id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7944 CUDA_ERROR_UNSUPPORTED_PTX_VERSION chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.21.2.el7.x86_64-x86_64-with-glibc2.17 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: 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 relion_post_flip.mrc Opened relion_post_flip.mrc as #1, grid size 200,200,200, pixel 1.76, shown at level 0.602, step 1, values float32 > open a3fit_1.pdb Chain information for a3fit_1.pdb #2 --- Chain | Description A | No description available > ui tool show ISOLDE > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 68 residues in model #2 to IUPAC-IUB standards. Chain information for a3fit_1.pdb --- Chain | Description 2.2/A | No description available Done loading forcefield Opened relion_post_flip.mrc as #2.1.1.1, grid size 200,200,200, pixel 1.76, shown at step 1, values float32 > volume #2.1.1.1 level 0.3262 > select /A 3512 atoms, 3591 bonds, 450 residues, 1 model selected ISOLDE: stopped sim > addh Summary of feedback from adding hydrogens to a3fit_1.pdb #2.2 --- notes | No usable SEQRES records for a3fit_1.pdb (#2.2) 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: /A TYR 450 Chain-final residues that are not actual C termini: 435 hydrogen bonds 3406 hydrogens added Launching using CUDA failed with the below message. Falling back to using OpenCL. Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) Traceback (most recent call last): File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1606, in start_sim self._prepare_sim() File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1564, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/openmm/app/simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/openmm/openmm.py"", line 5210, in __init__ this = _openmm.new_Context(*args) openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py"", line 2749, in _start_sim_or_toggle_pause self.start_sim() File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py"", line 2804, in start_sim sm.start_sim() File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 677, in start_sim sh.start_sim() File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1611, in start_sim self._prepare_sim() File ""/home/zhuyun/.local/share/ChimeraX/1.3/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1551, in _prepare_sim platform = openmm.Platform.getPlatformByName(params.platform) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/openmm/openmm.py"", line 18377, in getPlatformByName return _openmm.Platform_getPlatformByName(name) openmm.OpenMMException: There is no registered Platform called ""OpenCL"" openmm.OpenMMException: There is no registered Platform called ""OpenCL"" File ""/usr/libexec/UCSF-ChimeraX/lib/python3.9/site- packages/openmm/openmm.py"", line 18377, in getPlatformByName return _openmm.Platform_getPlatformByName(name) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.27.04 OpenGL renderer: Quadro P2000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: X11DPi-N(T) OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 40 Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz Cache Size: 14080 KB Memory: total used free shared buff/cache available Mem: 141G 10G 109G 233M 20G 129G Swap: 63G 0B 63G Graphics: 03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: 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: 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-ArtiaX: 0.3 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 geomdl: 5.3.1 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 pandas: 1.5.0 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 starfile: 0.4.11 suds-jurko: 0.6 superqt: 0.3.5 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 typing-extensions: 4.3.0 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Third Party duplicate Tom Goddard all ChimeraX