id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5670 OpenMM: Error uploading array TabulatedFunction ria2@… Tristan Croll "The following bug report has been submitted: Platform: Linux-4.19.0-17-amd64-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) 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 /storage/ria2/NanoCage/iSpy/iSpyAAAA-10-04-2021/phenix- refine/Autosharpen_9/sharpened_map.ccp4 format ccp4 Opened sharpened_map.ccp4 as #1, grid size 380,380,380, pixel 1.33, shown at level 0.925, step 2, values float32 open /storage/ria2/NanoCage/iSpy/iSpyAAAA-10-04-2021/phenix- refine/RealSpaceRefine_10/iSpy-AAAA_model_min_real_space_refined_010.pdb format pdb Chain information for iSpy-AAAA_model_min_real_space_refined_010.pdb #2 --- Chain | Description ? | No description available volume #1 step 1 volume #1 level 13.41 volume #1 color #40bfba74 ui tool show ISOLDE set selectionWidth 4 Chain information for iSpy-AAAA_model_min_real_space_refined_010.pdb --- Chain | Description 2.2/? | No description available Done loading forcefield Opened sharpened_map.ccp4 as #2.1.1.1, grid size 380,380,380, pixel 1.33, shown at step 1, values float32 clipper spotlight radius 25.00 clipper spotlight radius 25.00 select clear volume #2.1.1.1 level 24.07 clipper spotlight radius 26.00 clipper spotlight radius 27.00 clipper spotlight radius 28.00 clipper spotlight radius 29.00 clipper spotlight radius 30.00 clipper spotlight radius 31.00 clipper spotlight radius 32.00 clipper spotlight radius 33.00 clipper spotlight radius 34.00 clipper spotlight radius 35.00 clipper spotlight radius 36.00 clipper spotlight radius 37.00 clipper spotlight radius 38.00 clipper spotlight radius 39.00 clipper spotlight radius 40.00 select #2 4480 atoms, 4524 bonds, 292 residues, 12 models selected ~select Nothing selected select #2.2 4480 atoms, 4524 bonds, 292 residues, 5 models selected Traceback (most recent call last): File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2726, in _start_sim_or_toggle_pause self.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2780, in start_sim sm.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 674, in start_sim sh.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1601, in start_sim self._prepare_sim() File ""/home/ria2/.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 ""/opt/chimerax/1.2.5-1/lib/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 ""/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site- packages/simtk/openmm/openmm.py"", line 17752, in __init__ this = _openmm.new_Context(*args) simtk.openmm.OpenMMException: Error uploading array TabulatedFunction: clEnqueueWriteBuffer (-4) simtk.openmm.OpenMMException: Error uploading array TabulatedFunction: clEnqueueWriteBuffer (-4) File ""/opt/chimerax/1.2.5-1/lib/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. ~select Nothing selected ui tool show ISOLDE set selectionWidth 4 Done loading forcefield select #2.2 4480 atoms, 4524 bonds, 292 residues, 11 models selected Traceback (most recent call last): File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2726, in _start_sim_or_toggle_pause self.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2780, in start_sim sm.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 674, in start_sim sh.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1601, in start_sim self._prepare_sim() File ""/home/ria2/.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 ""/opt/chimerax/1.2.5-1/lib/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 ""/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site- packages/simtk/openmm/openmm.py"", line 17752, in __init__ this = _openmm.new_Context(*args) simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6) simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6) File ""/opt/chimerax/1.2.5-1/lib/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/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2726, in _start_sim_or_toggle_pause self.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/isolde.py"", line 2780, in start_sim sm.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 674, in start_sim sh.start_sim() File ""/home/ria2/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1601, in start_sim self._prepare_sim() File ""/home/ria2/.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 ""/opt/chimerax/1.2.5-1/lib/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 ""/opt/chimerax/1.2.5-1/lib/ucsf-chimerax/lib/python3.8/site- packages/simtk/openmm/openmm.py"", line 17752, in __init__ this = _openmm.new_Context(*args) simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6) simtk.openmm.OpenMMException: Error initializing context: clCreateContext (-6) File ""/opt/chimerax/1.2.5-1/lib/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 460.84 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: To Be Filled By O.E.M. Model: To Be Filled By O.E.M. OS: Debian GNU/Linux 10 buster Architecture: 64bit ELF Virutal Machine: none CPU: 64 AMD Ryzen Threadripper 2990WX 32-Core Processor Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 125Gi 76Gi 43Gi 367Mi 6.2Gi 47Gi Swap: 73Gi 3.1Gi 70Gi Graphics: 09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1) Subsystem: ASUSTeK Computer Inc. GP102 [GeForce GTX 1080 Ti] [1043:85e5] 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: 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 moderate Third Party can't reproduce all ChimeraX