Out of memory reading trajectory

[hassan@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
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 "C:/Users/hassan/OneDrive - National Institutes of Health/from-
> petri/BCBB/topo/coor_at_500ns.pdb"

Summary of feedback from opening C:/Users/hassan/OneDrive - National
Institutes of Health/from-petri/BCBB/topo/coor_at_500ns.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK MODEL PROTEIN G  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 2/11/23 22:22: 1 CREATED BY USER: hassan  
  
Ignored bad PDB record found on line 162675  
TER 162673 SOD 160  
  
Chain information for coor_at_500ns.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open "C:/Users/hassan/OneDrive - National Institutes of Health/from-
> petri/BCBB/topo/top3a_MD.dynamics_final-22_nonbin.pdb"

Summary of feedback from opening C:/Users/hassan/OneDrive - National
Institutes of Health/from-
petri/BCBB/topo/top3a_MD.dynamics_final-22_nonbin.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK MODEL PROTEIN G  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 1/24/23 10:50:14 CREATED BY USER: hassan  
  
Ignored bad PDB record found on line 162724  
TER 162722 SOD 158  
  
Chain information for top3a_MD.dynamics_final-22_nonbin.pdb #2  
---  
Chain | Description  
? | No description available  
  

> show atoms

> hide atoms

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker coor_at_500ns.pdb, chain (blank) (#1) with
top3a_MD.dynamics_final-22_nonbin.pdb, chain (blank) (#2), sequence alignment
score = 2997.6  
RMSD between 402 pruned atom pairs is 1.348 angstroms; (across all 619 pairs:
2.073)  
  

> show atoms

> hide atoms

> tile

2 models tiled  

> tile spacingFactor 0.8

2 models tiled  

> open "C:/Users/hassan/OneDrive - National Institutes of Health/from-
> petri/BCBB/topo/complex_500ns.pdb"

Summary of feedback from opening C:/Users/hassan/OneDrive - National
Institutes of Health/from-petri/BCBB/topo/complex_500ns.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK MODEL PROTEIN G  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 2/11/23 22:35:34 CREATED BY USER: hassan  
  
Ignored bad PDB record found on line 161794  
TER 161792 SOD 169  
  
Chain information for complex_500ns.pdb #3  
---  
Chain | Description  
? | No description available  
  

> mmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker coor_at_500ns.pdb, chain (blank) (#1) with complex_500ns.pdb, chain
(blank) (#3), sequence alignment score = 3024.6  
RMSD between 484 pruned atom pairs is 1.227 angstroms; (across all 619 pairs:
1.835)  
  

> ~tile

> hide #2 models

> mmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker coor_at_500ns.pdb, chain (blank) (#1) with complex_500ns.pdb, chain
(blank) (#3), sequence alignment score = 3024.6  
RMSD between 484 pruned atom pairs is 1.227 angstroms; (across all 619 pairs:
1.835)  
  

> color #3 #00aaff transparency 0

> color #1 #ffaa00 transparency 0

> show #1#!3 atoms

> select ::name="TIP3"

452844 atoms, 301896 bonds, 150948 residues, 3 models selected  

> hide sel & #1#!3 atoms

> hide #!3 models

> select ::name="CLA"

474 atoms, 474 residues, 3 models selected  

> style sel & #1 sphere

Changed 158 atom styles  

> color (#1 & sel) lime

> select ::name="SOD"

487 atoms, 487 residues, 3 models selected  

> color (#1 & sel) red

> select add #3

162109 atoms, 112262 bonds, 1 pseudobond, 50826 residues, 4 models selected  

> select subtract #3

318 atoms, 318 residues, 2 models selected  

> select add #2

162881 atoms, 111704 bonds, 51904 residues, 2 models selected  

> select subtract #2

160 atoms, 160 residues, 1 model selected  

> select add #1

162672 atoms, 111670 bonds, 51729 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #1 atoms

