Opened 4 years ago

Closed 4 years ago

#5607 closed defect (limitation)

volume step 2: out of graphics memory

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

Description

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd W1362_G1_montage_chimera

Current working directory is: /Users/dparrell/Desktop/W1362_G1_montage_chimera  

> cd W1362_G1_montage_chimera

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd ./W1362_G1_montage_chimera

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd /Desktop/W1362_G1_montage_chimera

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd /Desktop/

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd ../

Current working directory is: /Users/dparrell/Desktop  

> cd W1362_G1_montage_chimera

Current working directory is: /Users/dparrell/Desktop/W1362_G1_montage_chimera  

> open
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ER_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ERMem_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__mitos_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__NPC_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__nucleus_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec.mrc
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__golgi_seg.hdf
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__ribosomes_seg.hdf

Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ER_seg.hdf as #1,
grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__ERMem_seg.hdf as #2,
grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf
as #3, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__mitos_seg.hdf as #4,
grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__NPC_seg.hdf as #5,
grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__nucleus_seg.hdf as
#6, grid size 1860,2496,326, pixel 27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec.mrc as #7, grid size
1860,2496,326, pixel 27.6,27.6,27.6, shown at step 1, values float32  
Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__golgi_seg.hdf as
#8, grid size 2800,3750,288, pixel 18.4, shown at step 1, values float32  
Opened
w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin4_rec_trim_preproc__ribosomes_seg.hdf as
#9, grid size 2800,3750,288, pixel 18.4, shown at step 1, values float32  

> volume #1 level 0.001684,0 level 0.1244,0.8 level 2.405,1

> volume #2 level 0.0008498,0 level 0.1642,0.8 level 2.124,1

> ui tool show "Map Coordinates"

> volume #9 level 0.0673,0 level 0.1073,0.8 level 0.1566,1

> save /Users/dparrell/Desktop/W1362_G1_montage_chimera/W1362_G1_Montage.cxs

> volume #7 level -0.8056,0 level 1.664,0.8 level 3.976,1

> volume #7 level -0.8056,0 level 1.664,0.8 level 3.976,1

> volume #7 color black color white color white

> volume #7 color black color white color white

> volume #7 level -3.905,0 level 1.664,0.8 level 3.976,1

> volume #7 level -3.905,0 level -0.4981,1 level 3.976,1

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> show #!7 models

> volume #7 level -4.036,0 level -0.4981,1 level 3.976,1

> volume #7 level -4.036,0 level 1.769,1 level 3.976,1

> volume #7 level -4.036,0 level 1.769,1 level 0.2873,0.5735

> volume #7 level -0.9976,0.04412 level 1.769,1 level 0.2873,0.5735

> volume #7 level -0.9976,0.04412 level 1.769,1 level 0.0757,1

> volume #7 level -0.6046,0 level 1.769,1 level 0.0757,1

> volume #7 level -0.6046,0 level 0.4156,1 level 0.0757,1

> volume #7 level -0.6046,0 level 4.757,1 level 0.0757,1

> volume #7 level -0.6046,0 level 4.757,1 level -0.15,1

> volume #7 level -2.458,0 level 4.757,1 level -0.15,1

> volume #7 level -2.458,0 level 4.757,1 level 0.3658,0.8824

> volume #7 level -2.168,0.01471 level 4.757,1 level 0.3658,0.8824

> volume #7 level -2.168,0.01471 level 1.726,1 level 0.3658,0.8824

> volume #8 level 0,0 level 0.3252,0.8 level 5.113,1

> volume #8 region 0,0,0,2799,3749,287 step 8

> volume #8 region 0,0,0,2799,3749,287 step 8

> volume #8 step 4

> volume #8 color #996600

> ui tool show "Hide Dust"

