Opened 2 years ago

Last modified 2 years ago

#9975 assigned defect

ISOLDE sim start: OpenMMException: Error compiling kernel: Compile Server Error

Reported by: yangxl@… Owned by: Tristan Croll
Priority: normal 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:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
I need to use the ISOLDE to refine my cryo-EM structure. However, when I clicked the "Start simulation", it reported "openmm. OpenMMException: Error compiling kernel: Compile Server Error. File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/openmm/openmm.py", line 2501, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) ". Wish to hear advices for this error, thanks!

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/Transcend/Experiments/Data Process/20231006-Titan2-EDATP-
> DT-1957-W29/cryosparc_P36_J1117_006_volume_map_sharp.mrc" format mrc

Opened cryosparc_P36_J1117_006_volume_map_sharp.mrc as #1, grid size
384,384,384, pixel 0.832, shown at level 0.196, step 2, values float32  

> open "/Volumes/Transcend/Experiments/Data Process/20231006-Titan2-EDATP-
> DT-1957-W29/ATP-re1117.pdb"

Chain information for ATP-re1117.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> hide #!1 models

> select ~protein

72 atoms, 66 bonds, 18 pseudobonds, 5 residues, 4 models selected  

> delete sel

> show #!1 models

> select subtract #1

Nothing selected  

> isolde start

> set selectionWidth 4

Populating font family aliases took 454 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 162 residues in model #2 to IUPAC-IUB
standards.  
Chain information for ATP-re1117.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
  

> clipper associate #1 toModel #2

Opened cryosparc_P36_J1117_006_volume_map_sharp.mrc as #2.1.1.1, grid size
384,384,384, pixel 0.832, shown at step 1, values float32  

> isolde sim start sel

> set selectionWidth 4

ISOLDE: stopped sim  

> ui tool show "Ramachandran Plot"

> addh #2.2

Summary of feedback from adding hydrogens to ATP-re1117.pdb #2.2  
---  
notes | Termini for ATP-re1117.pdb (#2.2) chain A determined from SEQRES
records  
Termini for ATP-re1117.pdb (#2.2) chain B determined from SEQRES records  
Termini for ATP-re1117.pdb (#2.2) chain C determined from SEQRES records  
Termini for ATP-re1117.pdb (#2.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A THR 73, /B MET 1, /C MET
1, /D SER 2  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 591, /B SER 325, /C ARG
288, /D ALA 609  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /B SER 325  
Missing OXT added to C-terminal residue /C ARG 288  
Missing OXT added to C-terminal residue /D ALA 609  
1278 hydrogen bonds  
13442 hydrogens added  
  

> isolde sim start sel

> set selectionWidth 4

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim  
sm.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim  
self._prepare_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim  
sm.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim  
self._prepare_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> select /D

9229 atoms, 9299 bonds, 608 residues, 1 model selected  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim  
sm.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim  
self._prepare_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  

> isolde sim start sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim  
sm.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim  
self._prepare_sim()  
File "/Users/yangxl/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/openmm/openmm.py", line 2501, in __init__  
_openmm.Context_swiginit(self, _openmm.new_Context(*args))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.20
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 428.40.10.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1519)
      Kernel Version: Darwin 19.6.0
      Time since boot: 64 days 21:34

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    pyqtgraph: 0.13.3
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (6)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE sim start: OpenMMException: Error compiling kernel: Compile Server Error

Reported by Xiaolin

comment:2 by Tristan Croll, 2 years ago 

Could you try updating to ChimeraX 1.6 and see if this persists?

On Fri, 13 Oct 2023 at 19:35, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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comment:3 by yangxl@…, 2 years ago 

Thank you for your kind reply. I've updated ChimeraX to 1.6 version as suggested. But when I run ISOLDE simulation, it reported another bug as shown below.  I don't know how to solve this problem. I hope you can help . Have a nice day! 

 
openmm.OpenMMException: There is no registered Platform called "HIP"

File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/openmm/openmm.py", line 18655, in getPlatformByName
return _openmm.Platform_getPlatformByName(name)

See log for complete Python traceback.

comment:4 by Tristan Croll, 2 years ago

I'm afraid that the ultimate conclusion here is likely to be "your laptop is a bit too old to run ISOLDE" (the MacBook Pro 11.4 was released in 2015, about 8 years ago). But I'm a little confused as to how it's gotten that error message - if a platform fails to register on startup, ISOLDE shouldn't be trying to use it. Would you mind doing a few things to help debug?

