CUDA_ERROR_UNKNOWN starting ISOLDE simulation

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-76-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
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)  

'clip' is a prefix of an existing command 'clipper'  

> open
> /home/frechara/Bureau/NuA4/Map/4_Fullmap/cryosparc_P4_J134__localfilter.mrc

Opened cryosparc_P4_J134__localfilter.mrc, grid size 384,384,384, pixel 1.1,
shown at level 0.195, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.2632

> open2 /home/frechara/Bureau/NuA4/Model/Tra1Pichia.pdb

Tra1Pichia.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for Tra1Pichia.pdb #2  
---  
Chain | Description  
A | No description available  
  

Unknown command: allign  

> help help:user

Invalid "inMap" argument: invalid density map specifier  

> fitmap #2 inMap #1

Fit molecule Tra1Pichia.pdb (#2) to map cryosparc_P4_J134__localfilter.mrc
(#1) using 30825 atoms  
average map value = 0.3566, steps = 84  
shifted from previous position = 0.766  
rotated from previous position = 0.785 degrees  
atoms outside contour = 14098, contour level = 0.26321  
  
Position of Tra1Pichia.pdb (#2) relative to cryosparc_P4_J134__localfilter.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99996776 0.00025547 0.00802631 -1.91619458  
-0.00034455 0.99993834 0.01109904 -1.87666095  
-0.00802298 -0.01110144 0.99990619 4.00070828  
Axis -0.81021438 0.58572446 -0.02189796  
Axis point 0.00000000 359.48994358 190.37992742  
Rotation angle (degrees) 0.78499814  
Shift along axis 0.36571482  
  

> toolshed show ISOLDE

> set selectionWidth 4

Tra1Pichia.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for Tra1Pichia.pdb  
---  
Chain | Description  
2.2/A | 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  

QWidget::repaint: Recursive repaint detected  

> select clear

> select up

97 atoms, 98 bonds, 1 model selected  

> select up

30825 atoms, 31466 bonds, 1 model selected  

No template found for residue A31 (CYS)  

Adding hydrogens  
Summary of feedback from adding hydrogens to Tra1Pichia.pdb #2.2  
---  
notes | No usable SEQRES records for Tra1Pichia.pdb (#2.2) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LEU 3825  
Chain-final residues that are not actual C termini:  
2882 hydrogen bonds  
31009 hydrogens added  
  
Traceback (most recent call last):  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1327, in __init__  
sim_params, residue_templates)  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1424, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/forcefield.py", line 1114, in createSystem  
raise Exception('User-supplied template %s does not match the residue %d (%s)'
% (tname, res.index+1, res.name))  
Exception: User-supplied template CYM does not match the residue 31 (CYS)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2699, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 606, in __init__  
if self._parse_explicit_template_error(e):  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 658, in
_parse_explicit_template_error  
self.isolde._handle_bad_template(residue)  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2791, in _handle_bad_template  
self.start_sim()  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "/home/frechara/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "/home/frechara/.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 CUDA: CUDA_ERROR_UNKNOWN (999) at
/opt/conda/conda-
bld/openmm_1567095858138/work/platforms/cuda/src/CudaContext.cpp:148  
  
Exception: Error initializing CUDA: CUDA_ERROR_UNKNOWN (999) at
/opt/conda/conda-
bld/openmm_1567095858138/work/platforms/cuda/src/CudaContext.cpp:148  
  
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 418.56
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Ubuntu 16.04 xenial
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) W-2125 CPU @ 4.00GHz
Cache Size: 8448 KB
Graphics:
	65:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)
	Subsystem: Dell Device [1028:11a3]
	Kernel driver in use: nvidia

[Tristan Croll]

The first exception ("User-supplied template CYM does not match the residue 31 (CYS)") is actually handled - it brings up a dialogue higlighting the offending residue, and asks the user what they want to do next (add hydrogens/ignore the residue/abort the simulation). In this case I'm fairly sure they'd just forgotten to add the hydrogens up front, and did so via the dialogue (which triggers a new attempt to start the simulation). The real problem is down below: CUDA_ERROR_UNKNOWN from OpenMM when trying to initialise the simulation context. Hard to know what to do with that... from some limited Googling it could be a misconfiguration of their driver, or some permission issue (a user on a Matlab forum found the error went away when they ran Matlab as root), or something else entirely. Since it's an anonymous bug report, I can't see any real way forward.

[Tristan Croll]

Would require further feedback from the user to debug.