openmm.OpenMMException: Error launching CUDA compiler

[jmkrieger@…]

The following bug report has been submitted:
Platform:        Linux-5.10.60.1-microsoft-standard-WSL2-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Followed https://isolde.cimr.cam.ac.uk/static/isolde/doc/tutorials/intro/cryo_intro/cryo_intro.html up to "isolde sim start sel" on Ubuntu 20.04 from WSL2 on Windows 11 laptop. 

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> 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 | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, 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

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at level 0.168, step 1, values float32  
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 | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  

> volume #1.1.1.1 level 0.1147

> volume #1.1.1.1 level 0.07516

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C
ALA 519  
1438 hydrogen bonds  
/A SER 520 is not terminus, removing H atom from 'C'  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11443 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

22948 atoms, 23065 bonds, 1720 residues, 14 models selected  

> isolde sim start sel

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  

Traceback (most recent call last):  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5210, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: Error launching CUDA compiler: 32512  
sh: 1: /usr/local/cuda/bin/nvcc: not found  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/cmd/cmd.py", line 103, in isolde_sim  
isolde.start_sim()  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1611, in start_sim  
self._prepare_sim()  
File "/home/jkrieger/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1551, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 18377, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
openmm.OpenMMException: There is no registered Platform called "OpenCL"  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 18377, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 22.0.0-devel (git-2bb2219 2022-01-07 focal-oibaf-ppa)
OpenGL renderer: D3D12 (NVIDIA GeForce GTX 1650 Ti)
OpenGL vendor: Microsoft Corporation
Manufacturer: unknown
Model: unknown
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: wsl
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       1.3Gi       258Mi        60Mi        13Gi        13Gi
	Swap:         4.0Gi       1.0Mi       4.0Gi

Graphics:
	unknown
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[pett]

Reported by James Krieger

[Tristan Croll]

Looks to me like there's something quite weird about your CUDA installation - for one thing, this is the first time I've ever seen the CUDA platform being found by OpenMM *without* the OpenCL platform also being found. For another, this is weird:

OpenGL version: 3.3 (Core Profile) Mesa 22.0.0-devel (git-2bb2219 2022-01-07 focal-oibaf-ppa)
OpenGL renderer: D3D12 (NVIDIA GeForce GTX 1650 Ti)
OpenGL vendor: Microsoft Corporation
Manufacturer: unknown
Model: unknown

I'd suggest reinstalling the latest Nvidia driver (official Nvidia, *not* Nouveau) and CUDA (for best performance, go with CUDA 11.2 to match the version OpenMM was compiled against). Please let me know if that helps.

[jmkrieger@…]

I have now reinstalled CUDA 11.2 and the NVIDIA driver from  
https://developer.nvidia.com/cuda-11.2.0-download-archive?target_os=Linux&target_arch=x[…]istro=WSLUbuntu&target_version=20&target_type=runfilelocal and then reinstalled ChimeraX and ISOLDE and everything is  
working.

Thanks very much again for your help, Tristan.

ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> escribió:

[Tristan Croll]

Great! To my knowledge the first instance of ISOLDE running under WSL2 - so really cool to know that can be done.

[jmkrieger@…]

Yes, indeed!

ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> escribió: