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#8312 feedback defect

ISOLDE: "start sim": No compatible OpenCL platform is available

Reported by:	dolezal@…	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:        Linux-6.1.5-060105-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Happens when I press "Start simulation" in Isolde

michal@mdpc:~$ clinfo 
Number of platforms                               1
  Platform Name                                   AMD Accelerated Parallel Processing
  Platform Vendor                                 Advanced Micro Devices, Inc.
  Platform Version                                OpenCL 2.1 AMD-APP (3452.0)
  Platform Profile                                FULL_PROFILE
  Platform Extensions                             cl_khr_icd cl_amd_event_callback 
  Platform Extensions function suffix             AMD
  Platform Host timer resolution                  1ns

  Platform Name                                   AMD Accelerated Parallel Processing
Number of devices                                 0

NULL platform behavior
  clGetPlatformInfo(NULL, CL_PLATFORM_NAME, ...)  No platform
  clGetDeviceIDs(NULL, CL_DEVICE_TYPE_ALL, ...)   No platform
  clCreateContext(NULL, ...) [default]            No platform
  clCreateContext(NULL, ...) [other]              
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_DEFAULT)  No devices found in platform
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_CPU)  No devices found in platform
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_GPU)  No devices found in platform
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_ACCELERATOR)  No devices found in platform
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_CUSTOM)  No devices found in platform
  clCreateContextFromType(NULL, CL_DEVICE_TYPE_ALL)  No devices found in platform

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> "/home/michal/Science/CryoEM/Phenix/GuaB1_EM_002/RealSpaceRefine_14/real_space_refined_010-coot-1_after
> isolde_ligands_real_space_refined_014.pdb"

Chain information for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb #1  
---  
Chain | Description  
A B C D E F G H | No description available  
  

> open /home/michal/Desktop/test.mrc

Opened test.mrc as #2, grid size 540,540,540, pixel 0.679, shown at level
0.00952, step 4, values float32  

> open /home/michal/Desktop/test_sharp100.mrc

Opened test_sharp100.mrc as #3, grid size 540,540,540, pixel 0.679, shown at
level 0.281, step 4, values float32  

> open /home/michal/Desktop/test_blur200.mrc

Opened test_blur200.mrc as #4, grid size 540,540,540, pixel 0.679, shown at
level 0.00317, step 4, values float32  

> open /home/michal/Desktop/test_blur50.mrc

Opened test_blur50.mrc as #5, grid size 540,540,540, pixel 0.679, shown at
level 0.00289, step 4, values float32  

> clipper associate #2 toModel #1

Opened test.mrc as #1.1.1.1, grid size 540,540,540, pixel 0.679, shown at
level 0.0312, step 1, values float32  
Chain information for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 314 residues in model #1.2 to IUPAC-IUB
standards.  

> clipper associate #3 toModel #1

Opened test_sharp100.mrc as #1.1.1.2, grid size 540,540,540, pixel 0.679,
shown at step 1, values float32  

> clipper associate #4 toModel #1

Opened test_blur200.mrc as #1.1.1.3, grid size 540,540,540, pixel 0.679, shown
at step 1, values float32  

> clipper associate #5 toModel #1

Opened test_blur50.mrc as #1.1.1.4, grid size 540,540,540, pixel 0.679, shown
at step 1, values float32  

