Opened 5 years ago

Closed 5 years ago

#4290 closed defect (duplicate)

Various session save/restore errors

Reported by: sitins07@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:/Useful things/EV6-EV8-EV9_j1661_session.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 684, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 565, in restore_snapshot  
m.add([model], _from_session=True)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 663, in add  
self.add(children, parent=model, _notify=False,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 663, in add  
self.add(children, parent=model, _notify=False,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 650, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 714, in _parent_for_added_model  
raise ValueError('Tried to add model %s to parent %s with incompatible id'  
ValueError: Tried to add model j1685_52A_run_class001.mrc #1.1 to parent group
#1.1 with incompatible id  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 684, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 565, in restore_snapshot  
m.add([model], _from_session=True)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 663, in add  
self.add(children, parent=model, _notify=False,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 663, in add  
self.add(children, parent=model, _notify=False,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 650, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 714, in _parent_for_added_model  
raise ValueError('Tried to add model %s to parent %s with incompatible id'  
ValueError: Tried to add model j1685_52A_run_class001.mrc #1.1 to parent group
#1.1 with incompatible id  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 533, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 1754, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 105, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 169, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 412, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 944, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 692, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 502, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 570, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 888, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\models.py", line 858, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\structure.py", line 132, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1548, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000002323A3A4880>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1548, in remove_structure  
self._structures.remove(s)  
  
See log for complete Python traceback.  
  

> open D:/Projects/translocation/G1/j1663_run_class001.mrc

Opened j1663_run_class001.mrc as #2, grid size 288,288,288, pixel 1.16, shown
at level 0.125, step 2, values float32  

> open D:/Projects/translocation/G1/j1664_run_class001.mrc

Opened j1664_run_class001.mrc as #3, grid size 288,288,288, pixel 1.16, shown
at level 0.0998, step 2, values float32  

> open D:/Projects/translocation/G1/j1687_run_class001.mrc

Opened j1687_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown
at level 0.0535, step 2, values float32  

> open D:/Projects/translocation/G1/j1685_run_class001.mrc

Opened j1685_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown
at level 0.055, step 2, values float32  

> open D:/Projects/translocation/G1/j1686_run_class001.mrc

Opened j1686_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown
at level 0.0777, step 2, values float32  

> close #1

> hide #!2 models

> show #!2 models

> rename #2-6 id #7

> rename #7 EV6_rotation-d4d5

> hide #!7 models

> open D:/Projects/translocation/G1/j1676_run_class001.mrc

Opened j1676_run_class001.mrc as #2, grid size 288,288,288, pixel 1.16, shown
at level 0.07, step 2, values float32  

> open D:/Projects/translocation/G1/j1677_run_class001.mrc

Opened j1677_run_class001.mrc as #3, grid size 288,288,288, pixel 1.16, shown
at level 0.0562, step 2, values float32  

> open D:/Projects/translocation/G1/j1689_run_class001.mrc

Opened j1689_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown
at level 0.0553, step 2, values float32  

> open D:/Projects/translocation/G1/j1693_run_class001.mrc

Opened j1693_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown
at level 0.114, step 2, values float32  

> open D:/Projects/translocation/G1/j1688_run_class001.mrc

Opened j1688_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown
at level 0.0556, step 2, values float32  

> rename #2-6 EV8_towards-head id #8

> rename #7 id #2

> rename #8 id #3

> hide #!3 models

> open D:/Projects/translocation/G1/j1680_run_class001.mrc

Opened j1680_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown
at level 0.0544, step 2, values float32  

> open D:/Projects/translocation/G1/j1679_run_class001.mrc

Opened j1679_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown
at level 0.061, step 2, values float32  

> open D:/Projects/translocation/G1/j1694_run_class001.mrc

Opened j1694_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown
at level 0.0522, step 2, values float32  

> open D:/Projects/translocation/G1/j1696_run_class001.mrc

Opened j1696_run_class001.mrc as #7, grid size 288,288,288, pixel 1.16, shown
at level 0.0603, step 2, values float32  

> open D:/Projects/translocation/G1/j1695_run_class001.mrc

Opened j1695_run_class001.mrc as #8, grid size 288,288,288, pixel 1.16, shown
at level 0.0533, step 2, values float32  

