isolde set gpuDeviceIndex: Specified DeviceIndex but not OpenCLPlatformIndex

[s.sommerhage@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Per defaut Isolde is not "using" my Nvidia GPU although ChimeraX uses it for 3D rendering. When I use the command "isolde set gpuDeviceIndex 1" I get the following error as soon as I start a simulation with Isolde:
isolde set gpuDeviceIndex 1
isolde sim start /A-T
Traceback (most recent call last):   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 230, in callback     bundle_info.run_provider(session, name, session.toolbar, display_name=display_name)   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397, in run_provider     return api._api_caller.run_provider(api, session, name, mgr, **kw)            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419, in run_provider     return cls._get_func(api, "run_provider")(session, name, mgr, **kw)            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\__init__.py", line 166, in run_provider     toolbar_command(session, name)   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command     run(session, f'isolde sim start {_current_residue_sel_string(session)}')   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run     results = command.run(text, log=log, return_json=return_json)               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3221, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim     isolde.start_sim()   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\isolde.py", line 896, in start_sim     sm.start_sim()   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim     sh.start_sim()   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim     self._prepare_sim()   File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in _prepare_sim     s = self._simulation = app.Simulation(self.topology, self._system,                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\app\simulation.py", line 106, in __init__     self.context = mm.Context(self.system, self.integrator, platform, platformProperties)                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__     _openmm.Context_swiginit(self, _openmm.new_Context(*args))                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^ openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) ^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback.

Log:
> functionkey F1 save session.cxs

UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\simon\Nextcloud\Dokumente\Promotion\Auswertungen\Insulin_Fibrils\reconstruction-20230721-SiSo-
> Ins_Glarg_Dil_2_Acqui_Grid2_2\atomic_model_building\pmL1\models\5layers.pdb
> format pdb

Chain information for 5layers.pdb #1  
---  
Chain | Description  
A C E G I K M O Q S | No description available  
B D F H J L N P R T | No description available  
  

> lighting full

> isolde set

> 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  

> help islode

No help found for 'islode'  

> help isolde

> isolde set gpuDeviceIndex 1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 5layers.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/E 1.2/G 1.2/I 1.2/K 1.2/M 1.2/O 1.2/Q 1.2/S | No description available  
1.2/B 1.2/D 1.2/F 1.2/H 1.2/J 1.2/L 1.2/N 1.2/P 1.2/R 1.2/T | No description available  
  

> open
> C:/Users/simon/Nextcloud/Dokumente/Promotion/Auswertungen/Insulin_Fibrils/reconstruction-20230721-SiSo-
> Ins_Glarg_Dil_2_Acqui_Grid2_2/atomic_model_building/pmL1/models/maps/job458_postprocess_masked-
> rhsymp-5layers_boxed.mrc

Opened job458_postprocess_masked-rhsymp-5layers_boxed.mrc as #2, grid size
320,320,320, pixel 1.02, shown at level 5.45e-06, step 2, values float32  

> volume #2 step 1

> volume #2 level 5.451e-06

> volume #2 level 0.02462

> clipper associate #2 toModel #1

Opened job458_postprocess_masked-rhsymp-5layers_boxed.mrc as #1.1.1.1, grid
size 320,320,320, pixel 1.02, shown at step 1, values float32  

> set bgColor gray

> set bgColor #80808000

> isolde sim start /A-T

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\\__init__.py", line 166, in run_provider  
toolbar_command(session, name)  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\app\simulation.py", line 106, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.  
  
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde set gpuDeviceIndex 1

> isolde sim start /A-T

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\\__init__.py", line 166, in run_provider  
toolbar_command(session, name)  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\app\simulation.py", line 106, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.  
  
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.  
  
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 581.42
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: de_DE.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 15 9520
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,834,945,024
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: de-DE

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AlphaFold: 1.0.1
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    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[Eric Pettersen]

Reported by Simon Sommerhage