Opened 6 years ago

Closed 3 years ago

#3021 closed defect (can't reproduce)

ISOLDE: various errors

Reported by: alfredo0712.florez@… 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-4.15.0-88-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.93 (2020-04-03)
Description
I was trying to star an ISOLDE simulation, and this bug was reported

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b5-cp37-cp37m-linux_x86_64.whl  
Successfully installed ChimeraX-Clipper-0.12.0 ChimeraX-ISOLDE-1.0b5  
Installed ChimeraX-Clipper (0.12.0)  
Installed ChimeraX-ISOLDE (1.0b5)  

> toolshed show Toolbar

> toolshed show Toolbar

> open /home/alfredo/Desktop/relion30-practice/RNAP-nuc-
> practice/run_class001.mrc

Opened run_class001.mrc, grid size 256,256,256, pixel 1.49, shown at level
0.00918, step 1, values float32  

> volume #1 level 0.002588

> open /home/alfredo/Desktop/relion30-practice/RNAP-nuc-
> practice/postprocess.mrc

Opened postprocess.mrc, grid size 256,256,256, pixel 1.49, shown at level
0.00982, step 1, values float32  

> volume #1 level 0.009324

> open /home/alfredo/Downloads/emd_3580.map

File not found: /home/alfredo/Downloads/emd_3580.map  

> open /home/alfredo/Desktop/relion30-practice/RNAP-nuc-
> practice/run_ct12_class001.mrc

File not found: /home/alfredo/Desktop/relion30-practice/RNAP-nuc-
practice/run_ct12_class001.mrc  

> open /home/alfredo/Documents/RNAP-ribosome-project/RR-
> crio-28JAN2020/relion_locres_filtered.mrc

Opened relion_locres_filtered.mrc, grid size 384,384,384, pixel 1.57, shown at
level 0.0278, step 2, values float32  

> volume #1 level 0.005576

> volume #1 level 0.06313

> toolshed show ISOLDE

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description  
A B C | capsid protein VP1  
  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | capsid protein VP1  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Summary of feedback from opening 20205 fetched from emdb  
---  
note | Fetching compressed map 20205 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz  
  
Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> volume #2 level 0.2719

> clipper associate #2 toModel #1

> toolshed show Toolbar

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> hide #!1.1.1 models

> show #!1.1.1 models

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> select clear

> select clear

> select clear

> select clear

> select clear

> select clear

> toolshed show Log

> toolshed show ISOLDE

> set bgColor white

> toolshed show "Command Line Interface"

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> ui favorite true ISOLDE

> ui favorite false ISOLDE

> toolshed show Toolbar

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain B determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /B THR 9  
Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29  
Chain-final residues that are actual C termini: /A SER 520  
Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519  
Missing OXT added to C-terminal residue /A SER 520  
1438 hydrogen bonds  
Adding 'H' to /A ASP 29  
Adding 'H' to /C ASP 29  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11439 hydrogens added  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1135, in _model_changes_cb  
self._update_iffy_rota_list()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2349, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2349, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

Unknown command: hideHC  

> isolde restrain ligands #1

QWidget::repaint: Recursive repaint detected  

> open 20205 fromDatabase emdb

Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

> select #1

22945 atoms, 23062 bonds, 14 models selected  
Traceback (most recent call last):  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> select clear

> help help:user

> select #1

22945 atoms, 23062 bonds, 18 models selected  
Traceback (most recent call last):  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> select clear

> isolde restrain ligands #1

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | Termini for 6out.pdb (#1.2) chain A determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain B determined from SEQRES records  
Termini for 6out.pdb (#1.2) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /B THR 9  
Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29  
Chain-final residues that are actual C termini: /A SER 520  
Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519  
1207 hydrogen bonds  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1135, in _model_changes_cb  
self._update_iffy_rota_list()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2349, in _update_iffy_rota_list  
if not table.isVisible():  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
Error processing trigger "changes":  
RuntimeError: wrapped C/C++ object of type QTableWidget has been deleted  
  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2349, in _update_iffy_rota_list  
if not table.isVisible():  
  
See log for complete Python traceback.  
  

> isolde restrain ligands #1

> select #1

22945 atoms, 23062 bonds, 18 models selected  
Traceback (most recent call last):  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  

> select clear

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/cmd.py", line 83, in isolde_sim  
raise RuntimeError('All atoms must be from the same model!')  
RuntimeError: All atoms must be from the same model!  
  
RuntimeError: All atoms must be from the same model!  
  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/cmd.py", line 83, in isolde_sim  
raise RuntimeError('All atoms must be from the same model!')  
  
See log for complete Python traceback.  
  

> select clear

Expected an objects specifier or a keyword  

> select #1

22945 atoms, 23062 bonds, 18 models selected  

> isolde sim start sel

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/cmd.py", line 88, in isolde_sim  
isolde.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2709, in start_sim  
sm.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 667, in start_sim  
sh.start_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1570, in start_sim  
self._prepare_sim()  
File "/home/alfredo/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_prepare_sim  
integrator, platform, properties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__  
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
Exception: Error initializing context: clGetPlatformIDs (-1001)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/simtk/openmm/openmm.py", line 11125, in __init__  
this = _openmm.new_Context(*args)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 19.2.8
OpenGL renderer: Mesa DRI Intel(R) HD Graphics 5500 (Broadwell GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: TOSHIBA
Model: Satellite L55-C
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 4 Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz
Cache Size: 3072 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 5500 [8086:1616] (rev 09)
	Subsystem: Toshiba America Info Systems HD Graphics 5500 [1179:f840]
	Kernel driver in use: i915

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: various errors

in reply to:  2 ; comment:2 by Tristan Croll, 6 years ago 

Looks like the root cause here is that your OpenCL driver is incorrectly configured. Everything beyond that point is the fallout. You’ll need to have a look and see if there’s an official driver for your particular GPU (note that you won’t get great performance on that hardware - ISOLDE’s really built to use more heavy-duty GPUs like the GTX 10-series or better).

comment:3 by Tristan Croll, 3 years ago

Resolution: → can't reproduce
Status: assigned → closed
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