Opened 2 years ago

Closed 2 years ago

#9913 closed defect (nonchimerax)

Numpy memory array during vop zone

Reported by: chimerax-bug-report@… 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: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open G:\\\structure\\\Dpp\\\dppabcdf\\\512259.mrc

Opened 512259.mrc as #1, grid size 384,384,384, pixel 1.04, shown at level
0.103, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.5262

> open G:/structure/Dpp/dppabcdf/512259-H_real_space_refined_002-coot-7.pdb

Summary of feedback from opening
G:/structure/Dpp/dppabcdf/512259-H_real_space_refined_002-coot-7.pdb  
---  
warning | Cannot find LINK/SSBOND residue SF4 (402 )  
  
Chain information for 512259-H_real_space_refined_002-coot-7.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide atoms

> show cartoons

> sequence chain #2/A

Alignment identifier is 2/A  

> select /E:1-1002

4057 atoms, 4163 bonds, 509 residues, 1 model selected  

> vop zone #1 nearatoms #2/E newmap true

Opened 512259.mrc zone as #3, grid size 384,384,384, pixel 1.04, shown at step
1, values float32  

> save G:/structure/Dpp/dppabcdf/A.mrc models #3

> select /A:2

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2-339

2625 atoms, 2686 bonds, 338 residues, 1 model selected  

> open G:/structure/Dpp/dppabcdf/A_cryonet.pdb

Summary of feedback from opening G:/structure/Dpp/dppabcdf/A_cryonet.pdb  
---  
warning | Ignored bad PDB record found on line 4  
REMARK INFO: [occupancy]=sse [bfactor]=score  
  
Chain information for A_cryonet.pdb #4  
---  
Chain | Description  
A | No description available  
  

> vop zone #1 nearatoms #2/B newmap true

Opened 512259.mrc zone as #5, grid size 384,384,384, pixel 1.04, shown at step
1, values float32  

> volume #5 level 0.2082

> save G:/structure/Dpp/dppabcdf/C.mrc models #5

> vop zone #1 nearatoms #2/A newmap true

Traceback (most recent call last):  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 31, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 60, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 258, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 326, in masked_grid_data  
putmask(masked, mask, matrix)  
File "<__array_function__ internals>", line 180, in putmask  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 54.0 MiB for an
array with shape (384, 384, 384) and data type bool  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 54.0 MiB for an
array with shape (384, 384, 384) and data type bool  
  
File "<__array_function__ internals>", line 180, in putmask  
  
See log for complete Python traceback.  
  

> vop zone #1 nearatoms #2/A newmap true

Traceback (most recent call last):  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 31, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 60, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 256, in zone_masked_grid_data  
mask = zone_mask(grid_data, zone_points, zone_radius,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 277, in zone_mask  
mask_3d = zeros(shape, int8)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 54.0 MiB for an
array with shape (384, 384, 384) and data type int8  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 54.0 MiB for an
array with shape (384, 384, 384) and data type int8  
  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 277, in zone_mask  
mask_3d = zeros(shape, int8)  
  
See log for complete Python traceback.  
  

> select add #2

13961 atoms, 14274 bonds, 15 pseudobonds, 1784 residues, 2 models selected  

> hide #4 models

> vop zone #1 nearatoms #2/A newmap true

Traceback (most recent call last):  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in volume_zone  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\vopcommand.py", line 1078, in <listcomp>  
zv = [zone_operation(v, near_atoms, range, bond_point_spacing,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 31, in zone_operation  
vz = zone_volume(v, points, radius, minimal_bounds, invert,  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_filter\zone.py", line 60, in zone_volume  
mg = map_data.zone_masked_grid_data(sg, points, radius, invert,
minimal_bounds)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 258, in zone_masked_grid_data  
masked_data = masked_grid_data(grid_data, mask)  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 216. MiB for an
array with shape (384, 384, 384) and data type float32  
  
File "F:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 324, in masked_grid_data  
masked = zeros(matrix.shape, matrix.dtype)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.1008
OpenGL renderer: AMD Radeon HD 5450
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 390
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 10,709,041,152
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i3-2120 CPU @ 3.30GHz
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: 2022.5.18.1
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    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: 2.2.4
    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
    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: 1.1.1
    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: 1.5.1
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    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: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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 (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Numpy memory array during vop zone

comment:2 by Tom Goddard, 2 years ago

Resolution: → nonchimerax
Status: assigned → closed

Not much memory being used but failed allocating 50 Mbytes.

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