ISOLDE: start_sim: Error initializing CUDA

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-28-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/yashaswini/Downloads/Amyloid_lipid_internship/L1/amyloid_beta_1-40_L1_final.pdb
> format pdb

Chain information for amyloid_beta_1-40_L1_final.pdb #1  
---  
Chain | Description  
A B C D E F G H I J | No description available  
  
Drag select of 26 atoms  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 10 residues in model #1 to IUPAC-IUB
standards.  
Chain information for amyloid_beta_1-40_L1_final.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J | No description
available  
  

> isolde sim start /D,F:32

> open
> /home/yashaswini/Downloads/Amyloid_lipid_internship/L1/postprocess_masked_SymImposed.mrc

Opened postprocess_masked_SymImposed.mrc as #2, grid size 250,250,250, pixel
1.05, shown at level 0.0369, step 1, values float32  

> isolde sim start /D,F:32

> clipper associate #2 toModel #1

Opened postprocess_masked_SymImposed.mrc as #1.1.1.1, grid size 250,250,250,
pixel 1.05, shown at step 1, values float32  

> isolde sim start /D,F:32

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to amyloid_beta_1-40_L1_final.pdb
#1.2  
---  
notes | No usable SEQRES records for amyloid_beta_1-40_L1_final.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for amyloid_beta_1-40_L1_final.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for amyloid_beta_1-40_L1_final.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for amyloid_beta_1-40_L1_final.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for amyloid_beta_1-40_L1_final.pdb (#1.2) chain E;
guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ASP 1, /B ASP 1, /C ASP
1, /D ASP 1, /E ASP 1, /F ASP 1, /G ASP 1, /H ASP 1, /I ASP 1, /J ASP 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A VAL 40, /B VAL 40, /C VAL
40, /D VAL 40, /E VAL 40, /F VAL 40, /G VAL 40, /H VAL 40, /I VAL 40, /J VAL
40  
Chain-final residues that are not actual C termini:  
389 hydrogen bonds  
2920 hydrogens added  
  

> isolde sim start /D,F:29-35

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error initializing CUDA: CUDA_ERROR_NO_DEVICE (100) at
/home/tcroll/openmm_build_env/openmm/platforms/cuda/src/CudaContext.cpp:140  

Traceback (most recent call last):  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1377, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 5931, in __init__  
this = _openmm.new_Context(*args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_NO_DEVICE (100) at
/home/tcroll/openmm_build_env/openmm/platforms/cuda/src/CudaContext.cpp:140  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1437, in start_sim  
self._prepare_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1364, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 11789, 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/python3.11/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim start /D,F:26-38

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1302, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim  
sm.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1364, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 11789, 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/python3.11/site-packages/openmm/openmm.py",
line 11789, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File "/home/yashaswini/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Inspiron 5406 2n1
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       2.8Gi       9.3Gi       780Mi       3.2Gi        11Gi
	Swap:          232Gi          0B       232Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	DeviceName: Onboard - Video	
	Subsystem: Dell TigerLake-LP GT2 [Iris Xe Graphics] [1028:0a05]

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.4.1
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    certifi: 2023.11.17
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    ChimeraX-ESMFold: 1.0
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    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
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    ChimeraX-Hbonds: 2.4
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    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
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    ChimeraX-WebCam: 1.0.2
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    comm: 0.2.1
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    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
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    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
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    pickleshare: 0.7.5
    pillow: 10.2.0
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    Pygments: 2.16.1
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    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
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    webcolors: 1.12
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9