id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5322 OpenMMException: Error compiling program: nvrtc: error: invalid value for --gpu-architecture soumya-joseph@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1160.42.2.el7.x86_64-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description I selected my PDB file (added H, fitted in map and clipper associated) and asked for an MD simulation for the entire pdb file and map (according to the tutorial). 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 Consurf/LARGE1ConsurfFlex-EMaligned_AB.pdb Chain information for LARGE1ConsurfFlex-EMaligned_AB.pdb #1 --- Chain | Description A B | No description available > open deepEMhancer/J223_halves_ddepemhanced.mrc Opened J223_halves_ddepemhanced.mrc as #2, grid size 720,720,720, pixel 0.401, shown at step 1, values float32 > volume #2 region 0,0,0,719,719,719 step 4 > volume #2 region 0,0,0,719,719,719 step 4 > volume #2 step 1 > volume #2 > volume #2 level 0.001 > volume #2 change image level -4.493e-05,0 level 0.07227,0.8 level 1.947,1 > volume #2 level 0.01 > addh Summary of feedback from adding hydrogens to LARGE1ConsurfFlex- EMaligned_AB.pdb #1 --- notes | No usable SEQRES records for LARGE1ConsurfFlex-EMaligned_AB.pdb (#1) chain A; guessing termini instead No usable SEQRES records for LARGE1ConsurfFlex-EMaligned_AB.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 120, /B ALA 120 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A SER 756, /B SER 756 Chain-final residues that are not actual C termini: 1223 hydrogen bonds 10398 hydrogens added > transparency #1 50 > transparency #1 0 > transparency #2 50 > Incomplete command: isolde > isolde start > set selectionWidth 4 Chain information for LARGE1ConsurfFlex-EMaligned_AB.pdb --- Chain | Description 1.2/A 1.2/B | No description available Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > addh Summary of feedback from adding hydrogens to LARGE1ConsurfFlex- EMaligned_AB.pdb #1.2 --- notes | No usable SEQRES records for LARGE1ConsurfFlex-EMaligned_AB.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for LARGE1ConsurfFlex-EMaligned_AB.pdb (#1.2) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A ALA 120, /B ALA 120 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A SER 756, /B SER 756 Chain-final residues that are not actual C termini: 1169 hydrogen bonds 0 hydrogens added > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule LARGE1ConsurfFlex-EMaligned_AB.pdb (#1.2) to map J223_halves_ddepemhanced.mrc (#2) using 20944 atoms average map value = 0.06938, steps = 268 shifted from previous position = 2.06 rotated from previous position = 3.27 degrees atoms outside contour = 13696, contour level = 0.01 > clipper associate #2 toModel #1 Opened J223_halves_ddepemhanced.mrc as #1.1.1.1, grid size 720,720,720, pixel 0.401, shown at step 1, values float32 > volume #1.1.1.1 level 0.0168 > volume #1.1.1.1 region 0,0,0,719,719,719 step 4 > volume #1.1.1.1 style surface region 0,0,0,719,719,719 step 4 > volume #1.1.1.1 step 1 > clipper spotlight radius 20 > select #1.1.1 4 models selected > ~select #1.1.1 Nothing selected > select #1.1.1 4 models selected > ~select #1.1.1 Nothing selected > select #1.2 20944 atoms, 21230 bonds, 1274 residues, 5 models selected Map is too large for fast cubic interpolation on the GPU! Switching to slower, more memory-efficient implementation. Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py"", line 2726, in _start_sim_or_toggle_pause self.start_sim() File ""/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF- ChimeraX/lib/python3.8/site-packages/chimerax/isolde/isolde.py"", line 2780, in start_sim sm.start_sim() File ""/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF- ChimeraX/lib/python3.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 674, in start_sim sh.start_sim() File ""/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF- ChimeraX/lib/python3.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1601, in start_sim self._prepare_sim() File ""/programs/x86_64-linux/chimerax/1.2.5-c7/libexec/UCSF- ChimeraX/lib/python3.8/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1561, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, File ""/programs/x86_64-linux/chimerax/1.2.5-c7/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 ""/programs/x86_64-linux/chimerax/1.2.5-c7/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 ""/programs/x86_64-linux/chimerax/1.2.5-c7/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 460.27.04 OpenGL renderer: RTX A6000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7049GP-TRT OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 96 Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz Cache Size: 36608 KB Memory: total used free shared buff/cache available Mem: 251G 18G 196G 288M 36G 232G Swap: 9G 0B 9G Graphics: 05:00.0 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 duplicate all ChimeraX