Context Navigation

← Previous Ticket
Next Ticket →

#7344 closed defect (nonchimerax)

MemoryError saving session

Reported by:	chimerax-bug-report@…	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-10-10.0.19043
ChimeraX Version: 1.4.dev202204210713 (2022-04-21 07:13:17 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4.dev202204210713 (2022-04-21)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "H:\\\OneDrive\\\A1
> structure\\\drawing\\\FSC\\\map\\\job107_capsid_postprocess.mrc"

Opened job107_capsid_postprocess.mrc as #1, grid size 800,800,800, pixel 1.07,
shown at step 1, values float32  

> volume #1 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> volume #1 level 0.005

> volume #1 change image level -0.0009892,0 level 0.007618,0.8 level 0.01748,1

> volume #1 level 0.008

> set bgColor white

> ui tool show "Surface Color"

> key red-white-blue :0.0 :0.5 :1.0 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right translate

> color radial #1.2 palette
> 310,#0000ff:320,#00ffff:330,#00ff00:340,#ffff00:350,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 320,#0000ff:330,#00ffff:340,#00ff00:350,#ffff00:60,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 310,#0000ff:320,#00ffff:330,#00ff00:340,#ffff00:350,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 330,#0000ff:335,#00ffff:340,#00ff00:345,#ffff00:350,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 310,#0000ff:335,#00ffff:340,#00ff00:345,#ffff00:350,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 310,#0000ff:320,#00ffff:340,#00ff00:345,#ffff00:350,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 310,#0000ff:320,#00ffff:330,#00ff00:345,#ffff00:360,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 280,#0000ff:300,#00ffff:320,#00ff00:340,#ffff00:360,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 280,#0000ff:300,#00ffff:320,#00ff00:360,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 280,#0000ff:300,#00ffff:350,#00ff00:360,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 280,#0000ff:300,#00ffff:350,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 280,#0000ff:300,#00ffff:330,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 300,#0000ff:310,#00ffff:330,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 320,#0000ff:330,#00ffff:340,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 310,#0000ff:330,#00ffff:340,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> color radial #1.2 palette
> 320,#0000ff:330,#00ffff:340,#00ff00:350,#ffff00:370,#ff0000 center
> 428,427.9,428

> save "H:/OneDrive/A1
> structure/drawing/FSC/流程图/job107_capsid_320_330_340_350_370.png" width 8000
> height 4765 supersample 4 transparentBackground true

> save "H:/OneDrive/A1 structure/drawing/FSC/流程图/job107_capsid.cxs"
> includeMaps true

Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\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 "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  

> save "H:/OneDrive/A1 structure/drawing/FSC/流程图/job107_capsid.cxs"
> includeMaps true

Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\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 "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  

> save "H:/OneDrive/A1 structure/drawing/FSC/picture/job107_capsid.cxs"
> includeMaps true

Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\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 "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 718, in write  
compressed = self._compressor.compress(data)  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "E:\ChimeraX 1.4.dev202204210713\bin\lib\site-
packages\lz4\frame\\__init__.py", line 258, in compress  
result = compress_chunk(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt runtime version: 6.2.4
Qt platform: windows

Manufacturer: LENOVO
Model: 82B6
OS: Microsoft Windows 10 专业版 (Build 19043)
Memory: 17,042,837,504
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics         
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.38.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.3
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202204210713
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16.5
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.32.0
    funcparserlib: 1.0.0a1
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.8
    PyQt6-commercial: 6.2.3
    PyQt6-Qt6: 6.2.4
    PyQt6-sip: 13.2.1
    PyQt6-WebEngine-commercial: 6.2.1
    PyQt6-WebEngine-Qt6: 6.2.4
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.3.0
    QtPy: 2.0.1
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Sessions
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → MemoryError saving session

comment:2 by Greg Couch, 3 years ago

Cc:	Greg Couch added; Tom Goddard removed
Owner:	changed from Greg Couch to Tom Goddard

Probably related to "save ... includeMaps True". Tom has large volume data that might be able to reproduce this.

comment:3 by Tom Goddard, 3 years ago

Resolution:	→ nonchimerax
Status:	assigned → closed

I'm surprised the ran out of memory lz4 compressing the ChimeraX session file. It included a map that was 800 x 800 x 800 32-bit floats, so a bit less than 2 Gbytes. Their machine had 16 Gbytes.

But it seems it was just out of memory.

Note: See TracTickets for help on using tickets.

Download in other formats: