openmm.OpenMMException: Error compiling kernel

[Alexandrea.Rizo@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
When starting ISOLDE and pressing the play button to begin the simulation. 

Log:
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 /Users/alexrizo/Downloads/cryosparc_P81_J158_007_volume_map.mrc

Opened cryosparc_P81_J158_007_volume_map.mrc as #1, grid size 512,512,512,
pixel 0.834, shown at level 0.0687, step 2, values float32  

> volume #1 level 0.1175

> volume #1 step 1

> set bgColor white

> volume #1 level 0.1894

> open
> /Volumes/southworth-2/southworth_lab/arizo/hsp104/hsp104_hsp70/modeling/Rosetta/7_RosettaRelax_afterCM_extended/Extended_state_best_model.pdb

Summary of feedback from opening
/Volumes/southworth-2/southworth_lab/arizo/hsp104/hsp104_hsp70/modeling/Rosetta/7_RosettaRelax_afterCM_extended/Extended_state_best_model.pdb  
---  
warnings | Ignored bad PDB record found on line 77502  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 77503  
#BEGIN_POSE_ENERGIES_TABLE complete_model_0004.pdb  
  
Ignored bad PDB record found on line 77504  
label fa_atr fa_rep fa_sol fa_intra_atr_xover4 fa_intra_rep_xover4
fa_intra_sol_xover4 lk_ball lk_ball_iso lk_ball_bridge lk_ball_bridge_uncpl
fa_elec fa_intra_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13
omega fa_dun_dev fa_dun_rot fa_dun_semi p_aa_pp hxl_tors ref rama_prepro
cart_bonded gen_bonded elec_dens_fast total  
  
Ignored bad PDB record found on line 77505  
weights 1 0.55 1 1 0.55 1 0.92 -0.38 -0.33 -0.33 1 1 1 1 1 1 1.25 0.48 0.69
0.76 0.78 0.61 1 1 0.5 0.5 1 50 NA  
  
Ignored bad PDB record found on line 77506  
pose -30445.4 4126.53 23615.3 -1971.81 953.027 1529 11755.4 -12671.7 -50.2998
-332.254 -9778.52 -1516.72 -2949.86 -688.652 -725.467 -680.92 1.8336 213.747
520.124 2695.86 4434.91 -892.815 719.755 -1424.96 1266.97 4798.92 0 -116734
-124232  
  
4865 messages similar to the above omitted  
  
Chain information for Extended_state_best_model.pdb #2  
---  
Chain | Description  
A F | No description available  
B | No description available  
C D E | No description available  
P | No description available  
  

> hide atoms

> show cartoons

> volume #1 level 0.2443

> clippper associate #2 to #1

Unknown command: clippper associate #2 to #1  

> clippper associate #1 to #2

Unknown command: clippper associate #1 to #2  

> clippper #1 to #2

Unknown command: clippper #1 to #2  

> clipper associate #1 toModel #2

Opened cryosparc_P81_J158_007_volume_map.mrc as #1.1.1.1, grid size
512,512,512, pixel 0.834, shown at level 0.511, step 1, values float32  
Chain information for Extended_state_best_model.pdb  
---  
Chain | Description  
1.2/A 1.2/F | No description available  
1.2/B | No description available  
1.2/C 1.2/D 1.2/E | No description available  
1.2/P | No description available  
  

> volume #1.1.1.1 level 0.1434

> volume #1.1.1.1 level -0.008976

> volume #1.1.1.1 level 0.1038

> volume #1.1.1.1 level 0.4244

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 414 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> ui mousemode right select

Traceback (most recent call last):  
File "/Users/alexrizo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/alexrizo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File "/Users/alexrizo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/Users/alexrizo/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File "/Users/alexrizo/Library/Application Support/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
"/private/var/folders/dn/zfww2zhn6_5dn17mhwpjcv6h0000gq/T/AppTranslocation/534E5B9F-80D4-4C00-ADDA-E6EF680D14D4/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/private/var/folders/dn/zfww2zhn6_5dn17mhwpjcv6h0000gq/T/AppTranslocation/534E5B9F-80D4-4C00-ADDA-E6EF680D14D4/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2470, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel:  
  
openmm.OpenMMException: Error compiling kernel:  
  
File
"/private/var/folders/dn/zfww2zhn6_5dn17mhwpjcv6h0000gq/T/AppTranslocation/534E5B9F-80D4-4C00-ADDA-E6EF680D14D4/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2470, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.22
OpenGL renderer: AMD Radeon R9 M290X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac15,1
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 431.140.6.0.0
      SMC Version (system): 2.22f16

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1419)
      Kernel Version: Darwin 19.6.0
      Time since boot: 33 days 1:04

Graphics/Displays:

    AMD Radeon R9 M290X:

      Chipset Model: AMD Radeon R9 M290X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6810
      Revision ID: 0x0000
      ROM Revision: 113-C408A0-730
      VBIOS Version: 113-C408A0-017
      EFI Driver Version: 01.00.730
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    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
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    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
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    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
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    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
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    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
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    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
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    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
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    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
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-ShowAttr: 1.0
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    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
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    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    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
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    ihm: 0.21
    imagecodecs: 2021.4.28
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    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: 21.0
    ParmEd: 3.2.0
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    Pillow: 8.3.2
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    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tristan Croll]

The error message itself doesn't give much to go on, but I think the most likely explanation here is that your hardware is a bit too old to handle ISOLDE's (OpenMM's) simulations. The Radeon R9 M290X came out in 2014, and yours has just 2GB of RAM - which would need to be shared between graphics and the the MD simulation. I suspect it ran out of memory and bailed out. Ultimately I'm afraid you'll need to find a newer/higher-end machine to use for ISOLDE.