id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3156 Error initializing context: clGetPlatformIDs gokhan_tolun@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-76-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.93 (2020-04-03) Description Happens when I try to start an ISOLDE simulation. Log: Startup Messages --- warning | QXcbConnection: XCB error: 1 (BadRequest), sequence: 169, resource id: 456, major code: 130 (Unknown), minor code: 47 note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-linux_x86_64.whl Successfully installed ChimeraX-Clipper-0.12.1 ChimeraX-ISOLDE-1.0b5 Installed ChimeraX-Clipper (0.12.1) Installed ChimeraX-ISOLDE (1.0b5) > toolshed show ISOLDE > set selectionWidth 4 Forcefield cache not found or out of date.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 > open2 /home/gokhan/Documents/structure/RNAP-HelD/6WVK_HelD.pdb > /home/gokhan/Documents/structure/RNAP-HelD/sharpened_map.ccp4 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/dialog.py"", line 146, in _qt_safe if data_format is None else "" format "" + StringArg.unparse(data_format.nicknames[0]))) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 86, in cmd_open Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2848, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 149, in provider_open models, status = collated_open(session, False, [data], data_format, opener_info.open, UnboundLocalError: local variable 'data_format' referenced before assignment UnboundLocalError: local variable 'data_format' referenced before assignment File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/open_command/cmd.py"", line 149, in provider_open models, status = collated_open(session, False, [data], data_format, opener_info.open, See log for complete Python traceback. > open2 /home/gokhan/Documents/structure/RNAP-HelD/6WVK_HelD.pdb Summary of feedback from opening <_io.textiowrapper name=""/home/gokhan/Documents/structure/RNAP-HelD/6WVK_HelD.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Duplicate atom serial number found: 5900 Duplicate atom serial number found: 5901 Duplicate atom serial number found: 23498 Duplicate atom serial number found: 23499 Chain information for 6WVK_HelD.pdb #1 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available F | No description available H | No description available Chain information for 6WVK_HelD.pdb --- Chain | Description 1.2/A 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/H | 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 > open2 /home/gokhan/Documents/structure/RNAP-HelD/sharpened_map.ccp4 Opened sharpened_map.ccp4, grid size 169,194,164, pixel 0.84,0.84,0.84, shown at level 3.3, step 1, values float32 Missing ""hbond"" keyword's argument > addh Summary of feedback from adding hydrogens to 6WVK_HelD.pdb #1.2 --- warnings | Not adding hydrogens to /A LYS 6 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 8 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 16 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 17 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 29 CB because it is missing heavy-atom bond partners 134 messages similar to the above omitted notes | No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain E; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A GLU 5, /B GLU 5, /C THR 2, /D VAL 4, /E MET 1, /F MET 1, /H GLN 4 Chain-initial residues that are not actual N termini: /C ARG 312, /C GLU 502, /C VAL 872 Chain-final residues that are actual C termini: /E LEU 69 Chain-final residues that are not actual C termini: /A THR 228, /B THR 228, /C GLU 1149, /C ASP 296, /C GLY 490, /C PRO 848, /D SER 1187, /F PHE 61, /H ALA 773 2582 hydrogen bonds Adding 'H' to /C ARG 312 Adding 'H' to /C GLU 502 Adding 'H' to /C VAL 872 /A THR 228 is not terminus, removing H atom from 'C' /B THR 228 is not terminus, removing H atom from 'C' /C GLU 1149 is not terminus, removing H atom from 'C' /C ASP 296 is not terminus, removing H atom from 'C' /C GLY 490 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 28056 hydrogens added > select H 28056 atoms, 1 model 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 ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. > close #1.1 > close session Deleting atomic symmetry model... > open2 /home/gokhan/Documents/structure/RNAP-HelD/6WVK_HelD.pdb Summary of feedback from opening <_io.textiowrapper name=""/home/gokhan/Documents/structure/RNAP-HelD/6WVK_HelD.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Duplicate atom serial number found: 5900 Duplicate atom serial number found: 5901 Duplicate atom serial number found: 23498 Duplicate atom serial number found: 23499 Chain information for 6WVK_HelD.pdb #1 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available F | No description available H | No description available > open2 /home/gokhan/Documents/structure/RNAP-HelD/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 288,288,288, pixel 0.84, shown at level 0.0104, step 2, values float32 > toolshed show ISOLDE > set selectionWidth 4 Chain information for 6WVK_HelD.pdb --- Chain | Description 1.2/A 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/H | No description available Done loading forcefield > addh Summary of feedback from adding hydrogens to 6WVK_HelD.pdb #1.2 --- warnings | Not adding hydrogens to /A LYS 6 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A LYS 8 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 16 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A ASP 17 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A GLU 29 CB because it is missing heavy-atom bond partners 134 messages similar to the above omitted notes | No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 6WVK_HelD.pdb (#1.2) chain E; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A GLU 5, /B GLU 5, /C THR 2, /D VAL 4, /E MET 1, /F MET 1, /H GLN 4 Chain-initial residues that are not actual N termini: /C ARG 312, /C GLU 502, /C VAL 872 Chain-final residues that are actual C termini: /E LEU 69 Chain-final residues that are not actual C termini: /A THR 228, /B THR 228, /C GLU 1149, /C ASP 296, /C GLY 490, /C PRO 848, /D SER 1187, /F PHE 61, /H ALA 773 2582 hydrogen bonds Adding 'H' to /C ARG 312 Adding 'H' to /C GLU 502 Adding 'H' to /C VAL 872 /A THR 228 is not terminus, removing H atom from 'C' /B THR 228 is not terminus, removing H atom from 'C' /C GLU 1149 is not terminus, removing H atom from 'C' /C ASP 296 is not terminus, removing H atom from 'C' /C GLY 490 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 28056 hydrogens added > set bgColor white > hide HC > select 56281 atoms, 56778 bonds, 17 pseudobonds, 14 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 ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. > select clear > select 56281 atoms, 56778 bonds, 17 pseudobonds, 20 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 ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. > select clear Traceback (most recent call last): File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. Traceback (most recent call last): File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. Traceback (most recent call last): File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2709, in start_sim sm.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""/home/gokhan/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""/usr/lib/ucsf-chimerax/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/lib/ucsf-chimerax/lib/python3.7/site- packages/simtk/openmm/openmm.py"", line 11125, in __init__ this = _openmm.new_Context(*args) Exception: Error initializing context: clGetPlatformIDs (-1001) Exception: Error initializing context: clGetPlatformIDs (-1001) File ""/usr/lib/ucsf-chimerax/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: 3.3.0 NVIDIA 435.21 OpenGL renderer: Tesla V100-PCIE-32GB/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: PowerEdge R740 OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 48 Intel(R) Xeon(R) Silver 4116 CPU @ 2.10GHz Cache Size: 16896 KB Graphics: 03:00.0 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. Integrated Matrox G200eW3 Graphics Controller [102b:0536] (rev 04) Subsystem: Dell Integrated Matrox G200eW3 Graphics Controller [1028:0715] Kernel driver in use: mgag200 }}} " defect closed normal Third Party can't reproduce all ChimeraX