> volume #1.1.1.1 level 0.006882

> volume #1.1.1.3 level -0.0001456

> volume #1.1.1.4 level 0.00154

> select clear

> view /A:502

> volume #1.1.1.1 level 0.02943

> volume #1.1.1.1 level 0.03094

> volume #1.1.1.2 level 0.2172

> volume show

> volume #1.1.1.2 level 0.1617

> show #!1.1.1.1 models

> show #!1.1.1.3 models

> show #!1.1.1.4 models

> hide #!1.1.1.2 models

> hide #!1.1.1.3 models

> hide #!1.1.1.4 models

> select add #1.1.1.1

3 models selected  

> select subtract #1.1.1.1

Nothing selected  

> select add #1.1.1.1

3 models selected  

> select subtract #1.1.1.1

Nothing selected  

> hide #!1.1.1.1 models

> show #!1.1.1.2 models

> volume #1.1.1.2 level 0.2888

> volume #1.1.1.2 level 0.2326

> volume #1.1.1.2 step 2

> volume #1.1.1.2 step 1

> volume #1.1.1.2 level 0.2799

> volume #1.1.1.2 level 0.1765

> show #!1.1.1.3 models

> volume #1.1.1.3 level 0.008468

> volume #1.1.1.3 level 0.01179

> hide #!1.1.1.3 models

> show #!1.1.1.4 models

> volume #1.1.1.4 level 0.02085

> color #1.1.1.4 #c061cb models transparency 0

> color #1.1.1.4 #9141ac models transparency 0

> color #1.1.1.3 #57e389 models transparency 0

> color #1.1.1.3 #33d17a models transparency 0

> color #1.1.1.3 #e01b24 models transparency 0

> show #!1.1.1.3 models

> volume #1.1.1.3 level 0.008863

> hide #!1.1.1.3 models

> hide #!1.1.1.1 models

> show #!1.1.1.1 models

> hide #!1.1.1.4 models

> view /A:501

> show #!1.1.1.2 models

> hide #!1.1.1.1 models

> volume #1.1.1.2 level 0.4037

> hide #!1.1.1.2 models

> show #!1.1.1.1 models

> show #!1.1.1.4 models

> volume #1.1.1.4 level 0.01819

> hide #!1.1.1.4 models

> show #!1.1.1.3 models

> volume #1.1.1.3 level 0.007348

> volume #1.1.1.3 level 0.006675

> hide #!1.1.1.4 models

> show #!1.1.1.4 models

> clipper spotlight

> clipper isolate sel maskRadius 4.0 focus false

> clipper spotlight

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

212 atoms, 213 bonds, 13 residues, 1 model selected  

> clipper isolate sel maskRadius 4.0 focus false

> clipper spotlight

> isolde sim start sel

Loading residue template for 5GP from internal database  
Loading residue template for ATP from internal database  
ISOLDE: stopped sim  
Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif  

> isolde parameterise sel override true

Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpyay2orim/ante.in.mol2 -fi mol2 -o /tmp/tmpyay2orim/ante.out.mol2 -fo
mol2 -c bcc -nc -14 -j 5 -s 2 -dr n  
(5GP) ``  
(5GP) `Welcome to antechamber 20.0: molecular input file processor.`  
(5GP) ``  
(5GP) `Info: Finished reading file (/tmp/tmpyay2orim/ante.in.mol2); atoms read
(24), bonds read (26).`  
(5GP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(5GP) ``  
(5GP) ``  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(5GP) `Info: Total number of electrons: 188; net charge: -14`  
(5GP) ``  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(5GP) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!`  
(5GP) `Cannot properly run "/usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue 5GP  
Check reply log for details  

> isolde parameterise sel override true

Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmps9qlu83f/ante.in.mol2 -fi mol2 -o /tmp/tmps9qlu83f/ante.out.mol2 -fo
mol2 -c bcc -nc -14 -j 5 -s 2 -dr n  
(5GP) ``  
(5GP) `Welcome to antechamber 20.0: molecular input file processor.`  
(5GP) ``  
(5GP) `Info: Finished reading file (/tmp/tmps9qlu83f/ante.in.mol2); atoms read
(24), bonds read (26).`  
(5GP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(5GP) ``  
(5GP) ``  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(5GP) `Info: Total number of electrons: 188; net charge: -14`  
(5GP) ``  
(5GP) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(5GP) `/usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber: Fatal Error!`  
(5GP) `Cannot properly run "/usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out".`  
Failure running ANTECHAMBER for residue 5GP  
Check reply log for details  

