Opened 5 years ago

Closed 5 years ago

#4178 closed defect (can't reproduce)

OpenMM: Error launching CUDA compiler: Value 'sm_75' is not defined for option 'gpu-architecture'

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-72-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kpwu/chimeraX/MSG-combined-
> refined_job8-0303-coot-2_real_space_refined.pdb

Chain information for MSG-combined-
refined_job8-0303-coot-2_real_space_refined.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/kpwu/chimeraX/cryosparc_P6_J318_007_volume_map.mrc

Opened cryosparc_P6_J318_007_volume_map.mrc, grid size 256,256,256, pixel
0.822, shown at level 0.0572, step 1, values float32  

> volume #2 level 0.277

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for MSG-combined-
refined_job8-0303-coot-2_real_space_refined.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to MSG-combined-
refined_job8-0303-coot-2_real_space_refined.pdb #1.2  
---  
notes | No usable SEQRES records for MSG-combined-
refined_job8-0303-coot-2_real_space_refined.pdb (#1.2) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A HIS 723  
587 hydrogen bonds  
/A HIS 723 is not terminus, removing H atom from 'C'  
5610 hydrogens added  
  
Traceback (most recent call last):  
File "/home/kpwu/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/kpwu/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2746, in start_sim  
sm.start_sim()  
File "/home/kpwu/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/kpwu/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/kpwu/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1562, in
_prepare_sim  
integrator, platform, properties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 18608, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error launching CUDA compiler: 256  
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'  
  
  
Exception: Error launching CUDA compiler: 256  
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'  
  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 18608, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 18.0.5
OpenGL renderer: llvmpipe (LLVM 6.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 48 Intel(R) Xeon(R) Silver 4116 CPU @ 2.10GHz
Cache Size: 16896 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           251G         14G         11G        1.3G        225G        234G
	Swap:          974M        973M        1.1M

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:096d]
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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: 0.29.20
    decorator: 4.4.2
    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: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenMM: Error launching CUDA compiler: Value 'sm_75' is not defined for option 'gpu-architecture'

comment:2 by Tristan Croll, 5 years ago

Resolution: → can't reproduce
Status: assigned → closed

Not much idea what's going on here. A quick Google of the error message brings up ​https://discuss.cryosparc.com/t/nvidia-rtx-2080-nvcc-fatal-value-sm-75-is-not-defined-for-option-gpu-architecture/2731 which suggests this happens with newer Nvidia GPUs if the CUDA version is older than 10 - but OpenMM is compiled against CUDA 10, and the option to use CUDA won't appear unless the correct CUDA version is available (the OpenMM CUDA plugins would fail to load, leading ISOLDE to exclude it from its options). I suppose it's possible that the CUDA 10 libraries are on the load path but the wrong nvcc version is first on the execution path, but that seems unlikely... It also looks like this is running in a virtual machine? With this being an anonymous report, I don't think there's much I can do.

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