Opened 11 months ago
Closed 11 months ago
#16365 closed defect (limitation)
volume splitbyzone: ArrayMemoryError
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Volume Data | Version: | |
Keywords: | Cc: | ||
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: 1.8 (2024-06-10 23:15:52 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/ekeme/Downloads/70S_Streptomyces_griseus.pdb Chain information for 70S_Streptomyces_griseus.pdb #1 --- Chain | Description | UniProt A | No description available | Ac | No description available | Ad | No description available | Ae | No description available | Af | No description available | Ag | No description available | Ai | No description available | Aj | No description available | Ak | No description available | Al | No description available | Am | No description available | An | No description available | Ao | No description available | Ap | No description available | Aq | No description available | Ar | No description available | As | No description available | At | No description available | B | No description available | B0 | No description available | B1 | No description available | B2 | No description available | B3 | No description available | Ba | No description available | Bb | No description available | Bc | No description available | Bd | No description available | Bf | No description available | Bg | No description available | Bh | No description available | Bi | No description available | Bj | No description available | Bk | No description available | Bl | No description available | Bm | No description available | Bn | No description available | Bo | No description available | Bp | No description available | Bq | No description available | Br | No description available | Bs | No description available | Bt | No description available | Bu | No description available | Bv | No description available | Bw | No description available | Bx | No description available | By | No description available | Bz | No description available | C E | No description available | RL31_STRGG 1-74 D F | No description available | h | No description available | > show cartoons > hide atoms > open C:/Users/ekeme/Downloads/Flipped_S.griseus_map_from_relion.mrc Opened Flipped_S.griseus_map_from_relion.mrc as #2, grid size 480,480,480, pixel 1.25, shown at level 0.0118, step 2, values float32 > color zone #2 near #1 > volume splitbyzone #2 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\cmd_line\tool.py", line 319, in execute cmd.run(cmd_text) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 378, in split_volumes_by_color_zone vlist.extend(split_volume_by_color_zone(v)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 321, in split_volume_by_color_zone grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color g = masked_grid_data(sg, mask, m) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data masked = zeros(matrix.shape, matrix.dtype) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 422. MiB for an array with shape (480, 480, 480) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 422. MiB for an array with shape (480, 480, 480) and data type float32 File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data masked = zeros(matrix.shape, matrix.dtype) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > ui tool show "Color Zone" > color zone #2 near #1 distance 1.25 > volume splitbyzone #2 Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzonegui.py", line 253, in _split_map run(self.session, cmd) File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\core\commands\cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 378, in split_volumes_by_color_zone vlist.extend(split_volume_by_color_zone(v)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 321, in split_volume_by_color_zone grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color g = masked_grid_data(sg, mask, m) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data masked = zeros(matrix.shape, matrix.dtype) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ numpy.core._exceptions._ArrayMemoryError: Unable to allocate 422. MiB for an array with shape (480, 480, 480) and data type float32 numpy.core._exceptions._ArrayMemoryError: Unable to allocate 422. MiB for an array with shape (480, 480, 480) and data type float32 File "C:\Program Files\ChimeraX 1.8\bin\Lib\site- packages\chimerax\map_data\arrays.py", line 341, in masked_grid_data masked = zeros(matrix.shape, matrix.dtype) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 3.3.0 - Build 30.0.101.1338 OpenGL renderer: Intel(R) HD Graphics 520 OpenGL vendor: Intel Python: 3.11.4 Locale: en_GB.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: Dell Inc. Model: Latitude E5470 OS: Microsoft Windows 10 Pro (Build 19045) Memory: 8,476,712,960 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-6200U CPU @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.6.2 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
Component: | Unassigned → Volume Data |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → volume splitbyzone: ArrayMemoryError |
comment:2 by , 11 months ago
Resolution: | → limitation |
---|---|
Status: | assigned → closed |
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Out of memory with volume split by zone on Windows 10 with only 8 GB of memory.