> rename #4-8 EV9_towards-decoding id #9

> rename #9 id #4

> close #1

> select all

35 models selected  

> volume sel & #!4.1-5 step 1

> show #!2 models

> show #!3 models

> show #!1 models

> select all

35 models selected  

> volume sel 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 "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\view.py", line 247, in _draw_scene  
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in draw_highlight_outline  
_draw_multiple(drawings, r, Drawing.HIGHLIGHT_DRAW_PASS)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1511, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 751, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 765, in draw_self  
self._draw_geometry(renderer, highlighted_only = True)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 785, in _draw_geometry  
ds.activate_bindings(renderer)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1858, in activate_bindings  
self.update_buffers()  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1846, in update_buffers  
b.update_buffer_data(data)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 2606, 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 "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\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 = (  
GL_ELEMENT_ARRAY_BUFFER,  
10076496,  
array([[ 0, 3, 1],  
[ 2, 3, 0],  
[ 5, 3, 7],  
...,  
...,  
GL_STATIC_DRAW,  
),  
cArgs = (  
GL_ELEMENT_ARRAY_BUFFER,  
10076496,  
array([[ 0, 3, 1],  
[ 2, 3, 0],  
[ 5, 3, 7],  
...,  
...,  
GL_STATIC_DRAW,  
),  
cArguments = (  
GL_ELEMENT_ARRAY_BUFFER,  
10076496,  
array([[ 0, 3, 1],  
[ 2, 3, 0],  
[ 5, 3, 7],  
...,  
...,  
GL_STATIC_DRAW,  
)  
)  
  

> volume sel level 0.025

> hide #!2 models

> show #!2 models

> save D:/Projects/translocation/G3/Figures/g3.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data  
s['array'] = b64encode(compress(dt.matrix().tobytes()))  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000002322335A0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x000002323AD2D9A0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000002323AD2D9D0>
'j1695_run_class001.mrc' -> <chimerax.map.session.GridDataState object at
0x0000023244C1E1C0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002323AD2D9A0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002323AD2D9D0> 'j1695_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1E1C0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002323AD2D9A0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002323AD2D9D0> 'j1695_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1E1C0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'j1695_run_class001.mrc' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'j1695_run_class001.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data  
s['array'] = b64encode(compress(dt.matrix().tobytes()))  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000002322335A0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x000002323AD2D9A0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000002323AD2D9D0>
'j1695_run_class001.mrc' -> <chimerax.map.session.GridDataState object at
0x0000023244C1E1C0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002323AD2D9A0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002323AD2D9D0> 'j1695_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1E1C0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002323AD2D9A0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002323AD2D9D0> 'j1695_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1E1C0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'j1695_run_class001.mrc' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'j1695_run_class001.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2.1 models

> show #!2.1 models

> save D:/Projects/translocation/G3/Figures/g3.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data  
s['array'] = b64encode(compress(dt.matrix().tobytes()))  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py", line
540, in compress  
f.write(data)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py", line
280, in write  
self.fileobj.write(self.compress.compress(data))  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000002322335A0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x000002324548ADF0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000002324548AA30>
'j1676_run_class001.mrc' -> <chimerax.map.session.GridDataState object at
0x0000023244C1ED90>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002324548ADF0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002324548AA30> 'j1676_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1ED90>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002324548ADF0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002324548AA30> 'j1676_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1ED90>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'j1676_run_class001.mrc' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'j1676_run_class001.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 280, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot  
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\map\session.py", line 311, in state_from_grid_data  
s['array'] = b64encode(compress(dt.matrix().tobytes()))  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py", line
540, in compress  
f.write(data)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py", line
280, in write  
self.fileobj.write(self.compress.compress(data))  
MemoryError  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 259, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 283, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x000002322335A0D0> ->
<chimerax.map.volume.VolumeSurface object at 0x000002324548ADF0> 'surface' ->
<chimerax.map.volume.Volume object at 0x000002324548AA30>
'j1676_run_class001.mrc' -> <chimerax.map.session.GridDataState object at
0x0000023244C1ED90>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\ui\gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 78, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 79, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 839, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 583, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002324548ADF0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002324548AA30> 'j1676_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1ED90>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x000002322335A0D0> -> <chimerax.map.volume.VolumeSurface object at
0x000002324548ADF0> 'surface' -> <chimerax.map.volume.Volume object at
0x000002324548AA30> 'j1676_run_class001.mrc' ->
<chimerax.map.session.GridDataState object at 0x0000023244C1ED90>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'j1676_run_class001.mrc' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'j1676_run_class001.mrc' ->  
  
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\session.py", line 261, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 431.94
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 33,716,879,360
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Xeon(R) W-2135 CPU @ 3.70GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.2.1
    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: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    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: 2.2
    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: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011140750
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    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: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    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: 2.1
    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: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 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: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    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: 1.2.2
    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: 1.3.1
    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: 0.29.21
    decorator: 4.4.2
    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
    imagecodecs-lite: 2020.1.31
    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: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    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: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.0.0
    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: 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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Cc: Greg Couch added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Various session save/restore errors

Reported by Valentyn Petrychenko

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

First error is session not restoring caused by a bad session file resulting from renumbering model numbers before the session was saved. That bug has been fixed in daily builds. The session file may open in ChimeraX 1.1 or 1.0 (the version it written with) because the old ChimeraX tolerated the bad model numbers.

The subsequent errors were all "out of memory". Nothing we can do about that. You have 32 Gbytes but must have had large maps open. The first out of memory error is the graphics failing to allocate 40 Mbytes, a very small amount. Following that saving the session got another out of memory error. Once you reach a point where even 40 Mbytes cannot be allocated the only hope of recovering is to close data in ChimeraX.

Note: See TracTickets for help on using tickets.