Error launching CUDA compiler

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007fe262ffd700 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1284 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007fe3c2787740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/openmm/openmm.py", line 5210 in __init__
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/openmm/app/simulation.py", line 105 in __init__
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1564 in _prepare_sim
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1611 in start_sim
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 677 in start_sim
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/isolde.py", line 2804 in start_sim
  File "/home/rodolpho/.local/share/ChimeraX/1.3/site-packages/chimerax/isolde/isolde.py", line 2749 in _start_sim_or_toggle_pause
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/rodolpho/Projects/isolde/AlphaFold_P39109.pdb

Chain information for AlphaFold_P39109.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/home/rodolpho/Desktop/Paper
> Figures/cryosparc_P5_J665_006_volume_map.mrc"

Opened cryosparc_P5_J665_006_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.822, shown at level 0.0378, step 2, values float32  

> open /home/rodolpho/Desktop/Maps/cryosparc_P5_J556_008_volume_map.mrc

Opened cryosparc_P5_J556_008_volume_map.mrc as #3, grid size 440,440,440,
pixel 0.822, shown at level 0.0336, step 2, values float32  

> select #1

12061 atoms, 12312 bonds, 1515 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,272.79,0,1,0,97.937,0,0,1,86.188

> view matrix models #1,1,0,0,200.8,0,1,0,90.597,0,0,1,71.699

> view matrix models #1,1,0,0,205.29,0,1,0,121.61,0,0,1,176.88

> view matrix models #1,1,0,0,180.02,0,1,0,175.24,0,0,1,154.1

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.59748,-0.28126,-0.75094,169.23,0.66571,-0.69606,-0.26896,184.58,-0.44705,-0.6606,0.60312,152.64

> view matrix models
> #1,-0.43379,0.7671,0.47263,170.97,-0.011205,0.51992,-0.85414,173.59,-0.90094,-0.37581,-0.21694,145.64

> view matrix models
> #1,-0.62042,0.70086,0.35197,169.71,-0.10572,0.36996,-0.92301,173.39,-0.77711,-0.60986,-0.15544,147.51

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.62042,0.70086,0.35197,179.11,-0.10572,0.36996,-0.92301,189.06,-0.77711,-0.60986,-0.15544,160.42

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.001951,0.89808,0.43983,182.12,-0.22971,0.42847,-0.87387,188.34,-0.97326,-0.09933,0.20714,158.79

> view matrix models
> #1,-0.04168,0.93475,0.35286,181.38,-0.26035,0.33081,-0.90707,188.42,-0.96461,-0.12968,0.22958,159.05

> view matrix models
> #1,-0.026782,0.94626,0.3223,181.29,-0.18579,0.31209,-0.93171,188.81,-0.98222,-0.084833,0.16745,158.52

> fitmap #1 inMap #2

Fit molecule AlphaFold_P39109.pdb (#1) to map
cryosparc_P5_J665_006_volume_map.mrc (#2) using 12061 atoms  
average map value = 0.05059, steps = 172  
shifted from previous position = 5.63  
rotated from previous position = 15.5 degrees  
atoms outside contour = 6515, contour level = 0.037814  
  
Position of AlphaFold_P39109.pdb (#1) relative to
cryosparc_P5_J665_006_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.00714924 0.83115953 0.55598806 183.70559372  
-0.12435823 0.55094702 -0.82522264 194.07614050  
-0.99221163 -0.07504141 0.09942268 159.33041930  
Axis 0.38120519 0.78671889 -0.48554711  
Axis point 166.84059959 0.00000000 71.46941543  
Rotation angle (degrees) 100.27598262  
Shift along axis 145.35046699  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 222 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AlphaFold_P39109.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Done loading forcefield  
Opened cryosparc_P5_J665_006_volume_map.mrc as #1.1.1.1, grid size
440,440,440, pixel 0.822, shown at step 1, values float32  

> volume #3 step 1

> volume #3 color #f400f419

> set bgColor white

> select #1

12061 atoms, 12312 bonds, 1515 residues, 12 models selected  

> hide sel atoms

> show sel cartoons

> isolde restrain distances #1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde release distances #1:857-880

> open "/home/rodolpho/Desktop/Paper Figures/ycf1_pka_valid.pdb"

Chain information for ycf1_pka_valid.pdb #2  
---  
Chain | Description  
A | No description available  
  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to ycf1_pka_valid.pdb #2/A GLN 202 CB because
it is missing heavy-atom bond partners  
Not adding hydrogens to ycf1_pka_valid.pdb #2/A THR 203 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to ycf1_pka_valid.pdb #2/A LEU 204 CB because it is
missing heavy-atom bond partners  
Not adding hydrogens to ycf1_pka_valid.pdb #2/A THR 205 CB because it is
missing heavy-atom bond partners  
notes | No usable SEQRES records for AlphaFold_P39109.pdb (#1.2) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: AlphaFold_P39109.pdb #1.2/A
MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold_P39109.pdb #1.2/A
ASN 1515  
Chain-final residues that are not actual C termini:  
1528 hydrogen bonds  
No usable SEQRES records for ycf1_pka_valid.pdb (#2) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini: ycf1_pka_valid.pdb #2/A MET
1  
Chain-initial residues that are not actual N termini: ycf1_pka_valid.pdb #2/A
ASN 335, ycf1_pka_valid.pdb #2/A ALA 882, ycf1_pka_valid.pdb #2/A ASP 900  
Chain-final residues that are actual C termini: ycf1_pka_valid.pdb #2/A ASN
1515  
Chain-final residues that are not actual C termini: ycf1_pka_valid.pdb #2/A
PHE 332, ycf1_pka_valid.pdb #2/A LYS 857, ycf1_pka_valid.pdb #2/A ALA 891  
1301 hydrogen bonds  
12269 hydrogens added  
  

> select #1:1490-1515

386 atoms, 388 bonds, 26 residues, 1 model selected  

> select #1

24327 atoms, 24578 bonds, 1515 residues, 18 models selected  

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 256  
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'  
  


===== Log before crash end =====

Log:
> set selectionWidth 4

UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 430.34
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen Threadripper 2950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         17G         29G        245M         79G        106G
	Swap:          4.0G        1.4G        2.6G

Graphics:
	0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 Rev. A] [10de:1e87] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:2183]	
	Kernel driver in use: nvidia
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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Version 1.3 and no reporter...