OpenMMException: invalid value for --gpu-architecture

[vds7@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.31.1.el7.x86_64-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)
I was trying to run isolde and this happened. 
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: invalid value for --gpu-architecture (-arch) File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-packages/simtk/openmm/openmm.py", line 17752, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. 

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  

> open
> /home/vds7/Documents/3602-870/Coot/3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb

Chain information for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb #1  
---  
Chain | Description  
A F H | No description available  
B | No description available  
C I L | No description available  
D J | No description available  
G | No description available  
K M | No description available  
  

> hide atoms

> show cartoons

> open
> /home/vds7/Documents/3602-870/cryosparc_P5_J103_008_volume_map_sharp.mrc

Opened cryosparc_P5_J103_008_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.701, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.8344

> volume #2 level 0.9676

> isolde start

> set selectionWidth 4

Chain information for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb  
---  
Chain | Description  
1.2/A 1.2/F 1.2/H | No description available  
1.2/B | No description available  
1.2/C 1.2/I 1.2/L | No description available  
1.2/D 1.2/J | No description available  
1.2/G | No description available  
1.2/K 1.2/M | No description available  
  
Done loading forcefield  

> clipper associate #2 toModel #1

Opened cryosparc_P5_J103_008_volume_map_sharp.mrc as #1.1.1.1, grid size
320,320,320, pixel 1.07, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to
3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb #1.2  
---  
notes | No usable SEQRES records for
3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for 3602-870_Complex_map_Fitting_6.29.21-coot-3.pdb
(#1.2) chain F; guessing termini instead  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A HIS 1, /B ALA 517, /C ASP
1, /D ALA 517, /F HIS 1, /G GLU 32, /H HIS 1, /I ASP 1, /J ALA 517, /K GLU 32,
/L ASP 1, /M GLU 32  
Chain-initial residues that are not actual N termini: /B GLN 563, /D HIS 564,
/G ASN 188, /G GLY 409, /J HIS 564, /K LYS 65, /K ASN 188, /K GLY 409, /M LYS
65, /M ASN 188, /M GLY 409  
Chain-final residues that are actual C termini: /A SER 126, /C VAL 107, /F SER
126, /H SER 126, /I VAL 107, /L VAL 107  
Chain-final residues that are not actual C termini: /B LEU 663, /B SER 553, /D
LEU 663, /D VAL 549, /G ARG 504, /G ASN 185, /G ASN 398, /J LEU 663, /J VAL
549, /K ARG 504, /K ALA 58, /K ASN 185, /K ASN 398, /M ARG 504, /M ALA 58, /M
ASN 185, /M ASN 398  
1559 hydrogen bonds  
Adding 'H' to /B GLN 563  
Adding 'H' to /D HIS 564  
Adding 'H' to /G ASN 188  
Adding 'H' to /G GLY 409  
Adding 'H' to /J HIS 564  
6 messages similar to the above omitted  
/B LEU 663 is not terminus, removing H atom from 'C'  
/D LEU 663 is not terminus, removing H atom from 'C'  
/G ARG 504 is not terminus, removing H atom from 'C'  
/J LEU 663 is not terminus, removing H atom from 'C'  
/K ARG 504 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
18956 hydrogens added  
  

> hide HC

> select all

38219 atoms, 38632 bonds, 11 pseudobonds, 2447 residues, 13 models selected  
Traceback (most recent call last):  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/vds7/.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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: invalid
value for --gpu-architecture (-arch)  
  
  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: invalid
value for --gpu-architecture (-arch)  
  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2726, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/vds7/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/vds7/.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 "/usr/libexec/UCSF-ChimeraX/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 "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: invalid
value for --gpu-architecture (-arch)  
  
  
simtk.openmm.OpenMMException: Error compiling program: nvrtc: error: invalid
value for --gpu-architecture (-arch)  
  
  
File "/usr/libexec/UCSF-ChimeraX/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 460.73.01
OpenGL renderer: GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: SYS-7049GP-TRT
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           187G        5.5G        179G         81M        2.1G        181G
	Swap:            9G          0B          9G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: Super Micro Computer Inc Device [15d9:096d]	
	Kernel modules: ast
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
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    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
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    RandomWords: 0.3.0
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    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
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    tifffile: 2020.9.3
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    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

[Eric Pettersen]

Reported by Victoria Stalls

[Tristan Croll]

Hmm... looks like the problem here is that the current version of OpenMM bundled with ChimeraX uses a version of CUDA (11.0) that isn't yet compatible with the RTX 30 series. The good news is that you can work around this for now with what should be a barely noticeable impact on performance: on the ISOLDE GUI, set the "Experience level" drop-down (bottom right) to "advanced". Then, in the cyan "Computational Platform" field that appears on the "Sim settings" tab, choose OpenCL in the drop-down menu. I'm afraid you'll need to do this every time you start ISOLDE right now (I'm working on implementing persistent user settings, hopefully for the next release). I've been talking to the OpenMM team about making it easier to update the version installed in ChimeraX - looks like it's time I pushed that to the top of the to-do list.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 12 July 2021 18:10
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>; vds7@duke.edu <vds7@duke.edu>
Subject: Re: [ChimeraX] #4888: OpenMMException: invalid value for --gpu-architecture (was: ChimeraX bug report submission)

#4888: OpenMMException: invalid value for --gpu-architecture
----------------------------------+---------------------------
          Reporter:  vds7@…       |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * cc: Tom Goddard (added)
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tristan Croll


Comment:

 Reported by Victoria Stalls

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4888#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

Yes, it appears ChimeraX on Linux and Windows uses OpenMM with CUDA 11.0 from September 2020. I'm not sure what you mean about RTX 30x0 not supporting CUDA 11.0 -- it was supported almost a year ago

​https://developer.nvidia.com/blog/cuda-11-1-introduces-support-rtx-30-series/

[Tristan Croll]

See the discussion at ​https://github.com/pytorch/pytorch/issues/47658 - it seems to be a problem specifically with the just-in-time compiler, fixed (possibly) in 11.1 or later. But I don't think that will be a help here without updating OpenMM, since libOpenMMCudaCompiler.so links specifically to libnvrtc.so.11.0.

[Tristan Croll]

Same problem pops up periodically with new hardware updates - see ​https://github.com/openmm/openmm/issues/1653.

[Tristan Croll]

According to discussion with the OpenMM team, the OpenMM build *should* be compatible with any 11.x version of CUDA - so if you update your system CUDA to the latest version you should be good to go.

[victoria.stalls@…]

Ok, thank you both for your help.


Best,

Victoria Stalls
Research Technician III, Acharya Lab
Duke Human Vaccine Institute, Division of Structural Biology
Duke University School of Medicine
Durham, NC 27710
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, July 14, 2021 4:16 PM
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>; Victoria Stalls <victoria.stalls@duke.edu>
Subject: Re: [ChimeraX] #4888: OpenMMException: invalid value for --gpu-architecture

#4888: OpenMMException: invalid value for --gpu-architecture
----------------------------------+---------------------------
          Reporter:  vds7@…       |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tristan Croll):

 According to discussion with the OpenMM team, the OpenMM build *should* be
 compatible with any 11.x version of CUDA - so if you update your system
 CUDA to the latest version you should be good to go.

--
Ticket URL: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4888*comment:6__;Iw!!OToaGQ!6WaOxt-Lo_EdmramWcN_vgCgLRS2sCSy3mQtzhpeeTu8IAIkgxm20QyTtglXXw$ >
ChimeraX <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!6WaOxt-Lo_EdmramWcN_vgCgLRS2sCSy3mQtzhpeeTu8IAIkgxm20Qw9aIuIsg$ >
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