GPU with insufficient OpenCL support leads to traceback in ISOLDE

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-14)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.92 (2020-01-14)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open emdb:1080

Summary of feedback from opening 1080 fetched from emdb  
---  
note | Fetching compressed map 1080 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-1080/map/emd_1080.map.gz  
  
Opened emd_1080.map, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32  

> volume #1 level 1.169

> help help:index.html

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> ui dockable true "Help Viewer"

> open 6out

Summary of feedback from opening 6out fetched from pdb  
---  
note | Fetching compressed mmCIF 6out from
http://files.rcsb.org/download/6out.cif  
  
6out title:  
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP
asymmetric unit in T=3 symmetry [more info...]  
  
Chain information for 6out #2  
---  
Chain | Description  
A B C | Capsid protein VP1  
  
6out title:  
Asymmetric focused reconstruction of human norovirus GI.1 Norwalk strain VLP
asymmetric unit in T=3 symmetry [more info...]  
  
Chain information for 6out  
---  
Chain | Description  
2.1/A 2.1/B 2.1/C | Capsid protein VP1  
  
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  
  

> open 20205 fromDatabase emdb

Summary of feedback from opening 20205 fetched from emdb  
---  
note | Fetching compressed map 20205 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-20205/map/emd_20205.map.gz  
  
Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> close #1

Invalid "toModel" argument: Must specify 1 model, got 0  

> close #2.2-3#3#2.1

> 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  
A B C | capsid protein VP1  
  
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  
1.1/A 1.1/B 1.1/C | capsid protein VP1  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emd_20205.map, 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

> volume #3 style mesh

> isolde start

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.1  
---  
notes | Termini for 6out.pdb (#1.1) chain A determined from SEQRES records  
Termini for 6out.pdb (#1.1) chain B determined from SEQRES records  
Termini for 6out.pdb (#1.1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /B THR 9  
Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29  
Chain-final residues that are actual C termini: /A SER 520  
Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519  
Missing OXT added to C-terminal residue /A SER 520  
1438 hydrogen bonds  
Adding 'H' to /A ASP 29  
Adding 'H' to /C ASP 29  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11439 hydrogens added  
  

> hide HC

> volume #3 style surface

> transparency 50

> isolde restrain ligands #1

QWidget::repaint: Recursive repaint detected  

> select #1

22945 atoms, 23062 bonds, 10 models selected  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 600, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 345, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/cmd.py", line 77, in isolde_sim  
isolde.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1516, in
_prepare_sim  
integrator, platform, properties)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: No compatible OpenCL platform is available  
  
Exception: No compatible OpenCL platform is available  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 600, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 345, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/cmd.py", line 77, in isolde_sim  
isolde.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1516, in
_prepare_sim  
integrator, platform, properties)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: No compatible OpenCL platform is available  
  
Exception: No compatible OpenCL platform is available  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 600, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 345, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/cmd.py", line 77, in isolde_sim  
isolde.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2706, in start_sim  
sm.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 653, in start_sim  
sh.start_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1555, in start_sim  
self._prepare_sim()  
File "/Users/yang/Library/Application Support/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1516, in
_prepare_sim  
integrator, platform, properties)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: No compatible OpenCL platform is available  
  
Exception: No compatible OpenCL platform is available  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 INTEL-10.4.14
OpenGL renderer: Intel HD Graphics 3000 OpenGL Engine
OpenGL vendor: Intel Inc.

[Tristan Croll]

The HD Graphics 3000 dates back to the 2011 MacBook models. I'll see about adding a catch and a more user-friendly message in this scenario.