> addh

Summary of feedback from adding hydrogens to
real_space_refined_010-coot-1_after isolde_ligands_real_space_refined_014.pdb
#1.2  
---  
warnings | Not adding hydrogens to /A GLU 129 CG because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A GLU 138 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 168 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 175 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 188 CB because it is missing heavy-atom bond
partners  
83 messages similar to the above omitted  
notes | No usable SEQRES records for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb (#1.2) chain B; guessing termini
instead  
No usable SEQRES records for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb (#1.2) chain C; guessing termini
instead  
No usable SEQRES records for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb (#1.2) chain D; guessing termini
instead  
No usable SEQRES records for real_space_refined_010-coot-1_after
isolde_ligands_real_space_refined_014.pdb (#1.2) chain E; guessing termini
instead  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A VAL 2, /B VAL 2, /C VAL
2, /D VAL 2, /E VAL 2, /F VAL 2, /G VAL 2, /H VAL 2  
Chain-initial residues that are not actual N termini: /A SER 402, /B SER 402,
/C SER 402, /D SER 402, /E SER 402, /F SER 402, /G SER 402, /H SER 402  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 481, /A ALA 394, /B
ALA 481, /B ALA 394, /C ALA 481, /C ALA 394, /D ALA 481, /D ALA 394, /E ALA
481, /E ALA 394, /F ALA 481, /F ALA 394, /G ALA 481, /G ALA 394, /H ALA 481,
/H ALA 394  
4011 hydrogen bonds  
/A ALA 481 is not terminus, removing H atom from 'C'  
/B ALA 481 is not terminus, removing H atom from 'C'  
/C ALA 481 is not terminus, removing H atom from 'C'  
/D ALA 481 is not terminus, removing H atom from 'C'  
/E ALA 481 is not terminus, removing H atom from 'C'  
3 messages similar to the above omitted  
197 hydrogens added  
  

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/__init__.py", line 187, in run_provider  
toolbar_command(session, name)  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/toolbar.py", line 17, in toolbar_command  
run(session, 'isolde sim start sel')  
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/cmd/cmd.py", line 111, in isolde_sim  
isolde.start_sim()  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/isolde.py", line 893, in start_sim  
sm.start_sim()  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 677, in start_sim  
sh.start_sim()  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1624, in start_sim  
self._prepare_sim()  
File "/home/michal/.local/share/ChimeraX/1.4/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1582, in
_prepare_sim  
s = self._simulation = app.Simulation(self.topology, self._system,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/simulation.py", line 103, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5248, in __init__  
this = _openmm.new_Context(*args)  
openmm.OpenMMException: No compatible OpenCL platform is available  
  
openmm.OpenMMException: No compatible OpenCL platform is available  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/openmm.py",
line 5248, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.1.0-devel
OpenGL renderer: AMD Radeon (TM) R9 380 Series (tonga, LLVM 14.0.1, DRM 3.49, 6.1.5-060105-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        12Gi        12Gi        50Mi       7.0Gi        18Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Tonga PRO [Radeon R9 285/380] [1002:6939] (rev f1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Radeon R9 380 Gaming 4G [1462:2015]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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-NIHPresets: 1.1.9
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 3 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: "start sim": No compatible OpenCL platform is available

Reported by Michal Dolezal

comment:2 by Tristan Croll, 3 years ago

Status:	assigned → feedback

Looks like you don't have the OpenCL drivers installed for your GPU. Some discussion of this at https://community.amd.com/t5/devgurus-discussion/amdgpu-install-on-ubuntu-22-04-1-lts/m-p/555201 - could you try the solution there and see if it helps?

Note that this GPU is a little old and under-resourced for ISOLDE - released in 2015 and with only 4GB of RAM, which it has to share between rendering the graphics and running the simulations. Performance will be quite low, and you may experience out-of-memory errors for larger selections.

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