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Opened 4 years ago
Last modified 4 years ago
#6237 assigned defect
Problem switching GPU
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19042
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
In ISOLDE tool tried to switch from Intel graphics to Nvidia to run MD on dedicated graphics processor on a laptop with Nvidia Optimus using command 'isolde set gpuDeviceIndex 0'. Any but '-1' integer value result in same error:
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py", line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
Tried to change settings in Nvidia utility to utilise Nvidia GPU wherever possible with no success in changing GPU for MD simulation. 3D rendering could be directed to Nvidia though.
CUDA is not installed, just latest video driver.
Log:
Startup Messages
---
warning | Registration file
'C:
\Users
\segurian
\AppData
\Local
\UCSF
\ChimeraX
\registration' has
expired
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
open C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\demo_data\6out\6out.pdb format pdb
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
open 20205 format ccp4 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
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
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
ISOLDE: started sim
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
isolde set gpuDeviceIndex 0
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex 1
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
isolde set gpuDeviceIndex 2
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
select clear
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex -1
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
isolde set gpuDeviceIndex NVIDIA
Invalid "gpuDeviceIndex" argument: Expected an integer
isolde set gpuDeviceIndex 3
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex -2
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex -1
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
isolde set gpuDeviceIndex -2
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex -3
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
isolde set gpuDeviceIndex 4
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
isolde set gpuDeviceIndex -1
ISOLDE: started sim
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
isolde set gpuDeviceIndex 1
Traceback (most recent call last):
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2749, in _start_sim_or_toggle_pause
self.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\isolde.py", line 2804, in start_sim
sm.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 677, in start_sim
sh.start_sim()
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1606, in start_sim
self._prepare_sim()
File "C:\Users\segurian\AppData\Local\UCSF\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 "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\openmm\app\simulation.py", line 105, in init
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\openmm\openmm.py",
line 4605, in init
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
isolde set gpuDeviceIndex -1
ISOLDE: started sim
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1168, in
_dihe_r_changed_cb
self.sim_handler.update_dihedral_restraints(all_changeds)
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1975, in
update_dihedral_restraints
force.update_targets(restraints.sim_indices,
File "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(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 "C:\Users\segurian\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1371, in
update_targets
f(int(self.this), n, pointer(ind), pointer(params))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
ISOLDE: started sim
OpenGL version: 3.3.0 NVIDIA 472.42
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 20L6SBKX00
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 34,227,970,048
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz
OSLanguage: en-US
Locale: ('ru_RU', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Sorry about this! I think this is my bad, for not keeping up with a change to the OpenMM API. Will see about correcting that for the next ISOLDE version. Meanwhile, I ran into a similar problem a few years back (#2546) with a user on a Windows machine with Optimus architecture. The problem is that you have both the (generally pretty useless) Intel OpenCL driver installed along with the Nvidia one, and the Intel one is coming first in the list. The super high-tech approach that worked back then was to simply delete (or, to play it more safely, rename) the Intel OpenCL dll as per the thread at https://www.daz3d.com/forums/discussion/243216/getting-a-fatal-error-on-launch-solved. Applications using OpenCL should then see your Nvidia GPU as the only option.