Opened 5 years ago

Closed 5 years ago

#4418 closed defect (can't reproduce)

Shell sluggish

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103230345 (2021-03-23 03:45:30 UTC)
Description
Bug found while trying to debug another bug :)

Every time I enter a line in the shell, there's a hang of about 5 seconds and an error gets raised in the log. While there is no error message in the shell itself, it looks like it's at least partially non-functional:

a = 1
a
(returns None)

m = session.isolde.selected_model
m.atoms.selected=True
(successfully selects atoms) 

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.dev202103230345 (2021-03-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.2.dev15-cp38-cp38-manylinux_2_17_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/home/tic20/.cache/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.2.dev15-cp38-cp38-manylinux_2_17_x86_64.whl  
Requirement already satisfied: ChimeraX-AtomicLibrary~=2.1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.2.dev15) (2.1)  
Requirement already satisfied: ChimeraX-Clipper~=0.15.0 in
/home/tic20/.local/share/ChimeraX/1.2/site-packages (from ChimeraX-
ISOLDE==1.2.dev15) (0.15.0)  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.2.dev15) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.2.dev202103230345 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.2.dev15) (1.2.dev202103230345)  
Requirement already satisfied: ChimeraX-Atomic~=1.12.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ISOLDE==1.2.dev15) (1.12)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.3)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.3)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-ConnectStructure~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.1)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.0)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.4)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.5)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (1.7)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.3)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.0.2)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-
ISOLDE==1.2.dev15) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/run/media/tic20/storage/.opt/UCSF/ChimeraX-daily/lib/python3.8/site-packages
(from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.12.0->ChimeraX-ISOLDE==1.2.dev15) (2.0)  
Installing collected packages: ChimeraX-ISOLDE  
Attempting uninstall: ChimeraX-ISOLDE  
Found existing installation: ChimeraX-ISOLDE 1.2.dev14  
Uninstalling ChimeraX-ISOLDE-1.2.dev14:  
Successfully uninstalled ChimeraX-ISOLDE-1.2.dev14  
Successfully installed ChimeraX-ISOLDE-1.2.dev15  
  

> isolde demo crystal_intro

> set selectionWidth 4

/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/ramaplot.py:347:
MatplotlibDeprecationWarning: shading='flat' when X and Y have the same
dimensions as C is deprecated since 3.3. Either specify the corners of the
quadrilaterals with X and Y, or pass shading='auto', 'nearest' or 'gouraud',
or set rcParams['pcolor.shading']. This will become an error two minor
releases later.  
pcolor_plot = self.axes.pcolormesh(*grid, logvalues, cmap = 'Greys')  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
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.  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
1.2/A | predicted microcompartment protein  
  
Done loading forcefield  

WARNING: multiple experimental reflection datasets found:  
(dataset) FOBS, SIGFOBS,  
(dataset) IOBS, SIGIOBS,  
(dataset) DANO, SIGDANO,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) I(+), SIGI(+), I(-), SIGI(-)  
Automatically choosing "(dataset) FOBS, SIGFOBS".  

Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 36,36,34, pixel 0.723, shown at
level 0.303, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 36,36,34, pixel 0.723, shown at
level -0.0572,0.0572, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 36,36,34, pixel 0.723,
shown at level 0.602, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 36,36,34, pixel 0.723,
shown at level 0.366, step 1, values float32  
Loaded crystallographic demo: PDB ID 3io0  

> select clear

Updating bulk solvent parameters...  

> select clear

Updating bulk solvent parameters...  
Updating bulk solvent parameters...  

> usage isolde

Subcommands are:

  * isolde add ligand
  * isolde add water
  * isolde adjust distances
  * isolde adjust torsions
  * isolde cisflip
  * isolde demo
  * isolde ignore
  * isolde ~ignore
  * isolde jumpto
  * isolde pepflip
  * isolde release distances
  * isolde release torsions
  * isolde remote rest info
  * isolde remote rest start
  * isolde remote rest stop
  * isolde remote xmlrpc
  * isolde replace ligand
  * isolde report
  * isolde reset forcefield
  * isolde restrain distances
  * isolde restrain ligands
  * isolde restrain single distance
  * isolde restrain torsions
  * isolde set
  * isolde sim
  * isolde start
  * isolde stepto
  * isolde tutorial

  

> isolde sim start #1

Updating bulk solvent parameters...  