> surface dust #7 size 165.71

No surfaces specified  

> volume #8 color #003399

> surface dust #8 size 359.75

> surface dust #8 size 731.31

> volume #9 color #cc6600 color white color white

> volume #9 region 0,0,0,2799,3749,287 step 8

> volume #9 region 0,0,0,2799,3749,287 step 8

> volume #9 color #996600

> volume #9 step 4

> volume #9 level 0.09678

> surface dust #9 size 530.03

> surface dust #9 size 40

> surface dust #9 size 400

> volume #1 region 0,0,0,1859,2495,325 step 8

> volume #1 region 0,0,0,1859,2495,325 step 8

> volume #1 step 4

> volume #1 color #339933

> volume #1 step 2

> surface dust #1 size 350

> volume #3 level 0,0 level 0.731,0.8 level 9.668,1

> volume #3 color #ff00cc color white color white

> volume #3 color #990099 color white color white

> volume #3 region 0,0,0,1859,2495,325 step 8

> volume #3 region 0,0,0,1859,2495,325 step 8

> volume #3 color #990099

> volume #3 step 2

> volume #3 level 0.8893

> volume #3 level 0.5651

> surface dust #3 size 255.38

> surface dust #3 size 259.83

> surface dust #3 size 498.76

> surface dust #3 size 490.56

> surface dust #3 size 312.24

> surface undust #3

> surface dust #3 size 312.24

> volume #2 region 0,0,0,1859,2495,325 step 8

> volume #2 region 0,0,0,1859,2495,325 step 8

> volume #2 step 4

> volume #2 color #006600

> surface dust #2 size 89.87

> surface dust #2 size 128.7

> surface undust #2

> surface dust #2 size 531.85

> volume #4 level 0.004534,0 level 0.4042,0.8 level 2.061,1

> volume #4 region 0,0,0,1859,2495,325 step 8

> volume #4 region 0,0,0,1859,2495,325 step 8

> volume #2 color #ffff33

> volume #2 color #666600

> volume #2 color #33cc66

> volume #4 color #ffff33

> volume #4 step 2

> surface dust #4 size 165.71

> surface undust #4

> surface dust #4 size 440.75

> surface dust #4 size 60

> surface dust #4 size 600

> surface dust #4 size 600

> cd W1362_G1_montage_chimera

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> surface dust #4 size 80

> surface dust #4 size 800

> surface dust #4 size 800

> surface undust #4

> surface dust #4 size 2745.3

> surface undust #4

> surface dust #4 size 2000

> volume #5 level 0,0 level 0.5777,0.8 level 2.881,1

> volume #5 region 0,0,0,1859,2495,325 step 8

> volume #5 region 0,0,0,1859,2495,325 step 8

> volume #5 step 4

> surface dust #5 size 165.71

> surface undust #5

> surface dust #5 size 800

> volume #6 level 0,0 level 0.07658,0.8 level 1.612,1

> volume #6 color #cc3300 color white color white

> volume #6 region 0,0,0,1859,2495,325 step 8

> volume #6 region 0,0,0,1859,2495,325 step 8

> volume #6 color #cc0000

> volume #6 step 2

> surface dust #6 size 984.22

> open
> /Users/dparrell/Desktop/W1362_G1_montage_chimera/w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_lp8.mrc

Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_lp8.mrc as #10, grid size
1860,2496,326, pixel 27.6,27.6,27.6, shown at step 1, values float32  

