Opened 20 months ago
Last modified 20 months ago
#14676 assigned defect
MemoryError saving session after many 'vop zone' commands
Reported by: | Owned by: | Greg Couch | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Sessions | Version: | |
Keywords: | Cc: | Tom Goddard | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.19044 ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\ligand-1.cxs Opened J1170_UDP_galactose_sharp.mrc as #2, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #3, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel 1.1, shown at level 0.2, step 1, values float32 Log from Fri Mar 1 10:35:41 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\PLO- > COL_J1170-ABUV-039-coot-3rd.pdb Chain information for PLO-COL_J1170-ABUV-039-coot-3rd.pdb #1 --- Chain | Description A B | No description available U V | No description available > open > E:\\\实验室\\\其它\\\14-课题整理\\\文章写作\\\数据整理\\\Helix\\\J1170_UDP_galactose_sharp.mrc Opened J1170_UDP_galactose_sharp.mrc as #2, grid size 384,384,384, pixel 1.1, shown at level 0.168, step 2, values float32 > volume #2 step 1 > set bgColor white > surface dust #2 size 11 > fitmap #1 inMap #2 Fit molecule PLO-COL_J1170-ABUV-039-coot-3rd.pdb (#1) to map J1170_UDP_galactose_sharp.mrc (#2) using 20968 atoms average map value = 0.7349, steps = 48 shifted from previous position = 0.0362 rotated from previous position = 0.0453 degrees atoms outside contour = 524, contour level = 0.16777 Position of PLO-COL_J1170-ABUV-039-coot-3rd.pdb (#1) relative to J1170_UDP_galactose_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99999975 0.00010916 0.00069553 -0.15080643 -0.00010941 0.99999993 0.00036115 -0.06983153 -0.00069549 -0.00036122 0.99999969 0.25366731 Axis -0.45645586 0.87896075 -0.13811606 Axis point 359.15309264 0.00000000 235.05042989 Rotation angle (degrees) 0.04533715 Shift along axis -0.02757823 > color red > color byhetero > hide atoms > volume hide > hide cartoons > select #1/B:337-353 146 atoms, 153 bonds, 17 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #3, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!3 hide > select ::name="AKG" 20 atoms, 18 bonds, 2 residues, 1 model selected > show sel atoms > select clear Drag select of 10 atoms, 9 bonds > name frozen B-AKG sel > hide sel atoms > select clear > hide atoms > select ::name="FE2" 2 atoms, 2 residues, 1 model selected > show sel atoms > select clear Drag select of 1 atoms > name frozen B-FE sel > select clear > hide atoms > select ::name="MN" 2 atoms, 2 residues, 1 model selected > show sel atoms > select clear Drag select of 1 atoms > name frozen B-MN sel > select clear > hide atoms > select ::name="NAG" 126 atoms, 130 bonds, 9 residues, 1 model selected > show sel atoms > select clear Drag select of 28 atoms, 29 bonds > name frozen B-NAG-1 sel > select clear Drag select of 14 atoms, 14 bonds > name frozen B-NAG-2 sel > select clear > hide atoms > select ::name="UDP" 50 atoms, 52 bonds, 2 residues, 1 model selected > show sel atoms > select clear Drag select of 25 atoms, 26 bonds > name frozen B-UDP sel > select clear > hide atoms > save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/ligand.cxs > select B-AKG 10 atoms, 9 bonds, 1 residue, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!4 hide > hide sel atoms > select B-FE 1 atom, 1 residue, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!5 hide > select B-MN 1 atom, 1 residue, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!6 hide > select B-NAG-1 28 atoms, 29 bonds, 2 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!7 hide > select B-NAG-2 14 atoms, 14 bonds, 1 residue, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!8 hide > select B-UDP 25 atoms, 26 bonds, 1 residue, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > volume #!9 hide > color #3 black models > color #3-9 black models > show #!4 models > hide #!4 models > show #!3 models > volume #!3 style mesh > hide #!3 models > show #!4 models > hide sel cartoons > volume #!4 style mesh > hide #!4 models > show #!3 models > volume all level 0.2 > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!4 models > save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/ligand-1.cxs ——— End of log from Fri Mar 1 10:35:41 2024 ——— opened ChimeraX session > close #4-9 > hide #!3 models > show #1/B:362-364 > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > hide sel atoms > select clear > hide atoms > close #4 > show #1/B:362-364 > vop zone #2 near sel range 1.7 newmap 1 no atoms specified for zone > hide atoms > select #1/B:362-364 25 atoms, 25 bonds, 3 residues, 1 model selected > select #1/B:362-364 25 atoms, 25 bonds, 3 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #4, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!4 hide > hide sel atoms > select #1/B:368-380 98 atoms, 98 bonds, 13 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #5, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!5 hide > select #1/B:402-409 68 atoms, 67 bonds, 8 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #6, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!6 hide > select #1/B:444-448 43 atoms, 43 bonds, 5 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #7, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!7 hide > select #1/B:469-474 46 atoms, 45 bonds, 6 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #8, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!8 hide > select #1/B:489-500 99 atoms, 101 bonds, 12 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #9, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!9 