Opened 2 years ago

Closed 2 years ago

#9670 closed defect (duplicate)

MemoryError open mmCIF

Reported by: han.tran.220143@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
hi. 

I tried to open the databank in the Quick Help section. However, my computer repoted out of memory problem everytime. What can I do about this?

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

> open 2bbv

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 320, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line
368, in thread_safe  
func(*args, **kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py",
line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py",
line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  

> open 2bbv

Traceback (most recent call last):  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 320, in intercept  
chimerax_intercept(request_info, *args, session=self.session,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line
368, in thread_safe  
func(*args, **kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, 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 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py",
line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\mmcif\\__init__.py",
line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 528.92
OpenGL renderer: NVIDIA GeForce MX250/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP Pavilion Laptop 15-cs3xxx
OS: Microsoft Windows 11 Home Single Language (Build 22621)
Memory: 16,951,066,624
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError open mmCIF

comment:2 by Eric Pettersen, 2 years ago

Status: assigned → feedback

Hi Han,

Thanks for reporting this problem. We _think_ we have fixed it, and the fix is in the current ChimeraX daily build. If you could try the daily build and let us know if it fixes the problem for you, we would greatly appreciate it.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Greg Couch, 2 years ago

Resolution: → duplicate
Status: feedback → closed

Duplicated of #8815.

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