> volume #10 level -0.2795,0 level 0.6702,0.8 level 1.786,1

> volume #10 level -1.638,0 level 0.6702,0.8 level 1.786,1

> volume #10 color black color #ffffb3 color #ffffb3

> volume #10 level -1.638,0 level 0.6702,0.8 level 1.786,1

> volume #10 level -1.638,0 level 0.06799,1 level 1.786,1

> volume #10 color black color white color #ffffb3

> volume #10 level -0.7891,0 level 0.06799,1 level 1.786,1

> volume #10 level -0.7891,0 level 0.4618,1 level 1.786,1

> volume #10 level -1.793,0 level 0.4618,1 level 1.786,1

> volume #10 level -1.793,0 level 0.2996,1 level 1.786,1

> volume #10 level -1.793,0 level 0.4436,1 level 1.786,1

> volume #10 level -1.649,0 level 0.4436,1 level 1.786,1

> volume #10 level -2.296,0 level 0.4436,1 level 1.786,1

> volume #10 level -2.296,0 level 0.2036,1 level 1.786,1

> volume #10 level -2.296,0 level 0.2036,1 level 1.786,1

> volume #10 color black color white color black

> volume #10 level -2.296,0 level 0.2036,1 level 1.795,1

> volume #10 color black color white color white

> volume #10 color black color white color #999999

> volume #10 color black color white color #666666

> volume #10 color black color white color white

> volume #10 color black color #666666 color white

> volume #10 level -2.296,0 level 0.2036,1 level 1.795,1

> volume #10 level -2.296,0 level -0.1874,1 level 1.795,1

> volume #10 level -2.296,0 level -0.1874,1 level 0.4349,1

> volume #10 color black color white color white

> volume #10 color black color #333333 color white

> volume #10 color black color #cccccc color white

> volume #10 color black color #999999 color white

> volume #10 color black color #999999 color white

> volume #10 color black color #999999 color white

> volume #10 level -2.296,0 level -0.02745,1 level 0.4349,1

> volume #10 level -2.296,0 level -0.02745,1 level 0.4349,1

> volume #10 level -2.296,0 level -0.02745,1 level 2.142,1

> volume #10 level -2.296,0 level -0.02745,1 level 0.3194,1

> volume #10 level -2.296,0 level -0.4008,1 level 0.3194,1

> volume #10 level -2.296,0 level -0.4008,1 level 0.7371,1

> volume #10 level -2.296,0 level -0.2408,1 level 0.7371,1

> volume #10 level -2.296,0 level -0.2408,1 level 0.7371,1

> volume #10 level -2.296,0 level -0.2408,1 level 0.4794,0.9853

> volume #10 level -2.296,0 level -1.361,0.3088 level 0.4794,0.9853

> volume #10 level -2.296,0 level -1.361,0.3088 level 1.742,1

> volume #10 level -2.296,0 level -0.143,1 level 1.742,1

> volume #10 level -2.296,0 level -0.143,1 level 0.4794,1

> volume #10 level -2.296,0 level -0.08079,1 level 0.4794,1

> volume #9 step 2

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
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 233, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1498, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1511, in _draw_multiple  
d.draw(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 751, in draw  
self.draw_self(renderer, draw_pass)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 758, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 785, in _draw_geometry  
ds.activate_bindings(renderer)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1858, in activate_bindings  
self.update_buffers()  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/drawing.py", line 1846, in update_buffers  
b.update_buffer_data(data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 2662, in update_buffer_data  
GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW)  
File "src/latebind.pyx", line 51, in OpenGL_accelerate.latebind.Curry.__call__  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/OpenGL/GL/VERSION/GL_1_5.py", line 89, in glBufferData  
return baseOperation( target, size, data, usage )  
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 = glBufferData,  
pyArgs = (  
34963,  
6935638752,  
array([[ 1, 2, 2625002],  
[ 2625001, 1, 2625002],  
[ 2625000, 0, 2...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
34963,  
6935638752,  
array([[ 1, 2, 2625002],  
[ 2625001, 1, 2625002],  
[ 2625000, 0, 2...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
34963,  
6935638752,  
array([[ 1, 2, 2625002],  
[ 2625001, 1, 2625002],  
[ 2625000, 0, 2...,  
GL_STATIC_DRAW,  
)  
)  
  

> volume #9 level 0.04339

> close #9

> graphics reset

Expected a keyword  

> graphics restart

> ui mousemode right "map eraser"

> volume erase #3 center -7789,-509.37,-1415.7 radius 34467 outside true

Opened w1362_G1_L1_3x3_tilt_1_AliSB_v2_bin3_rec_preproc__lipid_drops_seg.hdf
copy as #11, grid size 1860,2496,326, pixel 27.6, shown at step 1, values
float32  

