delayed command registration for 'isolde' failed: OpenMM library not loaded

[e.orlova@…]

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501170719 (2025-01-17 07:19:08 UTC)
Description
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2477, in lazy_register raise RuntimeError
"ISOLDAVersion 1.8.dev0  failed to install properly

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501170719 (2025-01-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Toolbar

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd  
api._api_caller.register_command(api, self, ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1403, in register_command  
return cls._get_func(api, "register_command")(ci.name, logger)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 170, in register_command  
cmd.register_isolde(logger)  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 462, in register_isolde  
register_isolde_set()  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/cmd/cmd.py",
line 343, in register_isolde_set  
from chimerax.isolde.openmm.sim_param_mgr import fidelity_modes  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/__init__.py", line 12, in <module>  
from .openmm_interface import SimManager, SimHandler, OpenmmThreadHandler, \  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 24, in <module>  
from chimerax.isolde._openmm_async import OpenmmThreadHandler as
_OpenmmThreadHandlerBase  
ImportError: dlopen(/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2475, in lazy_register  
deferred.call()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2403, in call  
return self.proxy()  
^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb  
s._register_cmd(ci, logger)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: register_command() failed for command
isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 215, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/__init__.py",
line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-packages/chimerax/isolde/toolbar.py",
line 19, in toolbar_command  
run(session, 'isolde start')  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3139, in run  
self._find_command_name(final, used_aliases=_used_aliases)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2863, in _find_command_name  
what.lazy_register(cmd_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
RuntimeError: delayed command registration for 'isolde' failed
(register_command() failed for command isolde in bundle ChimeraX-ISOLDE:  
dlopen(/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so, 0x0002): Library
not loaded: @rpath/libOpenMM.8.0.dylib  
Referenced from: <5B912790-F8B3-3EB5-8165-758BE6829F1E>
/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/_openmm_async.cpython-311-darwin.so  
Reason: tried: '/Users/ubcg55a/Library/Application
Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Users/ubcg55a/Library/Application Support/ChimeraX/1.10/lib/python/site-
packages/chimerax/isolde/libOpenMM.8.0.dylib' (no such file),
'/Applications/ChimeraX_Daily.app/Contents/lib/libOpenMM.8.0.dylib' (no such
file),
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/libOpenMM.8.0.dylib'
(no such file), '/usr/lib/libOpenMM.8.0.dylib' (no such file, not in dyld
cache))  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2477, in lazy_register  
raise RuntimeError(  
  
See log for complete Python traceback.  
  

> toolshed show

Window position QRect(1393,1179 100x30) outside any known screen, using
primary screen  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: Z14W000E4B/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 7 days, 14 hours, 12 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    anyio: 4.8.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
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    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-Clipper: 0.23.0
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    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202501170719
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
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    ChimeraX-IUPAC: 1.0
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    ChimeraX-MapFit: 2.0
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    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.0
    PyQt6-Qt6: 6.8.1
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.1
    PyQt6_sip: 13.9.1
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

[pett]

Reported by Elena Orlova

[Tristan Croll]

The root cause of this is that ISOLDE shouldn't actually be able to be installed in the ChimeraX 1.10.dev... builds. The reason why it is is my fault - I messed up the version-requirement specifier in ISOLDE 1.8, so it thinks it's compatible with any ChimeraX 1.* version greater than or equal to 1.8. That's unfortunately a bit of a difficult egg to unscramble... will try to get a ChimeraX 1.10.dev compatible build together as time permits, but it might be a while.

[Tristan Croll]

Ugh… sorry, Eric - it appears my comment reverted your milestone
assignment.

On Tue, 21 Jan 2025 at 16:40, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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>
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[pett]

No problem. Since it's not really something to fix in ChimeraX per se, the milestone was superfluous anyway. Maybe Greg could edit the Toolshed requirements for the current ISOLDE so that it can't be installed in 1.10? Reassigning to Greg.

[Zach Pearson]

FYI Tristan, we're trying the PyPi OpenMM in the daily builds. I'm not sure if I ever made it clear in my last email that I made or was going to make the change. If you encounter troubles let me know, and we can choose an appropriate Anaconda OpenMM.

[Tristan Croll]

Did some experimentation with a prerelease build of OpenMM-PyPI a while
back. Pretty sure I can make it work.

On Tue, 21 Jan 2025 at 17:19, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>