OpenMM: Error initializing CUDA: CUDA_ERROR_UNKNOWN

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-58-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.2.2-cp38-cp38-manylinux_2_17_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.16.0 ChimeraX-ISOLDE-1.2.2  
Installed ChimeraX-Clipper (0.16.0)  
Installed ChimeraX-ISOLDE (1.2.2)  
Downloading bundle ChimeraX_Clipper-0.16.0-cp38-cp38-manylinux_2_17_x86_64.whl  
Bundle installation canceled  

> open /home/edu/Desktop/C1Rdelta11/zflip_J339.mrc

Opened zflip_J339.mrc as #1, grid size 520,520,520, pixel 0.87, shown at level
0.149, step 4, values float32  

> open /home/edu/Desktop/C1Rdelta11/J339-coot-1_edited.pdb

Chain information for J339-coot-1_edited.pdb #2  
---  
Chain | Description  
2 6 C D E F G H K M O S T U V W X | No description available  
4 | No description available  
A B I Q R | No description available  
J b t u v w x y z | No description available  
Z | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
  

> volume #1 step 1

> volume #1 level 0.1753

> set bgColor white

> lighting soft

> style stick

Changed 63133 atom styles  

> transparency 50

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for J339-coot-1_edited.pdb  
---  
Chain | Description  
2.2/2 2.2/6 2.2/C 2.2/D 2.2/E 2.2/F 2.2/G 2.2/H 2.2/K 2.2/M 2.2/O 2.2/S 2.2/T
2.2/U 2.2/V 2.2/W 2.2/X | No description available  
2.2/4 | No description available  
2.2/A 2.2/B 2.2/I 2.2/Q 2.2/R | No description available  
2.2/J 2.2/b 2.2/t 2.2/u 2.2/v 2.2/w 2.2/x 2.2/y 2.2/z | No description
available  
2.2/Z | No description available  
2.2/p | No description available  
2.2/q | No description available  
2.2/r | No description available  
2.2/s | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  
Opened zflip_J339.mrc as #2.1.1.1, grid size 520,520,520, pixel 0.87, shown at
step 1, values float32  

> volume #2.1.1.1 level 0.4485

> addh hbond

Missing "hbond" keyword's argument  

> addh hond true

Expected a keyword  

> addh

Summary of feedback from adding hydrogens to J339-coot-1_edited.pdb #2.2  
---  
notes | No usable SEQRES records for J339-coot-1_edited.pdb (#2.2) chain 2;
guessing termini instead  
No usable SEQRES records for J339-coot-1_edited.pdb (#2.2) chain 4; guessing
termini instead  
No usable SEQRES records for J339-coot-1_edited.pdb (#2.2) chain 6; guessing
termini instead  
No usable SEQRES records for J339-coot-1_edited.pdb (#2.2) chain A; guessing
termini instead  
No usable SEQRES records for J339-coot-1_edited.pdb (#2.2) chain B; guessing
termini instead  
32 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /2 HIS 26, /4 HIS 26, /6 HIS
26, /A SER 25, /B SER 25, /C HIS 26, /D HIS 26, /E HIS 26, /F HIS 26, /G HIS
26, /H HIS 26, /I SER 25, /J GLU 315, /K HIS 26, /M HIS 26, /O HIS 26, /Q SER
25, /R SER 25, /S HIS 26, /T HIS 26, /U HIS 26, /V HIS 26, /W HIS 26, /X HIS
26, /Z SER 25, /b GLU 315, /p ALA 5, /q ALA 36, /r ALA 283, /s SER 283, /t GLU
315, /u GLU 315, /v GLU 315, /w GLU 315, /x GLU 315, /y GLU 315, /z GLU 315  
Chain-initial residues that are not actual N termini: /4 ASP 55, /Z GLU 329,
/p GLU 315  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /2 THR 357, /4 THR 357, /4
PHE 53, /6 THR 357, /A THR 357, /B THR 357, /C THR 357, /D THR 357, /E THR
357, /F THR 357, /G THR 357, /H THR 357, /I THR 357, /J VAL 336, /K THR 357,
/M THR 357, /O THR 357, /Q THR 357, /R THR 357, /S THR 357, /T THR 357, /U THR
357, /V THR 357, /W THR 357, /X THR 357, /Z THR 357, /Z MET 327, /b VAL 336,
/p VAL 336, /p ALA 10, /q ALA 41, /r SER 287, /s ALA 287, /t VAL 336, /u VAL
336, /v VAL 336, /w VAL 336, /x VAL 336, /y VAL 336, /z VAL 336  
5435 hydrogen bonds  
Adding 'H' to /4 ASP 55  
Adding 'H' to /Z GLU 329  
Adding 'H' to /p GLU 315  
/2 THR 357 is not terminus, removing H atom from 'C'  
/4 THR 357 is not terminus, removing H atom from 'C'  
/6 THR 357 is not terminus, removing H atom from 'C'  
/A THR 357 is not terminus, removing H atom from 'C'  
/B THR 357 is not terminus, removing H atom from 'C'  
33 messages similar to the above omitted  
63478 hydrogens added  
  

> volume #2.1.1.1 level 0.2942

Traceback (most recent call last):  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/edu/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/home/edu/Downloads/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/home/edu/Downloads/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_UNKNOWN
(999) at /tmp/mmbuild/openmm/platforms/cuda/src/CudaContext.cpp:138  
  
simtk.openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_UNKNOWN
(999) at /tmp/mmbuild/openmm/platforms/cuda/src/CudaContext.cpp:138  
  
File "/home/edu/Downloads/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: Quadro M620/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 3520
OS: Linux Mint 19.3 tricia
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        3.4G        1.7G        200M         10G         11G
	Swap:          975M        1.0M        974M

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:591b] (rev 04)	
	Subsystem: Dell Device [1028:07a9]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Tristan Croll]

That's a very small GPU for what looks to be a very large model (the Quadro M620 has just 2GB of RAM). My guess is that it ran out of memory.

[Tristan Croll]

Actually, looking at where it crashed it's probably not a memory issue. More likely it boils down to the very poor support for these hybrid Intel/Nvidia GPU combinations (Nvidia Optimus) in Linux. My first serious GPU laptop had this architecture, and it was an absolute nightmare to get set up. Anyway, won't be able to do anything without input from the user.