> hide #1 atoms

> open "C:/Users/hassan/OneDrive - National Institutes of Health/from-
> petri/BCBB/topo/dynamics_large.dcd"

Specified structure has 162672 atoms whereas the coordinates are for 161791
atoms  

> open "C:/Users/hassan/OneDrive - National Institutes of Health/from-
> petri/BCBB/topo/dynamics_large.dcd"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\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 "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\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 "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 457, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\md_crds\\__init__.py", line 100, in open  
num_coords = read_coords(session, data, structure_model, md_type,  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\md_crds\read_coords.py", line 36, in read_coords  
num_frames = _set_model_dcd_coordinates(session, model, dcd, replace, start,
step, end)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\md_crds\read_coords.py", line 86, in
_set_model_dcd_coordinates  
model.add_coordset(base+num_frames, asarray(dcd[i], float64, order = 'C'))  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.70 MiB for an
array with shape (161791, 3) and data type float64  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 3.70 MiB for an
array with shape (161791, 3) and data type float64  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\md_crds\read_coords.py", line 86, in
_set_model_dcd_coordinates  
model.add_coordset(base+num_frames, asarray(dcd[i], float64, order = 'C'))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 391.25
OpenGL renderer: NVS 315/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 8,508,436,480
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Xeon(R) CPU E5-1603 v4 @ 2.80GHz
OSLanguage: en-US

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
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    jupyter-core: 4.10.0
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    line-profiler: 3.4.0
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    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
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    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
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Hi Sergio,

ChimeraX is trying to read your entire trajectory. I don't know how many frames you have in your trajectory, but it takes about 3.7MB per frame, so you could figure out how much it's trying to use. I would recommend using some kind of preprocessing program to reduce the trajectory to a number of frames that will only take a few GB (or less) for ChimeraX to read. You could also try using the start/end/step options to the 'open' command to read in a subset of the frames.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[hassan@…]

thank you, Eric.

I finally solved the problem without any need to process the trajectory. The error message was clear about the memory issue, but when I checked, it certainly was not the memory in my machine.

Long story short, the problem was that the structure showing on the screen was not the one that corresponded to the trajectory. The correct one was 'hidden.' Once I switched to showing the correct one and hiding the wrong one, the trajectory was read and processed without problems.

Does this make sense?

I tried to close or recall the ticket, but there was no way for me to do it.

thanks, and have a good day
s

_____________________________________
Sergio A. Hassan
https://bioinformatics.niaid.nih.gov/cmm/
BCBB/NIAID/NIH/DHHS
301 761 7221 (office) 301 741 5579 (mobile)

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, February 13, 2023 2:07 PM
Cc: Hassan, Sergio (NIH/NIAID) [E] <hassan@mail.nih.gov>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [EXTERNAL] Re: [ChimeraX] #8479: Out of memory reading trajectory

#8479: Out of memory reading trajectory
-------------------------------------------+--------------------
          Reporter:  hassan@…              |      Owner:  pett
              Type:  defect                |     Status:  closed
          Priority:  normal                |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:  limitation            |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+--------------------
Changes (by pett):

 * status:  accepted => closed
 * resolution:   => limitation


Comment:

 Hi Sergio,
         ChimeraX is trying to read your entire trajectory.  I don't know
 how many frames you have in your trajectory, but it takes about 3.7MB per
 frame, so you could figure out how much it's trying to use.  I would
 recommend using some kind of preprocessing program to reduce the
 trajectory to a number of frames that will only take a few GB (or less)
 for ChimeraX to read.  You could also try using the start/end/step options
 to the 'open' command to read in a subset of the frames.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F8479%23comment%3A2&data=05%7C01%7Chassan%40mail.nih.gov%7Caff7e8805b5b4a8d3dac08db0df5d585%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638119121728814682%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=hOl3xGuOBoByYBBV00HptNr85RR4VyH365DBoBn79hs%3D&reserved=0>
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[Eric Pettersen]

Glad you got it working fairly easily!

--Eric