Opened 4 years ago

Closed 4 years ago

#5514 closed defect (duplicate)

volume erase: out of 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.  

> open /Users/dparrell/Desktop/RSV_Montage_chimera/RSV_Montage.cxs

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec.mrc as #1, grid size
2790,3744,448, pixel 18.4,18.4,18.4, shown at step 1, values float32  
Opened RSV_clean.mrc as #4, grid size 2800,3750,448, pixel 18.4,18.4,18.4,
shown at level 0.056, step 2, values float32  
Opened F-prot_clean.mrc as #6, grid size 2800,3750,448, pixel 18.4,18.4,18.4,
shown at level 0.0692, step 2, values float32  
Opened
W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__membrane_seg.hdf as
#7, grid size 2800,3750,448, pixel 18.4, shown at level 0.0915, step 4, values
float32  
Opened membrane_clean.mrc as #2, grid size 2800,3750,448, pixel
18.4,18.4,18.4, shown at level 0.0915, step 4, values float32  
Log from Sat Oct 30 11:12:24 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/dparrell/Desktop/RSV_Montage_chimera/W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec.mrc

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec.mrc as #1, grid size
2790,3744,448, pixel 18.4,18.4,18.4, shown at step 1, values float32  

> volume #1 level -1.932,0 level 4.176,0.8 level 26.58,1

> volume #1 level -1.932,0 level 4.176,0.8 level 26.58,1

> volume #1 color black color white color white

> volume #1 level -1.932,0 level 4.176,0.8 level 26.58,1

> volume #1 color black color white color white

> volume #1 level -12.86,0 level 4.176,0.8 level 26.58,1

> volume #1 level -12.86,0 level 4.176,1 level 26.58,1

> volume #1 level -15.7,0 level 4.176,1 level 26.58,1

> volume #1 level -15.7,0 level 2.696,1 level 26.58,1

> volume #1 level -15.7,0 level 3.56,1 level 26.58,1

> cd ./RSV_Montage_chimera

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

> open
> /Users/dparrell/Desktop/RSV_Montage_chimera/W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__RSV_seg.hdf

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__RSV_seg.hdf as
#2, grid size 2800,3750,448, pixel 18.4, shown at step 1, values float32  

> volume #2 region 0,0,0,2799,3749,447 step 8

> volume #2 region 0,0,0,2799,3749,447 step 8

> volume #2 step 4

> ui tool show "Map Coordinates"

> ui tool show "Hide Dust"

> surface dust #2 size 1411.6

> volume #2 color #ff0099

> volume #2 color #ff00cc

> volume #2 color #cc3399

> volume #2 color #cc0099

> volume #2 color magenta

> volume #2 color #ff33cc

> volume #2 color #cc00cc

> volume #2 step 2

> surface dust #2 size 120

> surface dust #2 size 1200

> surface dust #2 size 12000

> surface dust #2 size 1200

> ui mousemode right "map eraser"

> surface dust #2 size 1239.7

> surface dust #2 size 291.81

> surface dust #2 size 120

> surface dust #2 size 1200

> surface dust #2 size 1200

> volume #2 step 4

> surface dust #2 size 1100

> surface dust #2 size 1100

> save actin_clean.mrc models #5

No volumes specified  

> surface dust #2 size 1000

> surface dust #2 size 1000

> save actin_clean.mrc models #5

No volumes specified  

> surface dust #2 size 90

> surface dust #2 size 900

> surface dust #2 size 900

> save actin_clean.mrc models #5

No volumes specified  

> surface dust #2 size 950

> surface dust #2 size 950

> save actin_clean.mrc models #5

No volumes specified  

> surface dust #2 size 948.86

> surface dust #2 size 944.93

> surface dust #2 size 944.28

> surface dust #2 size 943.63

> surface dust #2 size 95

> surface dust #2 size 950

> surface dust #2 size 950

> save actin_clean.mrc models #5

No volumes specified  

> volume erase #2 center 20275,19540,819.03 radius 23730

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__RSV_seg.hdf
copy as #4, grid size 2800,3750,448, pixel 18.4, shown at step 1, values
float32  

