id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4888 OpenMMException: invalid value for --gpu-architecture vds7@… Tristan Croll "{{{ 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 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 }}} " defect closed normal Third Party fixed Tom Goddard all ChimeraX