hide > select #1/B:528-531 37 atoms, 39 bonds, 4 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #10, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!10 hide > select #1/B:537-544 75 atoms, 78 bonds, 8 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #11, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!11 hide > select #1/B:549-554 51 atoms, 51 bonds, 6 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #12, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!12 hide > select #1/B:574-587 117 atoms, 118 bonds, 14 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #13, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!13 hide > hide sel atoms > select #1/B:614-617 33 atoms, 32 bonds, 4 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #14, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!14 hide > select #1/B:620-630 103 atoms, 105 bonds, 11 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #15, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > volume #!15 hide > select #1/B:632-638 49 atoms, 49 bonds, 7 residues, 1 model selected > vop zone #2 near sel range 1.7 newmap 1 Opened J1170_UDP_galactose_sharp.mrc zone as #16, grid size 384,384,384, pixel 1.1, shown at step 1, values float32 > close #16 > save E:/实验室/其它/14-课题整理/文章写作/数据整理/Helix/plod-2.cxs Traceback (most recent call last): File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 912, in save session.save(output, version=version, include_maps=include_maps) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 641, in save fserialize(stream, data) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\safesave.py", line 147, in write self._f.write(buf) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line 740, in write compressed = self._compressor.compress(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line 258, in compress result = compress_chunk( ^^^^^^^^^^^^^^^ MemoryError MemoryError File "D:\ChimeraX\ChimeraX\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 "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 165, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\info.py", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core\toolshed\\__init__.py", line 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\\__init__.py", line 37, in run_provider providers.run_provider(session, name) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\providers.py", line 56, in run_provider what(session) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\toolbar\providers.py", line 38, in _file_save show_save_file_dialog(session) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\save_command\dialog.py", line 62, in display run(session, cmd) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\save_command\cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "D:\ChimeraX\ChimeraX\bin\Lib\site- packages\chimerax\core_formats\\__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 912, in save session.save(output, version=version, include_maps=include_maps) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\session.py", line 641, in save fserialize(stream, data) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\chimerax\core\safesave.py", line 147, in write self._f.write(buf) File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line 740, in write compressed = self._compressor.compress(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "D:\ChimeraX\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py", line 258, in compress result = compress_chunk( ^^^^^^^^^^^^^^^ MemoryError MemoryError File "D:\ChimeraX\ChimeraX\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 536.99 OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: zh_CN.cp936 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Acer Model: Predator PHN16-71 OS: Microsoft Windows 10 专业版 (Build 19044) Memory: 16,886,128,640 MaxProcessMemory: 137,438,953,344 CPU: 20 13th Gen Intel(R) Core(TM) i5-13500HX OSLanguage: zh-CN Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (4)
comment:1 by , 20 months ago
Cc: | added |
---|---|
Component: | Unassigned → Sessions |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → MemoryError saving session after many 'vop zone' commands |
comment:2 by , 20 months ago
comment:3 by , 20 months ago
Are we using the default "frame" format for lz4, or instead "block" or "streaming"? Looking at the docs here: https://pypi.org/project/lz4/ it sounds like "frame" does make a copy and "streaming" does not, based on snippets from the page you get from clicking on the "streaming" link:
"Streaming" API : This is designed for complex things. For example, compress huge stream data in restricted memory environment."
--and--
"Streaming API doesn't keep a mirror copy of dependent (de)compressed memory"
--but--
"Experimental bindings for the the streaming format specification are also included, but further work on those is required."
comment:4 by , 20 months ago
ChimeraX session compression uses PyPi lz4 module lz4.frame.open() as shown below from core/session.py. So maybe a switch to streaming would avoid these memory errors.
def lz4_open(path): import lz4.frame f = SaveFile(path, open=lambda path: lz4.frame.open(path, 'wb')) return f
The session save memory errors are always in the LZ4 compressor. Maybe it is not simply streaming the compressed data to the file but instead makes a whole compressed copy in memory.
The vop zone command with "newmap 1" option is making lots of new volumes that will be saved in the session since there is no file for those maps.