> volume #4 step 4

> surface dust #4 size 950

> save RSV_clean.mrc models #4

> open
> /Users/dparrell/Desktop/RSV_Montage_chimera/W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__F-
> prot_seg.hdf

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__F-prot_seg.hdf
as #5, grid size 2800,3750,448, pixel 18.4, shown at step 1, values float32  

> volume #5 region 0,0,0,2799,3749,447 step 8

> volume #5 region 0,0,0,2799,3749,447 step 8

> volume #5 change image level 0,0 level 0.07064,0.8 level 2.77,1

> volume #5 step 4

> surface dust #5 size 605.62

> surface dust #5 size 50

> surface dust #5 size 500

> surface dust #5 size 500.5

> surface dust #5 size 503.97

> surface dust #5 size 563.97

> surface dust #5 size 563.97

> save RSV_clean.mrc models #4

> surface dust #5 size 60

> surface dust #5 size 600

> volume erase #5 center 20275,19540,819.03 radius 23730

Opened W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__F-prot_seg.hdf
copy as #6, grid size 2800,3750,448, pixel 18.4, shown at step 1, values
float32  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  

> volume #6 step 4

> surface dust #6 size 600

> volume erase #6 center -17047,-39096,8575 radius 23730

> volume erase #4 center -11038,-37139,9605.9 radius 23730

> volume erase #4 center -35237,4110.7,-3951.8 radius 23730

> volume erase #6 center -35237,4110.7,-3951.8 radius 23730

> volume erase #4 center -29542,45690,-3852.9 radius 23730

> volume erase #6 center -29542,45690,-3852.9 radius 23730

> surface dust #6 size 600

> volume erase #6 center 3148.2,41191,5132.3 radius 23730

> volume erase #4 center 3148.2,41191,5132.3 radius 23730

> save F-prot_clean.mrc models #6

> volume erase #6 center 949.5,-30221,-2735.8 radius 23730

> volume erase #4 center 949.5,-30221,-2735.8 radius 23730

> volume erase #6 center -11903,-6356.5,2018.6 radius 5112.1

> volume erase #4 center -11903,-6356.5,2018.6 radius 5112.1

> save /Users/dparrell/Desktop/RSV_Montage_chimera/RSV_Montage.cxs

> volume erase #4 center -14796,-1404.9,-483.51 radius 5112.1

> volume erase #4 center -14238,579.88,-2252.5 radius 5112.1

> volume erase #4 center -25244,-23268,-2591.5 radius 5112.1

> volume erase #4 center -554.69,-248.74,1780.5 radius 6631.9

> volume erase #6 center -554.69,-248.74,1780.5 radius 6631.9

> open
> /Users/dparrell/Desktop/RSV_Montage_chimera/W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__membrane_seg.hdf

Opened
W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__membrane_seg.hdf as
#7, grid size 2800,3750,448, pixel 18.4, shown at step 1, values float32  

