Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7470 closed defect (duplicate)

Start simulation: openmm.OpenMMException: Error compiling kernel: Compile Server Error

Reported by: lorenzo.finci@… 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-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

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/fincili/Desktop/Documents/RAS_data/20210517_Ras/phenix/RealSpaceRefine_311/real_space_refined_301_final_coot_081222_real_space_refined_311.pdb

Chain information for
real_space_refined_301_final_coot_081222_real_space_refined_311.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/fincili/Desktop/Documents/RAS_data/20210517_Ras/ccpem/LocScale_38/loc_scale.mrc

Opened loc_scale.mrc as #2, grid size 256,256,256, pixel 0.858, shown at level
0.0726, step 1, values float32  

> set bgColor white

> clipper associate #2 toModel #1

Opened loc_scale.mrc as #1.1.1.1, grid size 256,256,256, pixel 0.858, shown at
level 0.14, step 1, values float32  
Chain information for
real_space_refined_301_final_coot_081222_real_space_refined_311.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  

> addh

Summary of feedback from adding hydrogens to
real_space_refined_301_final_coot_081222_real_space_refined_311.pdb #1.2  
---  
notes | No usable SEQRES records for
real_space_refined_301_final_coot_081222_real_space_refined_311.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for
real_space_refined_301_final_coot_081222_real_space_refined_311.pdb (#1.2)
chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLY 10, /B GLY 10  
Chain-initial residues that are not actual N termini: /A LYS 267, /A TYR 507,
/B LYS 267  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 530, /A GLU 224, /A
ARG 490, /B ASP 545, /B GLU 224  
733 hydrogen bonds  
Adding 'H' to /A LYS 267  
Adding 'H' to /A TYR 507  
Adding 'H' to /B LYS 267  
/A LYS 530 is not terminus, removing H atom from 'C'  
/B ASP 545 is not terminus, removing H atom from 'C'  
7805 hydrogens added  
  

> volume #1.1.1.1 level 0.08484

> volume #1.1.1.1 style surface

> transparency 50

> volume #1.1.1.1 style mesh

> volume #1.1.1.1 level 0.08969

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 54 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  
Loading residue template for ATP from internal database  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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
"/opt/sbgrid/i386-mac/chimerax/1.3/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: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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.  
  

> volume #1.1.1.1 level 0.1188

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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
"/opt/sbgrid/i386-mac/chimerax/1.3/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: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.  
  

> volume #1.1.1.1 style image

> volume #1.1.1.1 style surface

> volume #1.1.1.1 change image level -0.003902,0 level 0.1714,0.8 level
> 0.249,1

> volume #1.1.1.1 level 0.07145

> volume #1.1.1.1 style mesh

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7fb59739e250>
contents scale of 1 - updating layer to match.  

[Repeated 1 time(s)]

Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x7fb59739e250>
contents scale of 2 - updating layer to match.  

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2749, in _start_sim_or_toggle_pause  
self.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/isolde.py", line 2804, in start_sim  
sm.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1606, in start_sim  
self._prepare_sim()  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1564, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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
"/opt/sbgrid/i386-mac/chimerax/1.3/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: Compile Server Error.  
  
openmm.OpenMMException: Error compiling kernel: Compile Server Error.  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/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.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1168, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1975, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.  
  




OpenGL version: 4.1 INTEL-14.7.28
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.8 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: 16 GB
      Boot ROM Version: 1731.140.2.0.0 (iBridge: 19.16.16064.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 4 days 6:46

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        D3218HN:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: X9R5K88H1U7E
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55

Locale: ('en_US', '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: 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
    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
    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: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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
    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

Change History (4)

comment:1 by Eric Pettersen, 3 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 → Start simulation: openmm.OpenMMException: Error compiling kernel: Compile Server Error

Reported by Lorenzo Finci

comment:2 by Tom Goddard, 3 years ago

Mac Intel graphics is pretty buggy, prone to crashing. You are using two displays, and ChimeraX logged warnings about some trouble handling the that one display was retina and one was not ("dpr" means display pixel resolution, 2 for retina displays, 1 for non-retina displays). I've seen these warnings reported before in ChimeraX crash reports.

Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x7fb59739e250> contents scale of 1 - updating layer to match.

The two displays and the flakey Mac Intel graphics may be related to the OpenMM error you report which appears to be a GPU shader compilation error.

openmm.OpenMMException: Error compiling kernel: Compile Server Error.

If this happens repeatedly you might try using just a single display.

comment:3 by Tristan Croll, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Sorry about not responding to this at the time... there was a spate of these issues a while back due to Apple releasing a faulty update to MacOS 10.15. Is it still an issue?

in reply to:  4 ; comment:4 by lorenzo.finci@…, 3 years ago 

Hi Tristan, 

Thank you, no it is not an issue anymore. 

Sincerely, 
lorenzo 

Lorenzo Ihsan Finci, Ph.D. (he/him) 

Scientist 

Ras Structural Biology Team, 
NCI Ras Initiative 


lorenzo.finci@nih.gov <mailto:email@nih.gov> [c] 


office: 301-846-1904 





frederick.cancer.gov <https://frederick.cancer.gov/> 

The Frederick National Laboratory for Cancer Research is operated by Leidos Biomedical Research, Inc. for the National Cancer Institute. 



<https://twitter.com/frednatlab> <https://www.linkedin.com/company/frederick-national-laboratory-for-cancer-research/> <https://www.facebook.com/FredNatLab> <https://www.instagram.com/frednatlab/> 







On 1/18/23, 9:38 AM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:


#7470: Start simulation: openmm.OpenMMException: Error compiling kernel: Compile
Server Error
--------------------------------------+---------------------------
Reporter: lorenzo.finci@… | Owner: Tristan Croll
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: duplicate | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+---------------------------
Changes (by Tristan Croll):


* status: assigned => closed
* resolution: => duplicate




Comment:


Sorry about not responding to this at the time... there was a spate of
these issues a while back due to Apple releasing a faulty update to MacOS
10.15. Is it still an issue?


--
Ticket URL: <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7470%23comment%3A3&data=05%7C01%7Clorenzo.finci%40nih.gov%7C660befb0744e4199a22108daf961b540%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638096495299680324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5iSNtfcKimOxg7RzeKISQSSwrIhJ2Br6KK7n7S7QcN8%3D&reserved=0> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7470%23comment%3A3&amp;data=05%7C01%7Clorenzo.finci%40nih.gov%7C660befb0744e4199a22108daf961b540%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638096495299680324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=5iSNtfcKimOxg7RzeKISQSSwrIhJ2Br6KK7n7S7QcN8%3D&amp;reserved=0&gt;>
ChimeraX <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7Clorenzo.finci%40nih.gov%7C660befb0744e4199a22108daf961b540%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638096495299680324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ocEb6MFM9HzFIQ6PfbPxs1kNurs1P3hnDd1mqRPHV0k%3D&reserved=0> <https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&amp;data=05%7C01%7Clorenzo.finci%40nih.gov%7C660befb0744e4199a22108daf961b540%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638096495299680324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=ocEb6MFM9HzFIQ6PfbPxs1kNurs1P3hnDd1mqRPHV0k%3D&amp;reserved=0&gt;>
ChimeraX Issue Tracker
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.
Note: See TracTickets for help on using tickets.