Out of memory mousing over large map

[m-schmid@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.2.dev202103272340 (2021-03-27 23:40:01 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202103272340 (2021-03-27)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open X:/TOXOPLASMA/CONOID_HEIGHT/T23_markers.cxs

Opened T23-axy150u8.hdf as #1, grid size 928,960,420, pixel 14.2, shown at
level 86, step 1, values uint8  
Log from Wed Mar 24 14:18:39 2021 Startup Messages  
---  
note | available bundle cache was for a different toolshed  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open X:/TOXOPLASMA/CONOID_HEIGHT/T23-axy150u8.hdf

Opened T23-axy150u8.hdf, grid size 928,960,420, pixel 14.2, shown at step 1,
values uint8  

> volume #1 region 0,0,0,927,959,419 step 4

> volume #1 region 0,0,0,927,959,419 step 1 colorMode opaque8 showOutlineBox
> true imageMode "box faces"

> volume #1

> volume #1 level 86

> volume #1 change image level 79,0 level 89.99,0.8 level 180,1

> surface dust #1 size 200

> color height #1 center 0,0,0 axis z palette rainbow

> vr nearClipDistance 0.5

started SteamVR rendering  
VR mode mark point  

> marker #2 position 5548,5882,-381.4 color yellow radius 1

VR mode resize markers  

> marker change #2 radius 100

> vr false

> hide #!1 models

> show #!1 models

> vr true

started SteamVR rendering  

> marker #2 position 4431,5961,-368.5 color yellow radius 100

> marker #2 position 4437,5993,-427.6 color yellow radius 100

> marker #2 position 3839,8375,2723 color yellow radius 100

> marker #2 position 4561,6188,2537 color yellow radius 100

> marker #2 position 4302,8658,2725 color yellow radius 100

> marker #2 position 5229,6375,2421 color yellow radius 100

> marker #2 position 4754,8946,2834 color yellow radius 100

> marker #2 position 5986,6881,2389 color yellow radius 100

> marker #2 position 3220,8130,2996 color yellow radius 100

> marker #2 position 3867,6099,2748 color yellow radius 100

> marker #2 position 2572,7752,3442 color yellow radius 100

> marker #2 position 3288,5557,3330 color yellow radius 100

> help marker

> vr false

> turn y 180

> marker delete #2:1

Deleted 1 markers  

> marker delete #2:2

Deleted 1 markers  

> marker delete #2:3

Deleted 1 markers  

> marker link #2:4,5 radius 20 color white

> marker link #2:6,7 radius 20 color white

> marker link #2:88,9 radius 20 color white

marker link command requires exactly 2 markers, got 1  

> marker link #2:8,9 radius 20 color white

> marker link #2:10,11 radius 20 color white

> marker link #2:12,13 radius 20 color white

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> save X:/TOXOPLASMA/CONOID_HEIGHT/T23_markers.cxs

> help distance

> distance #2:4 #2:5

Distance between /M mark 4 M and mark 5 M: 2309.883Å  

> distance #2:6 #2:7

Distance between /M mark 6 M and mark 7 M: 2482.802Å  

> distance #2:8 #2:9

Distance between /M mark 8 M and mark 9 M: 2445.361Å  

> distance #2:10 #2:11

Distance between /M mark 10 M and mark 11 M: 2145.351Å  

> distance #2:12 #2:13

Distance between /M mark 12 M and mark 13 M: 2311.031Å  

> save X:/TOXOPLASMA/CONOID_HEIGHT/T23_markers.cxs

——— End of log from Wed Mar 24 14:18:39 2021 ———

opened ChimeraX session  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\core\updateloop.py", line 139, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 738, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\view.py", line 787, in picked_object  
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\view.py", line 819, in picked_object_on_segment  
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\map\volume.py", line 1112, in first_intercept  
pd = Drawing.first_intercept(self, mxyz1, mxyz2, exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1036, in first_intercept  
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1053, in first_intercept_children  
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1031, in first_intercept  
p = self._first_intercept_excluding_children(mxyz1, mxyz2)  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1062, in
_first_intercept_excluding_children  
ta = self.masked_triangles  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1322, in masked_triangles  
return ta if tm is None else ta[tm,:]  
MemoryError: Unable to allocate 649. MiB for an array with shape (56693420, 3)
and data type int32  
  
MemoryError: Unable to allocate 649. MiB for an array with shape (56693420, 3)
and data type int32  
  
File "C:\Program Files\ChimeraX 1.2.dev202103272340\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1322, in masked_triangles  
return ta if tm is None else ta[tm,:]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUS
Model: All Series
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,086,476,288
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.12
    ChimeraX-AtomicLibrary: 3.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103272340
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.3.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Tom Goddard]

User error. Out of memory, as the error message says

MemoryError: Unable to allocate 649. MiB for an array with shape (56693420, 3) and data type int32

Could improve error message but this is a rare case. Computer has 16 Gbytes so they were very close to being out of memory and memory errors could occur all over the place, so a better message in this one place would likely not help.

[Eric Pettersen]

FYI, my Mail.app's spidey sense believes this bug was submitted by Michael Schmid

[Tom Goddard]

Hi Mike,

You reported this ChimeraX out of memory that happened when you moused over a large map surface.

MemoryError: Unable to allocate 649. MiB for an array with shape (56693420, 3) and data type int32

Your machine has 16 Gbytes of memory but is apparently so low on memory it cannot allocate 649 Mbytes. For handling large data sets 16 Gbytes is not much. I have 32 Gbytes or 64 Gbytes on the machines I use for larger data -- memory is cheap.

Tom