Opened 4 years ago

Closed 3 years ago

#4896 closed defect (can't reproduce)

OpenMMException: No compatible OpenCL platform is available

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.13.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 2cv5

2cv5 title:  
Crystal structure of human nucleosome core particle [more info...]  
  
Chain information for 2cv5 #1  
---  
Chain | Description  
A E | Histone H3.1  
B F | Histone H4  
C G | Histone H2A.a  
D H | Histone H2B K  
I J | DNA (146-mer)  
  
Non-standard residues in 2cv5 #1  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> open
> /Users/gageleighton/Downloads/cryosparc_P22_J183_008_volume_map_sharp.mrc

Opened cryosparc_P22_J183_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.91, shown at level 0.125, step 1, values float32  

> volume #2 level 0.3311

> ui tool show ISOLDE

> set selectionWidth 4

2cv5 title:  
Crystal structure of human nucleosome core particle [more info...]  
  
Chain information for 2cv5  
---  
Chain | Description  
1.2/A 1.2/E | Histone H3.1  
1.2/B 1.2/F | Histone H4  
1.2/C 1.2/G | Histone H2A.a  
1.2/D 1.2/H | Histone H2B K  
1.2/I 1.2/J | DNA (146-mer)  
  
Non-standard residues in 2cv5 #1.2  
---  
CL — chloride ion  
MN — manganese (II) ion  
  
Done loading forcefield  
Opened cryosparc_P22_J183_008_volume_map_sharp.mrc as #1.1.1.1, grid size
256,256,256, pixel 0.91, shown at step 1, values float32  

> close #1

> open 6jr1

Summary of feedback from opening 6jr1 fetched from pdb  
---  
note | Fetching compressed mmCIF 6jr1 from
http://files.rcsb.org/download/6jr1.cif  
  
6jr1 title:  
Crystal structure of the human nucleosome phased with 16 selenium atoms [more
info...]  
  
Chain information for 6jr1 #1  
---  
Chain | Description  
A E | Histone H3.1  
B F | Histone H4  
C G | Histone H2A type 1-B/E  
D H | Histone H2B type 1-J  
I J | DNA (146-mer)  
  
Non-standard residues in 6jr1 #1  
---  
CL — chloride ion  
MN — manganese (II) ion  
  
6jr1 title:  
Crystal structure of the human nucleosome phased with 16 selenium atoms [more
info...]  
  
Chain information for 6jr1  
---  
Chain | Description  
1.2/A 1.2/E | Histone H3.1  
1.2/B 1.2/F | Histone H4  
1.2/C 1.2/G | Histone H2A type 1-B/E  
1.2/D 1.2/H | Histone H2B type 1-J  
1.2/I 1.2/J | DNA (146-mer)  
  
Non-standard residues in 6jr1 #1.2  
---  
CL — chloride ion  
MN — manganese (II) ion  
  

> open /Users/gageleighton/Downloads/cryosparc_P26_J66_003_volume_map.mrc

Opened cryosparc_P26_J66_003_volume_map.mrc as #2, grid size 320,320,320,
pixel 0.88, shown at level 0.0476, step 2, values float32  
Opened cryosparc_P26_J66_003_volume_map.mrc as #1.1.1.1, grid size
320,320,320, pixel 0.88, shown at step 1, values float32  

> close #1.1.1.1

> open
> /Users/gageleighton/Downloads/cryosparc_P22_J183_008_volume_map_sharp.mrc

Opened cryosparc_P22_J183_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 0.91, shown at level 0.125, step 1, values float32  

> volume #2 level 0.3397

Opened cryosparc_P22_J183_008_volume_map_sharp.mrc as #1.1.1.1, grid size
256,256,256, pixel 0.91, shown at step 1, values float32  

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 6jr1 #1.2  
---  
warning | Unknown hybridization for atom (SE) of residue type MSE; not adding
hydrogens to it  
notes | Termini for 6jr1 (#1.2) chain A determined from SEQRES records  
Termini for 6jr1 (#1.2) chain B determined from SEQRES records  
Termini for 6jr1 (#1.2) chain C determined from SEQRES records  
Termini for 6jr1 (#1.2) chain D determined from SEQRES records  
Termini for 6jr1 (#1.2) chain E determined from SEQRES records  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /I DA 1, /J DA 147  
Chain-initial residues that are not actual N termini: /A PRO 38, /B ASP 24, /C
ARG 11, /D SER 32, /E LYS 37, /F ARG 17, /G ALA 14, /H ARG 33  
Chain-final residues that are actual C termini: /I DT 146, /J DT 292  
Chain-final residues that are not actual C termini: /A GLU 133, /B GLY 101, /C
LYS 118, /D ALA 124, /E ARG 134, /F GLY 101, /G LYS 118, /H ALA 124  
2652 hydrogen bonds  
Adding 'H' to /B ASP 24  
Adding 'H' to /C ARG 11  
Adding 'H' to /D SER 32  
Adding 'H' to /E LYS 37  
Adding 'H' to /F ARG 17  
2 messages similar to the above omitted  
/A GLU 133 is not terminus, removing H atom from 'C'  
/B GLY 101 is not terminus, removing H atom from 'C'  
/C LYS 118 is not terminus, removing H atom from 'C'  
/D ALA 124 is not terminus, removing H atom from 'C'  
/E ARG 134 is not terminus, removing H atom from 'C'  
3 messages similar to the above omitted  
10751 hydrogens added  
  

> hide

> hide

> hide HC

> isolde restrain ligands #1

> select #1

23308 atoms, 23540 bonds, 377 pseudobonds, 1624 residues, 16 models selected  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd/cmd.py", line 95, in _sim_start_cb  
isolde.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/Users/gageleighton/Library/Application Support/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
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/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
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 2671, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
simtk.openmm.OpenMMException: No compatible OpenCL platform is available  
  
Error processing trigger "frame drawn":  
simtk.openmm.OpenMMException: No compatible OpenCL platform is available  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 2671, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> ui windowfill toggle

> ui windowfill toggle

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd/cmd.py", line 95, in _sim_start_cb  
isolde.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim  
sm.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim  
sh.start_sim()  
File "/Users/gageleighton/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim  
self._prepare_sim()  
File "/Users/gageleighton/Library/Application Support/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
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/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
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 2671, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
simtk.openmm.OpenMMException: No compatible OpenCL platform is available  
  
Error processing trigger "frame drawn":  
simtk.openmm.OpenMMException: No compatible OpenCL platform is available  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 2671, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  




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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro8,2
      Processor Name: Intel Core i7
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 87.0.0.0.0
      SMC Version (system): 1.69f4
      Sudden Motion Sensor:
          State: Enabled

Software:

    System Software Overview:

      System Version: macOS 10.13.6 (17G14042)
      Kernel Version: Darwin 17.7.0
      Time since boot: 1 day 20:50

Graphics/Displays:

    Intel HD Graphics 3000:

      Chipset Model: Intel HD Graphics 3000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 512 MB
      Vendor: Intel
      Device ID: 0x0116
      Revision ID: 0x0009
      Automatic Graphics Switching: Supported
      gMux Version: 1.9.23
      Displays:
        SwitchResX4 - Color LCD:
          Display Type: LCD
          Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus)
          UI Looks like: 1680 x 1050
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Eric Pettersen, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenMMException: No compatible OpenCL platform is available

comment:2 by Tristan Croll, 4 years ago

Hmm... that's one I haven't seen before. Possibly to do with the ancient version of MacOS. Will see if I can dig anything up tomorrow.

comment:3 by Tristan Croll, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
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