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#15416 closed defect (limitation)

ISOLDE update coordinates: RuntimeError: clWaitForEvents

Reported by:	singuang.chen@…	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:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/AW Lab/Desktop/Cryo-EM/8g1i.pdb"

8g1i.pdb title:  
SPCAS9 with sgRNA and target DNA [more info...]  
  
Chain information for 8g1i.pdb #1  
---  
Chain | Description | UniProt  
A | crispr-associated endonuclease CAS9/CSN1 | CAS9_STRP1 1-1368  
B | SGRNA |  
C | DNA E2_TS |  
D | DNA E2_NTS |  
  

> open "C:/Users/AW Lab/Desktop/Cryo-EM/240526_SpCas9_WTsgRNA.cif"

Summary of feedback from opening C:/Users/AW Lab/Desktop/Cryo-
EM/240526_SpCas9_WTsgRNA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 240526_SpCas9_WTsgRNA.cif #2  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ba | No description available  
Bb Bc | No description available  
Bd Be | No description available  
Bf | No description available  
Bg | No description available  
Bh | No description available  
Bi | No description available  
Bj | No description available  
Bk Cc | No description available  
Ca | No description available  
Cb | No description available  
  

> style stick

Changed 23784 atom styles  

> show cartoons

> hide atoms

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 240526_SpCas9_WTsgRNA.cif, chain Ad (#2) with 8g1i.pdb, chain A
(#1), sequence alignment score = 1228  
RMSD between 197 pruned atom pairs is 1.108 angstroms; (across all 306 pairs:
2.291)  
  

> color #1 red

> color #2 #005500ff

> color #2 #ffaa00ff

> color #2 #0055ffff

> set bgColor white

> select #1:775-915

1122 atoms, 1133 bonds, 2 pseudobonds, 137 residues, 2 models selected  

> select #1:775-917

1141 atoms, 1153 bonds, 2 pseudobonds, 139 residues, 2 models selected  

> select #1:775-919

1161 atoms, 1173 bonds, 2 pseudobonds, 141 residues, 2 models selected  

> select #1:775-921

1178 atoms, 1190 bonds, 2 pseudobonds, 143 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> open "C:/Users/AW Lab/Desktop/Cryo-EM/J247_003_volume_map_sharp.mrc"

Opened J247_003_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.23,
shown at level 0.118, step 1, values float32  

> volume #3 level 0.1832

> hide #!2 models

> volume #3 level 0.216

> clipper associate #3 toModel #1

Opened J247_003_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel
1.23, shown at level 0.432, step 1, values float32  
8g1i.pdb title:  
SPCAS9 with sgRNA and target DNA [more info...]  
  
