Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8830 closed defect (can't reproduce)

MemoryError opening mmCIF

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output 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-10-10.0.19045
ChimeraX Version: 1.6rc202304072249 (2023-04-07 22:49:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Opening up a DNA file and it blinked the screen and the error came up

Log:
UCSF ChimeraX version: 1.6rc202304072249 (2023-04-07)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> vr true

started SteamVR rendering  

> open 1i6h from pbd

No such database 'pbd'  

> open 1i6h fromDatabase pdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\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 "C:\Program Files\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 "C:\Program Files\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\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 "C:\Users\VR Admin\Downloads\DNA.pdb" format pdb

Summary of feedback from opening C:\Users\VR Admin\Downloads\DNA.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK 3DNA v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org  
  
Chain information for DNA.pdb #101  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\nucleotides\\_data.py", line 522, in rebuild  
_rebuild_molecule('internal', mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\nucleotides\\_data.py", line 676, in _rebuild_molecule  
nd.add_shapes(all_shapes)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 266, in add_shapes  
all_triangles[i] = triangles + num_vertices  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.52 KiB for an
array with shape (300, 3) and data type int32  
  
Error processing trigger "new frame":  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.52 KiB for an
array with shape (300, 3) and data type int32  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\shapedrawing.py", line 266, in add_shapes  
all_triangles[i] = triangles + num_vertices  
  
See log for complete Python traceback.  
  
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.  
  
Unable to allocate 1.28 MiB for an array with shape (111992, 3) and data type
uint32  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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\bin\lib\site-
packages\chimerax\graphics\view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 247, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1542, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1555, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 768, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 775, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 802, in _draw_geometry  
ds.activate_bindings(renderer)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1915, in activate_bindings  
self.update_buffers()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1903, in update_buffers  
b.update_buffer_data(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 2697, in update_buffer_data  
d = data.astype(self.value_type, order = 'C')  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 1.28 MiB for an
array with shape (111992, 3) and data type uint32  
  

Invalid texture upload for 0x1bfe9f1a720 layer=0 mip=0  




OpenGL version: 3.3.0 NVIDIA 512.59
OpenGL renderer: NVIDIA GeForce GTX 1070/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: Alienware
Model: Alienware 15 R3
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 17,046,728,704
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
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: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    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: 1.6rc202304072249
    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
    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: 1.10.2
    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: 6.3.0
    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: 23.0
    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: 3.2.0
    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
    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: 6.2
    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, 3 years ago

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

comment:2 by Greg Couch, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed

comment:3 by Greg Couch, 3 years ago

See #8815

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