no OpenCL or compatible CUDA drivers

[jianghai.zhu@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-45-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
After starting ISOLDE, I got the following warning.

WARNING: no OpenCL or compatible CUDA drivers detected! While it is theoretically possible to run ISOLDE using CPU only, in practice it is prohibitively slow. If you have a suitable GPU in your machine, please check that you have the recommended drivers from the manufacturer installed. The current required CUDA version is 11.2 - if installed, please make sure this is on your library path before starting ChimeraX.

As you see from the "Gathered Information" below, ChimeraX is using NVIDIA driver 550.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> mousemode shift middleMode center

> functionkey F1 clip near -2

> functionkey F2 clip near 2

> functionkey F3 clip far -2

> functionkey F4 clip far 2

> ui tool hide "command line interface"

> ui tool show clix

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Data/Stalled_Ribosome/PP/70S_PP_MD_peptide_3.cif

Summary of feedback from opening
/Data/Stalled_Ribosome/PP/70S_PP_MD_peptide_3.cif  
---  
warning | Unable to fetch template for 'MKL': will connect using distance criteria  
  
Chain information for 70S_PP_MD_peptide_3.cif #1  
---  
Chain | Description  
3 | 50S ribosomal protein bL37  
A | 23S rRNA  
B | 5S rRNA  
BA | 16S rRNA  
BB | Conserved domain protein  
BC | 30S ribosomal protein S3  
BD | 30S ribosomal protein S4  
BE | 30S ribosomal protein S5  
BF | 30S ribosomal protein S6  
BG | 30S ribosomal protein S7  
BH | 30S ribosomal protein S8  
BI | 30S ribosomal protein S9  
BJ | 30S ribosomal protein S10  
BK | 30S ribosomal protein S11  
BL | 30S ribosomal protein S12  
BM | 30S ribosomal protein S13  
BN | 30S ribosomal protein S14 type Z  
BO | 30S ribosomal protein S15  
BP | 30S ribosomal protein S16  
BQ | 30S ribosomal protein S17  
BR | 30S ribosomal protein S18 2  
BS | 30S ribosomal protein S19  
BT | 30S ribosomal protein S20  
BV | 30S ribosomal protein S2  
BW | P/P-site Phe-tRNA(Phe)  
BX | mRNA  
C | 50S ribosomal protein L2  
D | 50S ribosomal protein L3  
E | 50S ribosomal protein L4  
F | 50S ribosomal protein L5  
G | 50S ribosomal protein L6  
H | 50S ribosomal protein L9  
I | 50S ribosomal protein L10  
J | 50S ribosomal protein L11  
K | 50S ribosomal protein L13  
L | 50S ribosomal protein L14  
M | 50S ribosomal protein L15  
N | 50S ribosomal protein L16  
O | 50S ribosomal protein L17  
P | 50S ribosomal protein L18  
Q | 50S ribosomal protein L19  
R | 50S ribosomal protein L20  
S | 50S ribosomal protein L21  
T | 50S ribosomal protein L22  
U | 50S ribosomal protein L23  
V | 50S ribosomal protein L24  
W | 50S ribosomal protein L25  
X | 50S ribosomal protein L27  
Y | LSU ribosomal protein L28P  
Z | 50S ribosomal protein L29  
a | 50S ribosomal protein L30  
b | 50S ribosomal protein L32  
c | 50S ribosomal protein L33 1  
d | 50S ribosomal protein L34  
e | 50S ribosomal protein L35  
f | 50S ribosomal protein L36  
g | 50S ribosomal protein L31  
s | nascent peptide chain  
  

> open /Data/Stalled_Ribosome/PP/smeg_70S_PP_2.01.mrc

Opened smeg_70S_PP_2.01.mrc as #2, grid size 576,576,576, pixel 0.918, shown
at level 0.0845, step 4, values float32  

> open /Data/Stalled_Ribosome/PP/smeg_70S_PP_2.01_deep.mrc

Opened smeg_70S_PP_2.01_deep.mrc as #3, grid size 640,640,640, pixel 0.826,
shown at level 0.00347, step 4, 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  

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 11.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 70S_PP_MD_peptide_3.cif  
---  
Chain | Description  
1.2/3 | 50S ribosomal protein bL37  
1.2/A | 23S rRNA  
1.2/B | 5S rRNA  
1.2/BA | 16S rRNA  
1.2/BB | Conserved domain protein  
1.2/BC | 30S ribosomal protein S3  
1.2/BD | 30S ribosomal protein S4  
1.2/BE | 30S ribosomal protein S5  
1.2/BF | 30S ribosomal protein S6  
1.2/BG | 30S ribosomal protein S7  
1.2/BH | 30S ribosomal protein S8  
1.2/BI | 30S ribosomal protein S9  
1.2/BJ | 30S ribosomal protein S10  
1.2/BK | 30S ribosomal protein S11  
1.2/BL | 30S ribosomal protein S12  
1.2/BM | 30S ribosomal protein S13  
1.2/BN | 30S ribosomal protein S14 type Z  
1.2/BO | 30S ribosomal protein S15  
1.2/BP | 30S ribosomal protein S16  
1.2/BQ | 30S ribosomal protein S17  
1.2/BR | 30S ribosomal protein S18 2  
1.2/BS | 30S ribosomal protein S19  
1.2/BT | 30S ribosomal protein S20  
1.2/BV | 30S ribosomal protein S2  
1.2/BW | P/P-site Phe-tRNA(Phe)  
1.2/BX | mRNA  
1.2/C | 50S ribosomal protein L2  
1.2/D | 50S ribosomal protein L3  
1.2/E | 50S ribosomal protein L4  
1.2/F | 50S ribosomal protein L5  
1.2/G | 50S ribosomal protein L6  
1.2/H | 50S ribosomal protein L9  
1.2/I | 50S ribosomal protein L10  
1.2/J | 50S ribosomal protein L11  
1.2/K | 50S ribosomal protein L13  
1.2/L | 50S ribosomal protein L14  
1.2/M | 50S ribosomal protein L15  
1.2/N | 50S ribosomal protein L16  
1.2/O | 50S ribosomal protein L17  
1.2/P | 50S ribosomal protein L18  
1.2/Q | 50S ribosomal protein L19  
1.2/R | 50S ribosomal protein L20  
1.2/S | 50S ribosomal protein L21  
1.2/T | 50S ribosomal protein L22  
1.2/U | 50S ribosomal protein L23  
1.2/V | 50S ribosomal protein L24  
1.2/W | 50S ribosomal protein L25  
1.2/X | 50S ribosomal protein L27  
1.2/Y | LSU ribosomal protein L28P  
1.2/Z | 50S ribosomal protein L29  
1.2/a | 50S ribosomal protein L30  
1.2/b | 50S ribosomal protein L32  
1.2/c | 50S ribosomal protein L33 1  
1.2/d | 50S ribosomal protein L34  
1.2/e | 50S ribosomal protein L35  
1.2/f | 50S ribosomal protein L36  
1.2/g | 50S ribosomal protein L31  
1.2/s | nascent peptide chain  
  




OpenGL version: 3.3.0 NVIDIA 550.107.02
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 24.04 Noble Numbat
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi       6.5Gi       238Gi        57Mi       8.5Gi       245Gi
	Swap:          8.0Gi          0B       8.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. GA102 [GeForce RTX 3090] [19da:1613]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-clix: 0.1.9
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    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: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11