OpenMM: Error launching CUDA compiler: Value 'sm_30' is not defined for option 'gpu-architecture'

[kostrewa@…]

The following bug report has been submitted:
Platform:        Linux-5.10.0-9-amd64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
open test.pdb
open test.mrc
clipper assoc #2 to #1
addh metalDist 1.0
isolde start
select #1
isolde sim start sel

Model and map belong to a PhD student's project. The error is reproducible with these files, but don't occur with other data, up to now. Neither me nor ISOLDE can find anything unusual in the coordinate file or in the cryo-EM map.
To exclude any CUDA problems, this error occurs with Debian's CUDA 11.2 from it's repsoitory and with Nvidia's CUDA 11.2.
Model and map are over 100 MB big. If you need those files, I will ask the PhD student whether he agrees to send his data.

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 test-gut.pdb

Summary of feedback from opening test-gut.pdb  
---  
warning | Ignored bad PDB record found on line 17518  
END  
  
Chain information for test-gut.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> open test-gut.mrc

Opened test-gut.mrc as #2, grid size 320,320,320, pixel 1.06, shown at level
0.000305, step 2, values float32  

> transparency 50

> volume #2 step 1

> volume #2 level 0.007667

> style stick

Changed 13068 atom styles  

> clipper associate #2 toModel #1

Opened test-gut.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06, shown at
level 0.0339, step 1, values float32  
Chain information for test-gut.pdb  
---  
Chain | Description  
1.2/A | No description available  
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  
  

> addh metalDist 1.0

Summary of feedback from adding hydrogens to test-gut.pdb #1.2  
---  
warnings | Not adding hydrogens to /E DC -34 P because it is missing heavy-
atom bond partners  
Not adding hydrogens to /F DA 28 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for test-gut.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for test-gut.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for test-gut.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for test-gut.pdb (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for test-gut.pdb (#1.2) chain E; guessing termini
instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET
1, /D MET 1, /E DC -34, /F DA 28  
Chain-initial residues that are not actual N termini: /A LEU 204, /B LEU 153,
/B ARG 354, /C GLN 875, /D THR 874  
Chain-final residues that are actual C termini: /E DT -4, /F DG 58  
Chain-final residues that are not actual C termini: /A ALA 395, /A GLY 189, /B
ALA 395, /B ILE 137, /B SER 341, /C VAL 1047, /C GLU 201, /D VAL 1047, /D LEU
200  
1293 hydrogen bonds  
Adding 'H' to /A LEU 204  
Adding 'H' to /B LEU 153  
Adding 'H' to /B ARG 354  
Adding 'H' to /C GLN 875  
Adding 'H' to /D THR 874  
/A ALA 395 is not terminus, removing H atom from 'C'  
/B ALA 395 is not terminus, removing H atom from 'C'  
/C VAL 1047 is not terminus, removing H atom from 'C'  
/D VAL 1047 is not terminus, removing H atom from 'C'  
12454 hydrogens added  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde sim start sel

No atoms selected!  

> select #1

25522 atoms, 25882 bonds, 5 pseudobonds, 1567 residues, 13 models selected  

> isolde sim start sel

Loading residue template for ADP from internal database  
Traceback (most recent call last):  
File "/gcm/opt/cryo/UCSF-ChimeraX-1.2.5-1-Debian/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/strubio/kostrewa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd/cmd.py", line 95, in _sim_start_cb  
isolde.start_sim()  
File "/home/strubio/kostrewa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/home/strubio/kostrewa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/home/strubio/kostrewa/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/home/strubio/kostrewa/.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 "/gcm/opt/cryo/UCSF-ChimeraX-1.2.5-1-Debian/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 "/gcm/opt/cryo/UCSF-ChimeraX-1.2.5-1-Debian/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__  
this = _openmm.new_Context(*args)  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 256  
nvcc fatal : Value 'sm_30' is not defined for option 'gpu-architecture'  
  
  
Error processing trigger "frame drawn":  
simtk.openmm.OpenMMException: Error launching CUDA compiler: 256  
nvcc fatal : Value 'sm_30' is not defined for option 'gpu-architecture'  
  
  
File "/gcm/opt/cryo/UCSF-ChimeraX-1.2.5-1-Debian/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 460.91.03
OpenGL renderer: Quadro K5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: FUJITSU
Model: CELSIUS R930
OS: Debian GNU/Linux 11 bullseye
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
Cache Size: 20480 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       2.8Gi        47Gi       186Mi        12Gi        59Gi
	Swap:          975Mi          0B       975Mi

Graphics:
	04:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K5000] [10de:11ba] (rev a1)	
	Subsystem: NVIDIA Corporation GK104GL [Quadro K5000] [10de:0965]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Eric Pettersen]

Reported by Dirk Kostrewa

[Tristan Croll]

This will go away as soon as I manage to get ISOLDE 1.3 out the door. The issue is that the CUDA 11.0 runtime compiler used by OpenMM doesn't recognise the 30-series GPUs - ChimeraX 1.3 (and hence ISOLDE 1.3) has a newer OpenMM version built against CUDA 11.2, which doesn't have this problem. Until then, if you switch the "Experience level" drop-down at the bottom of the ISOLDE panel to "advanced", you'll get a new option on the "Sim settings" tab allowing you to switch the computational platform from CUDA to OpenCL.