Opened 3 years ago

Closed 3 years ago

#7583 closed defect (nonchimerax)

glTexImage3D: out of memory

Reported by: eddy731@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Utz Ermel
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-46-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
open the tomogram in ChimeraX by ArtiaX

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /media/clark/Tomo2/tet/Agro/25/25_rec.mrc

Opened 25_rec.mrc as #1, grid size 1023,1440,600, pixel 13.6,13.6,13.6, shown
at step 1, values float32  

> volume #1 region 0,0,0,1022,1439,599 step 4

[Repeated 1 time(s)]

> volume #1 change image level 138.5,0 level 177,0.8 level 442.7,1

> volume #1 style mesh

> volume #1 style image

> volume #1 region 0,0,296,1022,1439,296 step 1 showOutlineBox true

> volume planes z style image imageMode "full region"

> mousemode rightMode "move planes"

> volume #1 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 0 tiltedSlabSpacing 13.6 tiltedSlabPlaneCount 10

> mousemode rightMode "rotate slab"

> volume #1 tiltedSlabAxis 0.1308,0.3775,0.9167 tiltedSlabOffset 4831

> volume #1 tiltedSlabAxis -0.2602,0.2336,0.9369 tiltedSlabOffset -1168

> volume #1 tiltedSlabAxis -0.3643,0.422,0.8302 tiltedSlabOffset -1105

> volume #1 tiltedSlabAxis -0.3751,0.07138,0.9242 tiltedSlabOffset -4817

> volume scale #1 factor -1

Opened 25_rec.mrc scaled as #2, grid size 1023,1440,600, pixel 13.6,13.6,13.6,
shown at step 1, values float32  

> volume #2 tiltedSlabAxis -0.5679,0.04529,0.8219 tiltedSlabOffset -6583

> volume #2 tiltedSlabAxis -0.3416,-0.09773,0.9348 tiltedSlabOffset -5755

> set bgColor white

> show #!1 models

> hide #!2 models

> volume #1 tiltedSlabAxis -0.2671,-0.1462,0.9525 tiltedSlabOffset -5906

> volume #1 tiltedSlabAxis -0.7231,-0.0757,0.6866 tiltedSlabOffset -9575

> volume #2 level -164.4,0 level -126.1,0.8 level 748.4,1

> volume #2 level -235.1,0.3906 level -126.1,0.8 level 748.4,1

> volume #2 level -235.1,0.3906 level -117.3,0.7375 level 748.4,1

> hide #!2 models

> volume #1 level 74.43,0.2188 level 177,0.8 level 442.7,1

> volume #1 tiltedSlabAxis -0.4834,-0.4985,0.7196 tiltedSlabOffset -1.026e+04

> toolshed show

Downloading bundle ChimeraX_ArtiaX-0.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/clark/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/1.4/site-packages  
sysconfig: /home/clark/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/typing-
extensions  
sysconfig: /home/clark/.local/include/python3.9/typing-extensions  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/bin  
sysconfig: /home/clark/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX  
sysconfig: /home/clark/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/pandas  
sysconfig: /home/clark/.local/include/python3.9/pandas  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/superqt  
sysconfig: /home/clark/.local/include/python3.9/superqt  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/starfile  
sysconfig: /home/clark/.local/include/python3.9/starfile  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/ChimeraX-ArtiaX  
sysconfig: /home/clark/.local/include/python3.9/ChimeraX-ArtiaX  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/clark/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/clark/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.3.1; however, version 22.2.2 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_ArtiaX-0.1-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.3 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.4)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-UI>=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.18.3)  
Requirement already satisfied: ChimeraX-Log>=1.1.4 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1.5)  
Requirement already satisfied: ChimeraX-BILD~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Collecting superqt  
Downloading superqt-0.3.5-py3-none-any.whl (59 kB)  
Requirement already satisfied: ChimeraX-Markers~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Geometry>=1.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.2)  
Requirement already satisfied: ChimeraX-IMOD~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand>=1.5 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.5.1)  
Collecting starfile  
Using cached starfile-0.4.11-py3-none-any.whl (27 kB)  
Requirement already satisfied: ChimeraX-ModelPanel>=1.2.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.3.2)  
Requirement already satisfied: ChimeraX-OpenCommand>=1.7 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.9)  
Requirement already satisfied: ChimeraX-MouseModes~=1.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-Atomic>=1.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.39.1)  
Requirement already satisfied: ChimeraX-Map~=1.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-ArtiaX==0.1) (1.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (2.6.6)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=7.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (7.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
Atomic>=1.1->ChimeraX-ArtiaX==0.1) (2.0.1)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (2.0.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (2.7)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.1->ChimeraX-
ArtiaX==0.1) (1.0.2)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-BILD~=1.0->ChimeraX-
ArtiaX==0.1) (1.2.2)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-BILD~=1.0->ChimeraX-
ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.1->ChimeraX-
ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-Map~=1.1->ChimeraX-
ArtiaX==0.1) (2.1)  
Requirement already satisfied: ChimeraX-StdCommands>=1.3.1,~=1.3 in
/usr/lib/ucsf-chimerax/lib/python3.9/site-packages (from ChimeraX-
ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1) (1.8)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
OpenCommand>=1.7->ChimeraX-ArtiaX==0.1) (1.0.1)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-UI>=1.0->ChimeraX-
ArtiaX==0.1) (1.0)  
Collecting pandas  
Downloading
pandas-1.4.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7
MB)  
Collecting typing-extensions  
Downloading typing_extensions-4.3.0-py3-none-any.whl (25 kB)  
Requirement already satisfied: qtpy>=1.1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1)
(2.1.0)  
Requirement already satisfied: pygments>=2.4.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1)
(2.11.2)  
Requirement already satisfied: packaging in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from superqt->ChimeraX-ArtiaX==0.1)
(21.3)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-
Map~=1.1->ChimeraX-ArtiaX==0.1) (2.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI>=1.0->ChimeraX-ArtiaX==0.1) (1.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from ChimeraX-
StdCommands>=1.3.1,~=1.3->ChimeraX-ModelPanel>=1.2.1->ChimeraX-ArtiaX==0.1)
(2.0)  
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from packaging->superqt->ChimeraX-
ArtiaX==0.1) (3.0.9)  
Requirement already satisfied: numpy>=1.18.5 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX-
ArtiaX==0.1) (1.22.1)  
Requirement already satisfied: python-dateutil>=2.8.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX-
ArtiaX==0.1) (2.8.2)  
Requirement already satisfied: pytz>=2020.1 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from pandas->starfile->ChimeraX-
ArtiaX==0.1) (2022.1)  
Requirement already satisfied: six>=1.5 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from python-
dateutil>=2.8.1->pandas->starfile->ChimeraX-ArtiaX==0.1) (1.16.0)  
Installing collected packages: typing-extensions, pandas, superqt, starfile,
ChimeraX-ArtiaX  
Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.4 starfile-0.4.11
superqt-0.3.5 typing-extensions-4.3.0  
\---  