Chain information for 8g1i.pdb  
---  
Chain | Description | UniProt  
1.2/A | crispr-associated endonuclease CAS9/CSN1 | CAS9_STRP1 1-1368  
1.2/B | SGRNA |  
1.2/C | DNA E2_TS |  
1.2/D | DNA E2_NTS |  
  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Ba C 1 P
because it is missing heavy-atom bond partners  
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bb C 0 P because it is
missing heavy-atom bond partners  
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bc C 0 P because it is
missing heavy-atom bond partners  
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Bd C 0 P because it is
missing heavy-atom bond partners  
Not adding hydrogens to 240526_SpCas9_WTsgRNA.cif #2/Be C 0 P because it is
missing heavy-atom bond partners  
12 messages similar to the above omitted  
notes | No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Aa;
guessing termini instead  
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ab; guessing
termini instead  
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ac; guessing
termini instead  
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ad; guessing
termini instead  
No usable SEQRES records for 240526_SpCas9_WTsgRNA.cif (#2) chain Ae; guessing
termini instead  
16 messages similar to the above omitted  
Chain-initial residues that are actual N termini: 240526_SpCas9_WTsgRNA.cif
#2/Aa ILE 15, 240526_SpCas9_WTsgRNA.cif #2/Ab VAL 1091,
240526_SpCas9_WTsgRNA.cif #2/Ac LYS 962, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
283, 240526_SpCas9_WTsgRNA.cif #2/Ae ILE 1128, 240526_SpCas9_WTsgRNA.cif #2/Af
ILE 687, 240526_SpCas9_WTsgRNA.cif #2/Ag ASP 715  
Chain-initial residues that are not actual N termini:
240526_SpCas9_WTsgRNA.cif #2/Aa ALA 58, 240526_SpCas9_WTsgRNA.cif #2/Aa GLU
133, 240526_SpCas9_WTsgRNA.cif #2/Aa GLY 174, 240526_SpCas9_WTsgRNA.cif #2/Aa
ASP 190, 240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1173, 240526_SpCas9_WTsgRNA.cif
#2/Ab LEU 1265, 240526_SpCas9_WTsgRNA.cif #2/Ad THR 321,
240526_SpCas9_WTsgRNA.cif #2/Ad GLU 435, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
521, 240526_SpCas9_WTsgRNA.cif #2/Ad THR 568, 240526_SpCas9_WTsgRNA.cif #2/Ad
PHE 595, 240526_SpCas9_WTsgRNA.cif #2/Ad ASP 622, 240526_SpCas9_WTsgRNA.cif
#2/Ad LEU 624, 240526_SpCas9_WTsgRNA.cif #2/Ad TYR 664,
240526_SpCas9_WTsgRNA.cif #2/Af GLY 725  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 240526_SpCas9_WTsgRNA.cif
#2/Aa PHE 193, 240526_SpCas9_WTsgRNA.cif #2/Aa ASN 54,
240526_SpCas9_WTsgRNA.cif #2/Aa ILE 126, 240526_SpCas9_WTsgRNA.cif #2/Aa PHE
172, 240526_SpCas9_WTsgRNA.cif #2/Aa ASP 188, 240526_SpCas9_WTsgRNA.cif #2/Ab
GLY 1375, 240526_SpCas9_WTsgRNA.cif #2/Ab LYS 1163, 240526_SpCas9_WTsgRNA.cif
#2/Ab LYS 1252, 240526_SpCas9_WTsgRNA.cif #2/Ac LYS 1008,
240526_SpCas9_WTsgRNA.cif #2/Ad ILE 678, 240526_SpCas9_WTsgRNA.cif #2/Ad ASN
317, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU 431, 240526_SpCas9_WTsgRNA.cif #2/Ad
HIS 519, 240526_SpCas9_WTsgRNA.cif #2/Ad TYR 529, 240526_SpCas9_WTsgRNA.cif
#2/Ad GLU 574, 240526_SpCas9_WTsgRNA.cif #2/Ad ILE 609,
240526_SpCas9_WTsgRNA.cif #2/Ad ASP 622, 240526_SpCas9_WTsgRNA.cif #2/Ad LEU
659, 240526_SpCas9_WTsgRNA.cif #2/Ae LYS 1132, 240526_SpCas9_WTsgRNA.cif #2/Af
ILE 767, 240526_SpCas9_WTsgRNA.cif #2/Af ASN 698, 240526_SpCas9_WTsgRNA.cif
#2/Ag LYS 718  
710 hydrogen bonds  
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa ALA 58  
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa GLU 133  
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa GLY 174  
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Aa ASP 190  
Adding 'H' to 240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1173  
10 messages similar to the above omitted  
240526_SpCas9_WTsgRNA.cif #2/Aa PHE 193 is not terminus, removing H atom from
'C'  
240526_SpCas9_WTsgRNA.cif #2/Ab GLY 1375 is not terminus, removing H atom from
'C'  
240526_SpCas9_WTsgRNA.cif #2/Ac LYS 1008 is not terminus, removing H atom from
'C'  
240526_SpCas9_WTsgRNA.cif #2/Ad ILE 678 is not terminus, removing H atom from
'C'  
240526_SpCas9_WTsgRNA.cif #2/Ae LYS 1132 is not terminus, removing H atom from
'C'  
2 messages similar to the above omitted  
Termini for 8g1i.pdb (#1.2) chain A determined from SEQRES records  
Termini for 8g1i.pdb (#1.2) chain B determined from SEQRES records  
Termini for 8g1i.pdb (#1.2) chain C determined from SEQRES records  
Termini for 8g1i.pdb (#1.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 8g1i.pdb #1.2/A LYS 4,
8g1i.pdb #1.2/A ALA 589, 8g1i.pdb #1.2/A SER 719, 8g1i.pdb #1.2/A VAL 922,
8g1i.pdb #1.2/A GLY 1030, 8g1i.pdb #1.2/A LYS 1059, 8g1i.pdb #1.2/A GLU 1253  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 8g1i.pdb #1.2/A ILE 580,
8g1i.pdb #1.2/A GLN 712, 8g1i.pdb #1.2/A ARG 765, 8g1i.pdb #1.2/A ASP 1012,
8g1i.pdb #1.2/A ILE 1050, 8g1i.pdb #1.2/A HIS 1241, 8g1i.pdb #1.2/A GLN 1364  
Chain-initial residues that are not actual 5' termini: 8g1i.pdb #1.2/D DG 28  
828 hydrogen bonds  
Adding 'H' to 8g1i.pdb #1.2/A LYS 4  
Adding 'H' to 8g1i.pdb #1.2/A ALA 589  
Adding 'H' to 8g1i.pdb #1.2/A SER 719  
Adding 'H' to 8g1i.pdb #1.2/A VAL 922  
Adding 'H' to 8g1i.pdb #1.2/A GLY 1030  
2 messages similar to the above omitted  
8g1i.pdb #1.2/A GLN 1364 is not terminus, removing H atom from 'C'  
8g1i.pdb #1.2/D DG 28 is not terminus, removing H atom from O5'  
8g1i.pdb #1.2/C DA 31 is not terminus, removing H atom from O3'  
20017 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 80 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> 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  

