard, 4 years ago

Resolution: → nonchimerax
Status: assigned → closed
Summary: Crash creating ribbon graphics, possibly during simulation → Crash in graphics driver deleting ribbon graphics, possibly during simulation

Crash in graphics driver while removing a ribbon in this ChimeraX line.

GL.glDeleteBuffers(1, [self.opengl_buffer])

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