> volume erase #11 center 21132,2852.5,-5239.7 radius 15480

> volume erase #11 center -34913,18658,16.618 radius 15480

> volume erase #11 center -37616,-29297,850.9 radius 15480

> volume erase #11 center -39648,-9397.8,1294.3 radius 15480

> volume erase #11 center -31759,-4966.8,-247.23 radius 9306.2

> volume erase #11 center -30740,2985.9,6991.5 radius 9306.2

> volume erase #11 center -30400,-17661,7080 radius 9306.2

> volume erase #11 center -22433,-12279,8883.7 radius 9306.2

> surface dust #3 size 307.11

> surface dust #3 size 223.51

> surface dust #3 size 223.51

> graphics restart

> surface dust #3 size 200

> surface dust #3 size 200

> graphics restart

> graphics restart

> surface dust #11 size 150

> volume erase #11 center -24935,7637.6,-3199.1 radius 3240

> volume erase #11 center -26311,2283.5,-5603 radius 3240

> volume erase #11 center -21785,-5301.1,-1777.9 radius 4446.3

> volume erase #11 center 4962.6,12813,-499.6 radius 16854

> volume erase #11 center 13277,-19909,-413.01 radius 11133

> volume erase #11 center -35306,-13571,-6981.1 radius 11133

> volume erase #11 center -33852,-25056,-2045.7 radius 11133

> volume erase #11 center -17764,41261,-2231.5 radius 12546

> volume erase #11 center -5494.8,11384,-1589.1 radius 12546

> volume erase #11 center -12243,-27373,-385.04 radius 2171.4

> volume erase #11 center -12230,-27677,-304.13 radius 2171.4

> volume erase #11 center -23427,-30536,-2959.7 radius 4308.4

> volume erase #11 center -25114,8951.4,1239.8 radius 4308.4

> volume erase #11 center -13684,-13144,-1186.5 radius 4170.5

> orient

Unknown command: orient  

> view orient

> surface dust #11 size 144.94

> surface dust #11 size 212.81

> surface dust #11 size 250

> save lipid_droplets_clean.mrc #11

> save /Users/dparrell/Desktop/W1362_G1_montage_chimera/W1362_G1_Montage.cxs




OpenGL version: 4.1 ATI-2.11.26
OpenGL renderer: AMD Radeon Pro Vega 64X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac Pro
      Model Identifier: iMacPro1,1
      Processor Name: Intel Xeon W
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 18
      L2 Cache (per Core): 1 MB
      L3 Cache: 24.8 MB
      Hyper-Threading Technology: Enabled
      Memory: 256 GB
      Boot ROM Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G9323)
      Kernel Version: Darwin 18.7.0
      Time since boot: 2:01

Graphics/Displays:

    Radeon Pro Vega 64X:

      Chipset Model: Radeon Pro Vega 64X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 16 GB
      Vendor: AMD (0x1002)
      Device ID: 0x686b
      Revision ID: 0x0000
      ROM Revision: 113-D0500D-114
      VBIOS Version: 113-D05001A1XX-021
      Option ROM Version: 113-D05001A1XX-021
      EFI Driver Version: 01.01.114
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Component: UnassignedVolume Data
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionvolume step 2: out of graphics memory

comment:2 by Tom Goddard, 4 years ago

Resolution: limitation
Status: assignedclosed

Tried to show a size 2800,3750,288 map at step 2 (3 Gvoxels, float32, 12 Gbytes) and graphics card did not have sufficient memory. The glBufferData call was trying to fill a 7 Gbyte texture. I don't understand that buffers size, would expect it to be only 1.5 Gbytes. Maybe it is blending multiple maps since the user has 11 maps open that are each 1-2 Gbytes in size and another map had exactly the same size. Graphics AMD Radeon Pro Vega 64X has 16 Gbytes of memory.

The user used "graphics restart" so they understood the error message.

Is there any way we can improve this? Obviously we can't render if the graphics is out of memory. We could give an error message without a traceback. We could continue rendering only omit the maps where the allocation failed. Seems like a good bit of work for a quite rare case which is handled clearly enough now.

Note: See TracTickets for help on using tickets.