Opened 5 years ago

Closed 5 years ago

#4316 closed defect (nonchimerax)

Out of memory rendering volume texture

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

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.0-64-generic-x86_64-with-debian-bullseye-sid
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  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  

> help help:user

> open /home/andrea/Avatar/2nd-series_RESCALED3x.tif

Opened 2nd-series_RESCALED3x.tif, grid size 1328,1286,624, pixel 1, shown at
step 1, values uint16  

> volume #1 region 0,0,0,1327,1285,623 step 4

> volume #1 region 0,0,0,1327,1285,623 step 4

> volume #1 step 1

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 "/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 "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 240, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1493, in draw_transparent  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1174, in draw_transparent  
draw()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1493, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1499, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 780, in draw  
pd = self._update_planes(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 545, in _update_planes  
pd = self._update_3d_texture_planes(view_dir)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 597, in _update_3d_texture_planes  
pd = self._texture_3d_planes()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 607, in _texture_3d_planes  
pd = Texture3dPlanes(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1144, in __init__  
self._fill_textures()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/image3d.py", line 1240, in _fill_textures  
t.reload_texture(td, now = True)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2970, in reload_texture  
self.fill_opengl_texture()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2980, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2874, in initialize_texture  
0, format, tdtype, data)  
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/PyOpenGL-3.1.5-py3.7.egg/OpenGL/platform/baseplatform.py", line 415,
in __call__  
return self( *args, **named )  
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_RG8,  
1328,  
1286,  
624,  
0,  
GL_RG,  
GL_UNSIGNED_BYTE,  
array([[[[113, 0],  
[118, 0],  
[120, 0],  
...,  
[ 77, 0],  
[ 74, 0]...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_RG8,  
1328,  
1286,  
624,  
0,  
GL_RG,  
GL_UNSIGNED_BYTE,  
array([[[[113, 0],  
[118, 0],  
[120, 0],  
...,  
[ 77, 0],  
[ 74, 0]...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_RG8,  
1328,  
1286,  
624,  
0,  
GL_RG,  
GL_UNSIGNED_BYTE,  
array([[[[113, 0],  
[118, 0],  
[120, 0],  
...,  
[ 77, 0],  
[ 74, 0]...,  
)  
)  
  
Exception ignored in: <function Drawing.__del__ at 0x7f1b107b2680>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1172, in __del__  
self.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1192, in delete  
raise RuntimeError("Don't have opengl context needed to delete texture from
drawing '%s' because drawing was never drawn" % self.name)  
RuntimeError: Don't have opengl context needed to delete texture from drawing
'Image3D 3d texture planes' because drawing was never drawn  
Exception ignored in: <function Texture.__del__ at 0x7f1b0fe65ef0>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2931, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

> show target m




OpenGL version: 4.5 (Core Profile) Mesa 20.2.6
OpenGL renderer: llvmpipe (LLVM 11.0.0, 256 bits)
OpenGL vendor: Mesa/X.org
Manufacturer: TYAN
Model: B7109F77DV14HR-2T-N
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 80 Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz
Cache Size: 28160 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          1.5Ti        27Gi       1.4Ti       384Mi        30Gi       1.4Ti
	Swap:         8.0Gi          0B       8.0Gi

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]	
	Kernel driver in use: ast
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: 2.1.3
    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: 1.3
    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, 5 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Out of memory rendering volume texture

comment:2 by Tom Goddard, 5 years ago

Cc: andrea.fera@… added
Resolution: → nonchimerax
Status: assigned → closed

Graphics reports out of memory trying to allocate an OpenGL 3D texture show a 10 Gbyte tiff 3d image at full resolution. Texture is 20 Gbytes. Graphics driver is Mesa, software rendering. I don't know what controls how big a 3D texture the Mesa driver will allow. The machine has 1.5 Tbytes memory so it has plenty. I suspect the driver simply won't allow a single large 3D texture, probably limited to 8 Gbytes. By switching ChimeraX to use multiple 2D textures it may be able to render. To use 2D texture rendering for volume model #1 use

volume #1 projectionMode 2d-z

https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid

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