Opened 5 years ago

Closed 5 years ago

#3568 closed defect (duplicate)

OpenCL problem?

Reported by: mks131@… 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-10-10.0.18362
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\Manoj\Documents\phenix_lin28\sharpened_map3.3.ccp4 format ccp4

Opened sharpened_map3.3.ccp4, grid size 376,376,376, pixel 0.649, shown at
level 3.05, step 2, values float32  

> open2 C:/Users/Manoj/Documents/phenix_lin28/lin28b_DNA.pdb

Chain information for lin28b_DNA.pdb #2  
---  
Chain | Description  
I | No description available  
J | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 525, in rebuild  
_rebuild_molecule('internal', mol)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 652, in
_rebuild_molecule  
hide_residues = make_ladder(nd, residues, mol._ladder_params)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 1237, in make_ladder  
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\nucleotides\\_data.py", line 733, in get_cylinder  
h = distance(p0, p1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 71, in distance  
return sqrt(distance_squared(p, q))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "new frame":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\geometry\vector.py", line 63, in distance_squared  
if len(p) == 3:  
  
See log for complete Python traceback.  
  

> volume #1 level 8.583

> toolshed show ISOLDE

> set selectionWidth 4

Chain information for lin28b_DNA.pdb  
---  
Chain | Description  
2.2/I | No description available  
2.2/J | No description available  
  
Done loading forcefield  

No template found for residue I-64 (DT)  

Adding hydrogens  
Summary of feedback from adding hydrogens to lin28b_DNA.pdb #2.2  
---  
notes | No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain I; guessing
termini instead  
No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain J; guessing termini
instead  
Chain-initial residues that are actual N termini: /I DT -64, /J DG -72  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /I DC 72, /J DA 64  
Chain-final residues that are not actual C termini:  
384 hydrogen bonds  
3098 hydrogens added  
  

No template found for residue I-64 (DT)  

Excluding residue  

> select clear

Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
Exception: Error creating array TabulatedFunction: clCreateBuffer (-61)  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py",
line 6265, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: Inspiron 7348
OS: Microsoft Windows 10 Home (Build 18362)
Memory: 8,501,149,696
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → OpenCL problem?

comment:2 by Tristan Croll, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Addressed this in #3566 before reading this one.

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