id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3143 Starting simulation: Error initializing context: clGetDeviceIDs florejo@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.3.11-100.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine ChimeraX Version: 0.93 (2020-04-03) Description Starting the MD simulation in the ISOLDE intro to cryoEM model building tutorial. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- note | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 > select clear > isolde start > isolde start > set bgColor white > addh Summary of feedback from adding hydrogens to 6out.pdb #1.2 --- notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records Termini for 6out.pdb (#1.2) chain B determined from SEQRES records Termini for 6out.pdb (#1.2) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > hide HC > isolde restrain ligands #1 QWidget::repaint: Recursive repaint detected > select #1 22945 atoms, 23062 bonds, 14 models selected > isolde sim start sel Traceback (most recent call last): File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 601, in customEvent func(*args, **kw) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 429, in defer cxcmd(session, topic) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 445, in cxcmd run(session, cmd) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/home/jonathan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/cmd.py"", line 88, in isolde_sim isolde.start_sim() File ""/home/jonathan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/jonathan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/jonathan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/jonathan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/simtk/openmm/app/simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetDeviceIDs (-1) Exception: Error initializing context: clGetDeviceIDs (-1) File ""/usr/local/chimerax-0.93/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. OpenGL version: 3.3 (Core Profile) Mesa 18.3.6 OpenGL renderer: llvmpipe (LLVM 7.0, 256 bits) OpenGL vendor: VMware, Inc. Manufacturer: Supermicro Model: SYS-7048A-T OS: Fedora 29 Architecture: 64bit ELF CPU: 48 Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz Cache Size: 30720 KB Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:85aa] Kernel driver in use: nvidia }}} " defect closed normal Third Party fixed all ChimeraX