Successfully installed ChimeraX-ArtiaX-0.1 pandas-1.4.4 starfile-0.4.11
superqt-0.3.5 typing-extensions-4.3.0  
Installed ChimeraX-ArtiaX (0.1)  
Downloading bundle ChimeraX_ArtiaX-0.1-py3-none-any.whl  
Bundle installation canceled  

> volume #1 tiltedSlabAxis -0.4427,-0.2399,0.864 tiltedSlabOffset -6704

> ui tool show Toolbar

> ui tool show ArtiaX

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> volume #1 tiltedSlabAxis -0.3586,-0.28,0.8905 tiltedSlabOffset -6226

> volume #1 tiltedSlabAxis -0.2321,0.1462,0.9616 tiltedSlabOffset -718.2

> artiax add tomo #1

Opened 25_rec.mrc as #3.1.1, grid size 1023,1440,600, pixel 13.6,13.6,13.6,
shown at level 176, step 1, values float32  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

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 = 1285,  
description = b'out of memory',  
baseOperation = glTexImage3D,  
pyArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
)  
)  
  
Traceback (most recent call last):  
File "/usr/lib/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/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 242, in _draw_scene  
draw_transparent(r, transparent_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1531, in draw_transparent  
r.draw_transparent(  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1242, in draw_transparent  
draw()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1533, in <lambda>  
lambda: _draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1539, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd = self._update_planes(renderer)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 548, in _update_planes  
pd = self._update_3d_texture_planes(view_dir)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 600, in _update_3d_texture_planes  
pd = self._texture_3d_planes()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 610, in _texture_3d_planes  
pd = Texture3dPlanes(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1147, in __init__  
self._fill_textures()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1243, in _fill_textures  
t.reload_texture(td, now = True)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 3058, in reload_texture  
self.fill_opengl_texture()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 3068, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2961, in initialize_texture  
GL.glTexImage3D(gl_target, 0, iformat, size[0], size[1], size[2],  
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 "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_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
),  
cArgs = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
),  
cArguments = (  
GL_TEXTURE_3D,  
0,  
GL_R32F,  
1023,  
1440,  
600,  
0,  
GL_RED,  
GL_FLOAT,  
array([[[156.30373, 157.8497 , 157.32513, ..., 147.21478, 145.89235,  
149.99055],  
[155.93594, 160.395...,  
)  
)  
  
Exception ignored in: <function Drawing.__del__ at 0x7f1ae9f061f0>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1189, in __del__  
self.delete()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1209, 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 0x7f1ae6bfdd30>  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 3019, 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  

> artiax add tomo #2

Opened 25_rec.mrc scaled as #3.1.2, grid size 1023,1440,600, pixel
13.6,13.6,13.6, shown at level -126, step 1, values float32  

> artiax tomo #3.1.2 sliceDirection 0,0,1

> artiax view xy




OpenGL version: 4.5 (Core Profile) Mesa 21.2.6
OpenGL renderer: llvmpipe (LLVM 12.0.0, 256 bits)
OpenGL vendor: Mesa/X.org

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virtual Machine: none
CPU: 96 Intel(R) Xeon(R) Gold 6240R CPU @ 2.40GHz
Cache Size: 36608 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi        12Gi       167Gi        93Mi        71Gi       236Gi
	Swap:         2.0Gi          0B       2.0Gi

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d]

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.1
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    pandas: 1.4.4
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    starfile: 0.4.11
    suds-community: 1.0.0
    superqt: 0.3.5
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 4.3.0
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Utz Ermel added
Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → glTexImage3D: out of memory

Reported by Yi-Ting Liao.

comment:2 by Tom Goddard, 3 years ago

Resolution: → nonchimerax
Status: assigned → closed

As the error message says "out of memory". You are trying to display a large map 1023 by 1440 by 600 with float values, about 3.5 GBytes, at full resolution and the graphics is saying it does not have enough memory. You can try using step 2 which shows every other grid point. Maybe ArtiaX makes it show step 1 -- we did not write ArtiaX so I don't know if it does that. Another approach is to bin your map by a factor of 2.

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