> ui tool show "Ramachandran Plot"

QWindowsWindow::setGeometry: Unable to set geometry 1920x1010+0+23 (frame:
1936x1049-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1009+0+23 (frame: 1936x1048-8-8) margins: 8, 31, 8, 8
minimum size: 454x1010 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=470, y=1049)))  

> clipper spotlight

> select add #1.1.1

19 atoms, 1 residue, 6 models selected  

> select subtract #1.1.1

19 atoms, 1 residue, 2 models selected  

> select ~sel & ##selected

23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected  

> select ~sel & ##selected

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

> select ~sel & ##selected

23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected  

> select ~sel & ##selected

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

> select ~sel & ##selected

23581 atoms, 24112 bonds, 6 pseudobonds, 1296 residues, 2 models selected  

> isolde restrain ligands #1

> select #1

23600 atoms, 24130 bonds, 6 pseudobonds, 1297 residues, 19 models selected  

> isolde sim start #1.2/B,A,C-D

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.2/B,A,C-D

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:195

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug selection"

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

> isolde tutorial

3 models selected  

> view /A:5

> view /A:57

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:1304

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.2

Sim termination reason: None  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:208

ISOLDE: started sim  

> volume show

> transparency 50

> isolde sim pause

> isolde sim resume

> volume #1.1.1.1 level 0.356

> volume #1.1.1.1 level 0.165

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
RuntimeError: clWaitForEvents  
  
Error processing trigger "new frame":  
RuntimeError: clWaitForEvents  
  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim pause

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:183

ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
RuntimeError: Error invoking kernel findBlocksWithInteractions:
clEnqueueNDRangeKernel (-5)  
  
Error processing trigger "new frame":  
RuntimeError: Error invoking kernel findBlocksWithInteractions:
clEnqueueNDRangeKernel (-5)  
  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim stop

[Repeated 4 time(s)]

> isolde sim pause

[Repeated 2 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:180-186

ISOLDE: started sim  

> isolde sim start #1.2/A:208

Simulation already running!  

> isolde sim start #1.2/A:208

Simulation already running!  

> isolde sim start #1.2/A:208

Simulation already running!  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:181

ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
RuntimeError: clWaitForEvents  
  
Error processing trigger "new frame":  
RuntimeError: clWaitForEvents  
  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 103, in coords  
return self.smoothed_coords  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde sim stop

[Repeated 2 time(s)]

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start #1.2/A:178

ISOLDE: started sim  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
^^^^^^^^^  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 101, in coords  
return self.current_coords  
^^^^^^^^^^^^^^^^^^^  
RuntimeError: clWaitForEvents  
  
Error processing trigger "new frame":  
RuntimeError: clWaitForEvents  
  
File "C:\Users\AW Lab\AppData\Local\UCSF\ChimeraX\1.7\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 101, in coords  
return self.current_coords  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2114
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.11.2
Locale: zh_HK.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: FUJITSU CLIENT COMPUTING LIMITED
Model: ESPRIMO D7011
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 33,877,090,304
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    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: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 17 months ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE update coordinates: RuntimeError: clWaitForEvents

Reported by Sin-Guang Chen

comment:2 by Tristan Croll, 17 months ago

Resolution:	→ limitation
Status:	assigned → closed

Unfortunately what this boils down to is that your GPU isn't capable of handling the simulation you're trying to run. The important line in the error message is:

RuntimeError: Error invoking kernel findBlocksWithInteractions:
clEnqueueNDRangeKernel (-5)

As per https://streamhpc.com/blog/2013-04-28/opencl-error-codes/, the error code -5 is CL_OUT_OF_RESOURCES. That's a little surprising given that the Intel UHD 630 shares the system RAM - while it's a slow GPU for ISOLDE's purposes, in my experience it can manage surprisingly big systems. Did you have a lot of other memory-hungry processes running at the same time, perhaps?

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