OpenMM: Context_swiginit: Error compiling kernel: symbol multiply defined

[ajitr@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
I'm attempting to start an ISOLDE simulation and get this bug where the simulation won't start.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ajit/Downloads/8j73.cif

8j73.cif title:  
Methylcrotonoyl-CoA carboxylase core-Dimer [more info...]  
  
Chain information for 8j73.cif #1  
---  
Chain | Description | UniProt  
G H I J K L M N O P Q R | Methylcrotonoyl-CoA carboxylase beta chain,
mitochondrial | MCCB_HUMAN 1-563  
  

> hide atoms

> show atoms

> show cartoons

> hide atoms

> open /Users/ajit/Downloads/emd_36024.map

Opened emd_36024.map as #2, grid size 320,320,320, pixel 1.1, shown at level
0.28, step 2, values float32  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 402 residues in model #1 to IUPAC-IUB
standards.  
8j73.cif title:  
Methylcrotonoyl-CoA carboxylase core-Dimer [more info...]  
  
Chain information for 8j73.cif  
---  
Chain | Description | UniProt  
1.2/G 1.2/H 1.2/I 1.2/J 1.2/K 1.2/L 1.2/M 1.2/N 1.2/O 1.2/P 1.2/Q 1.2/R |
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial | MCCB_HUMAN 1-563  
  

> clipper associate #2 toModel #1

Opened emd_36024.map as #1.1.1.1, grid size 320,320,320, pixel 1.1, shown at
step 1, values float32  

> addh #1.2

Summary of feedback from adding hydrogens to 8j73.cif #1.2  
---  
notes | Termini for 8j73.cif (#1.2) chain G determined from SEQRES records  
Termini for 8j73.cif (#1.2) chain H determined from SEQRES records  
Termini for 8j73.cif (#1.2) chain I determined from SEQRES records  
Termini for 8j73.cif (#1.2) chain J determined from SEQRES records  
Termini for 8j73.cif (#1.2) chain K determined from SEQRES records  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /G LEU 31, /H LEU 31, /I
LEU 31, /J LEU 31, /K LEU 31, /L LEU 31, /M LEU 31, /N LEU 31, /O LEU 31, /P
LEU 31, /Q LEU 31, /R LEU 31  
Chain-final residues that are actual C termini: /G MET 563, /H MET 563, /I MET
563, /J MET 563, /K MET 563, /L MET 563, /M MET 563, /N MET 563, /O MET 563,
/P MET 563, /Q MET 563, /R MET 563  
Chain-final residues that are not actual C termini:  
6263 hydrogen bonds  
Adding 'H' to /G LEU 31  
Adding 'H' to /H LEU 31  
Adding 'H' to /I LEU 31  
Adding 'H' to /J LEU 31  
Adding 'H' to /K LEU 31  
7 messages similar to the above omitted  
49008 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> volume #1.1.1.1 level 0.3594

> isolde sim start /G:562

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/Users/ajit/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error compiling kernel: Linking globals named
'_Z8atom_addPVU3AS1mm': symbol multiply defined!  
  
openmm.OpenMMException: Error compiling kernel: Linking globals named
'_Z8atom_addPVU3AS1mm': symbol multiply defined!  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/openmm.py", line 2469, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-14.0.32 355.11.11.10.10.143
OpenGL renderer: NVIDIA GeForce GT 755M OpenGL Engine
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 8 GB
      Boot ROM Version: 433.140.2.0.0
      SMC Version (system): 2.15f7

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H15)
      Kernel Version: Darwin 19.6.0
      Time since boot: 45 minutes

Graphics/Displays:

    NVIDIA GeForce GT 755M:

      Chipset Model: NVIDIA GeForce GT 755M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 1 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fea
      Revision ID: 0x00a2
      ROM Revision: 3782
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    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: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
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    glfw: 2.6.4
    grako: 3.16.5
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    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
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    Pygments: 2.16.1
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    PyQt6-commercial: 6.3.1
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    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
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    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Eric Pettersen]

Reported by Ajit

[Tristan Croll]

Unfortunately this is one that can't be fixed other than by running on a newer machine - as per the discussion at ​https://github.com/openmm/openmm/issues/3982#issuecomment-1493803321, OpenMM is no longer compatible with the Nvidia GPUs on old Macs. Sorry I can't be more helpful.