Opened 2 years ago

Closed 2 years ago

#9742 closed defect (limitation)

Unable to allocate memory for surface

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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  

> open C:\Users\Safe\Desktop\Portable\moleculas\4fby.cif format mmcif

Summary of feedback from opening
C:\Users\Safe\Desktop\Portable\moleculas\4fby.cif  
---  
warnings | Atom MN1 has no neighbors to form bonds with according to residue
template for OEC /A:412  
Atom MN2 has no neighbors to form bonds with according to residue template for
OEC /A:412  
Atom MN3 has no neighbors to form bonds with according to residue template for
OEC /A:412  
Atom MN4 has no neighbors to form bonds with according to residue template for
OEC /A:412  
Atom CA1 has no neighbors to form bonds with according to residue template for
OEC /A:412  
Atom MN1 has no neighbors to form bonds with according to residue template for
OEC /G:413  
Atom MN2 has no neighbors to form bonds with according to residue template for
OEC /G:413  
Atom MN3 has no neighbors to form bonds with according to residue template for
OEC /G:413  
Atom MN4 has no neighbors to form bonds with according to residue template for
OEC /G:413  
Atom CA1 has no neighbors to form bonds with according to residue template for
OEC /G:413  
  
4fby.cif title:  
fs X-ray diffraction of Photosystem II [more info...]  
  
Chain information for 4fby.cif #1  
---  
Chain | Description | UniProt  
A G | Photosystem Q(B) protein 1 | PSBA1_THEEB 1-344  
B N | Photosystem II core light harvesting protein | Q8DIQ1_THEEB 1-510  
C P | Photosystem II CP43 protein | Q8DIF8_THEEB 13-473  
D Q | Photosystem II D2 protein | PSBD_THEEB 1-352  
E R | Cytochrome b559 subunit alpha | PSBE_THEEB 2-84  
F S | Cytochrome b559 subunit beta | PSBF_THEEB 2-45  
H W | Photosystem II reaction center protein H | PSBH_THEEB 2-66  
I a | Photosystem II reaction center protein I | PSBI_THEEB 1-38  
J b | Photosystem II reaction center protein J | PSBJ_THEEB 2-40  
K c | Photosystem II reaction center protein K | PSBK_THEEB 10-46  
L d | Photosystem II reaction center protein L | PSBL_THEEB 1-37  
M e | Photosystem II reaction center protein M | PSBM_THEEB 1-36  
O f | Photosystem II manganese-stabilizing polypeptide | PSBO_THEEB 27-272  
T g | Photosystem II reaction center protein T | PSBT_THEEB 1-32  
U h | Photosystem II 12 kDa extrinsic protein | PSBU_THEEB 31-134  
V i | Cytochrome c-550 | CY550_THEEB 27-163  
X j | Photosystem II reaction center protein X | PSBX_THEEB 11-50  
Y k | Photosystem II reaction center protein Y |  
Z l | Photosystem II reaction center protein Z | PSBZ_THEEB 1-62  
m y | Photosystem II reaction center protein ycf12 | YCF12_THEEB 1-46  
  
Non-standard residues in 4fby.cif #1  
---  
BCR — β-carotene  
BCT — bicarbonate ion  
CA — calcium ion  
CL — chloride ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
LMT — dodecyl-β-D-maltoside  
OEC — oxygen evolving system  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
  

> style sphere

Changed 50232 atom styles  

> style ball

Changed 50232 atom styles  

> undo

[Repeated 1 time(s)]

> style ball

Changed 50232 atom styles  

> undo

> hide atoms

> undo

No Surface models open  
[Repeated 1 time(s)]

> style ball

Changed 50232 atom styles  

> style sphere

Changed 50232 atom styles  

> undo

[Repeated 1 time(s)]

> show cartoons

[Repeated 1 time(s)]

> show atoms

[Repeated 1 time(s)]

> cartoon

> color white

> undo

> style ball

Changed 50232 atom styles  

> show surfaces

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 1.15 MiB for an array with shape (100702, 3) and data type
uint32  
  
Traceback (most recent call last):  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 215, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 609, in _compute_shadowmaps  
shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 1438, in use_shadow_map  
draw_depth(r, sdrawings, opaque_only = not
r.material.transparent_cast_shadows)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1567, in draw_depth  
draw_opaque(r, drawings)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1542, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1555, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 768, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 775, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 802, in _draw_geometry  
ds.activate_bindings(renderer)  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1915, in activate_bindings  
self.update_buffers()  
File "C:\Users\Safe\Desktop\Portable\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1903, in update_buffers  
b.update_buffer_data(data)  
File "C:\Users\Safe\Desktop\Portable\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 1.15 MiB for an
array with shape (100702, 3) and data type uint32  
  

Invalid texture upload for 0x21eabb4f6d0 layer=0 mip=0  




OpenGL version: unknown
Could not make opengl context current

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

Manufacturer: LENOVO
Model: 11A5S06B00
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 6,372,569,088
MaxProcessMemory: 137,438,953,344
CPU: 4 AMD Athlon PRO 300GE w/ Radeon Vega Graphics   
OSLanguage: es-MX

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 (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Unable to allocate memory for surface

comment:2 by Tom Goddard, 2 years ago

Resolution: → limitation
Status: assigned → closed

Surprising that a numpy memory allocation failed for just 1 Mbyte of memory. The user machine has a very small amount of memory 6 Gbytes. The had opened an mmCIF and maybe the Windows mmCIF out of memory bug was in play here and used up almost all the memory.

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