  1. Copy the full traceback from the ChimeraX log for the "no registered Platform" error.
  2. On the ISOLDE panel, switch the "Experience level" drop-down in the top right corner to "Advanced", then open the cyan "Computational Platform" widget on the General tab and list the entries you see in the drop-down menu there.
  3. Open the ChimeraX Python shell (Tools/General/Shell), enter the commands below, and copy/paste the result into a reply. 
from openmm import Platform
Platform.getPluginLoadFailures()

Thanks,
Tristan

comment:5 by yangxl@…, 2 years ago 

Hi, I did what you suggested and the corresponding reports are attached below. Actually, when I changed computational platform to CPU, it had an error report, but it worked. I wonder if this is working properly.

1. Complete Logs

select /D:272-332

881 atoms, 891 bonds, 61 residues, 1 model selected


isolde sim start /D:272-332
set selectionWidth 4

Loading residue template for ATP from internal database


  Traceback (most recent call last):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 205, in callback
    bundle_info.run_provider(session, name, session.toolbar, display_name=display_name)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386, in run_provider
    return api._api_caller.run_provider(api, session, name, mgr, **kw)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider
    return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/__init__.py", line 183, in run_provider
    toolbar_command(session, name)
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command
    run(session, f'isolde sim start {_current_residue_sel_string(session)}')
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run
    results = command.run(text, log=log, return_json=return_json)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run
    result = ci.function(session, **kw_args)
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
    isolde.start_sim()
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/isolde.py", line 896, in start_sim
    sm.start_sim()
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 401, in start_sim
    sh.start_sim()
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1432, in start_sim
    self._prepare_sim()
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1364, in _prepare_sim
    platform = openmm.Platform.getPlatformByName(params.platform)
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/openmm/openmm.py", line 18655, in getPlatformByName
    return _openmm.Platform_getPlatformByName(name)
openmm.OpenMMException: There is no registered Platform called "HIP"

openmm.OpenMMException: There is no registered Platform called "HIP"

File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/openmm/openmm.py", line 18655, in getPlatformByName
return _openmm.Platform_getPlatformByName(name)

See log for complete Python traceback.


isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000

2. Computational Platform List:

OpenCL

CPU

Reference

When I chose CPU to simulate, it reported the following:

select /C:120-230

1759 atoms, 1771 bonds, 111 residues, 1 model selected


isolde sim start /C:120-230

ISOLDE: started sim
Traceback (most recent call last):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 138, in invoke
    return self._func(self._name, data)
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 909, in _dihe_r_changed_cb
    self.sim_handler.update_dihedral_restraints(all_changeds)
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1816, in update_dihedral_restraints
    force.update_targets(restraints.sim_indices,
  File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in update_targets
    _openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this), indices, params)
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range

Error processing trigger "changes":
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of range

File "/Users/yangxl/Library/Application Support/ChimeraX/1.6/site-packages/chimerax/isolde/openmm/custom_forces.py", line 1301, in update_targets
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this), indices, params)

See log for complete Python traceback.



3. Commands results :

{{{
from openmm import Platform
Platform.getPluginLoadFailures()
}}}
  Cell In[2], line 2
    from openmm import Platform
    ^
SyntaxError: invalid syntax




Thanks!

Xiaolin

comment:6 by Tristan Croll, 2 years ago 

Thanks for this. Could you repeat step 3 again, but make sure to remove all
spaces from the start of the line? Looks like the SyntaxError it returned
is because the first line is indented. Also, what happens if you switch the
platform to OpenCL rather than CPU?

On Mon, Oct 16, 2023 at 1:15 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
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