> volume #7 step 4

> volume #7 region 0,0,0,2799,3749,447 step 32

> volume #7 region 0,0,0,2799,3749,447 step 32

> volume #7 step 4

> surface dust #7 size 650.73

> volume #7 change image level 0,0 level 0.2699,0.8 level 3.057,1

> volume #7 level 0.1371

> surface undust #7

> surface dust #7 size 4230.6

> volume erase #4 center 8669.9,1221.9,124.52 radius 6631.9

> volume erase #6 center 8669.9,1221.9,124.52 radius 6631.9

> volume erase #4 center -1095.4,6801.8,1735 radius 7840.8

> volume erase #6 center -1095.4,6801.8,1735 radius 7840.8

> volume erase #6 center -8586.1,10886,8265.2 radius 7840.8

> volume erase #4 center -8586.1,10886,8265.2 radius 7840.8

> volume erase #6 center -18591,17500,8101.7 radius 7840.8

> volume erase #4 center 22352,-27772,4465.9 radius 16718

> volume erase #4 center 33775,-7386.8,-10269 radius 16718

> volume erase #4 center -8183.1,-7689.9,-4767.6 radius 5043

> volume erase #4 center -5482,11016,-4188.3 radius 5043

> volume erase #4 center 8981.4,-7806.4,5359.6 radius 5043

> volume erase #4 center -14370,8109.8,2967.8 radius 5043

> volume erase #4 center 14998,-4318.5,-6430.2 radius 5043

> volume erase #6 center 8257.6,-9113.8,6011 radius 5043

> volume erase #6 center 14330,-8245.4,6514.3 radius 5043

> volume erase #6 center -6218.9,10043,-5279.7 radius 5043

> volume erase #6 center 9612.2,-611.22,-822.84 radius 5043

> volume erase #6 center -15376,25037,-6996.8 radius 5043

> save F-prot_clean.mrc models #6

> save RSV_clean.mrc models #4

> save /Users/dparrell/Desktop/RSV_Montage_chimera/RSV_Montage.cxs

> close #5

> close #2

> volume #7 step 8

> volume #7 level 0.09151

> volume #7 step 4

> view orient

> surface dust #7 size 4292.4

> surface dust #7 size 2668.7

> volume #7 step 2

> surface dust #7 size 3668.7

> surface dust #7 size 3668.7

> view orient

> volume #7 step 4

> volume #4 step 2

> volume #6 step 2

> volume erase #7 center -26492,17915,840.64 radius 20172

Opened
W1106_G3_target86_tilt_4_AliSB_v2_bin2_rec_highpass_050__membrane_seg.hdf copy
as #2, grid size 2800,3750,448, pixel 18.4, shown at step 1, values float32  
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,  
5178912264,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
34963,  
5178912264,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
34963,  
5178912264,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
)  
)  
  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  

> volume #2 step 4

> surface dust #2 size 1454.1

> save /Users/dparrell/Desktop/RSV_Montage_chimera/RSV_Montage.cxs

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/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
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/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 612, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack/_packer.pyx", line 286, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 292, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 289, in msgpack._cmsgpack.Packer.pack  
File "msgpack/_packer.pyx", line 225, in msgpack._cmsgpack.Packer._pack  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
ValueError: bytes object is too large  
  
ValueError: bytes object is too large  
  
File "msgpack/_packer.pyx", line 196, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> save membrane_clean.mrc models #2

> save /Users/dparrell/Desktop/RSV_Montage_chimera/RSV_Montage.cxs

——— End of log from Sat Oct 30 11:12:24 2021 ———

opened ChimeraX session  

> ui tool show "Hide Dust"

> surface dust #2 size 18.41

> ui tool show "Map Eraser"

> surface dust #2 size 18.41

> surface undust #2

> surface dust #2 size 3070.4

> surface undust #2

> surface dust #2 size 14015

> cd ./RSV_Montage_chimera

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

> volume erase #2 center 26676,-26226,8162.7 radius 11468

Opened membrane_clean.mrc copy as #5, grid size 2800,3750,448, pixel
18.4,18.4,18.4, shown at step 1, values float32  
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,  
5028638016,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
34963,  
5028638016,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
34963,  
5028638016,  
array([[ 609110, 1, 609111],  
[ 609110, 0, 1],  
[ 0, 2, ...,  
GL_STATIC_DRAW,  
)  
)  
  
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value
encountered in log  
h.show_data(log(counts + 1))  




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: 1 day 3:45

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 Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → volume erase: out of memory

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

OpenGL out of memory, duplicate of #5384, error message has been improved.
Session save error, duplicate of #5501, error message has been improved.

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