> select clear

> isolde sim start #1

Updating bulk solvent parameters...  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd.py", line 88, in isolde_sim  
isolde.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 968, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> isolde sim start #1

> select clear

> isolde report

> isolde set timeStepsPerGuiUpdate 50

> isolde set timeStepsPerGuiUpdate 100

> isolde set timeStepsPerGuiUpdate 20

Updating bulk solvent parameters...  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  

> select clear

> isolde report

> isolde set timeStepsPerGuiUpdate 50

> usage isolde rep

isolde report [report] [interval an integer]  
— Report the current simulation performance to the status bar  
report: true or false  

> isolde report false

> isolde report interval 50

Updating bulk solvent parameters...  
Updating bulk solvent parameters...  

> select clear

Updating bulk solvent parameters...  

> isolde restrain distances #1

> isolde restrain torsions #1

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  
Updating bulk solvent parameters...  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  

> select clear

Updating bulk solvent parameters...  

> select #1

3348 atoms, 3371 bonds, 229 residues, 30 models selected  
Updating bulk solvent parameters...  

> select clear

> isolde sim start #1

Updating bulk solvent parameters...  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd.py", line 88, in isolde_sim  
isolde.start_sim()  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
sm = self._sim_manager = Sim_Manager(self, self.selected_model, main_sel,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__  
mobile_atoms = self.expand_mobile_selection(selected_atoms, expansion_mode)  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 968, in
expand_mobile_selection  
sel = selections.expand_selection_along_chains(core_atoms,  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
TypeError: Selected atoms must all be in the same model!  
  
TypeError: Selected atoms must all be in the same model!  
  
File "/home/tic20/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/selections.py", line 40, in
expand_selection_along_chains  
raise TypeError('Selected atoms must all be in the same model!')  
  
See log for complete Python traceback.  
  

> select clear

> ui tool show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  
ERROR:tornado.general:Uncaught exception in ZMQStream callback  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  
ERROR:tornado.general:Uncaught exception in zmqstream callback  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events  
self._handle_recv()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv  
self._run_callback(callback, msg)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  
ERROR:asyncio:Exception in callback BaseAsyncIOLoop._handle_events(150, 1)  
handle: <Handle BaseAsyncIOLoop._handle_events(150, 1)>  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/asyncio/events.py", line 81, in
_run  
self._context.run(self._callback, *self._args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/tornado/platform/asyncio.py", line 189, in _handle_events  
handler_func(fileobj, events)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 451, in _handle_events  
self._handle_recv()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv  
self._run_callback(callback, msg)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event  
event_f()  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 214, in <lambda>  
self.schedule(lambda : self._really_send(*args, **kwargs))  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 222, in _really_send  
self.socket.send_multipart(msg, *args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/socket.py", line 62, in send_multipart  
self.message_sent += 1  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 604, in __set__  
self.set(obj, value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 593, in set  
obj._notify_trait(self.name, old_value, new_value)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1217, in _notify_trait  
self.notify_change(Bunch(  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1227, in notify_change  
return self._notify_observers(change)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/traitlets/traitlets.py", line 1264, in _notify_observers  
c(event)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/inprocess/ipkernel.py", line 130, in _io_dispatch  
ident, msg = self.session.recv(self.iopub_socket, copy=False)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/jupyter_client/session.py", line 807, in recv  
msg_list = socket.recv_multipart(mode, copy=copy)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 246, in __getattr__  
warnings.warn("Accessing zmq Socket attribute %s on BackgroundSocket" % attr,  
DeprecationWarning: Accessing zmq Socket attribute recv_multipart on
BackgroundSocket  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         10G         32G        370M         20G         51G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.12
    ChimeraX-AtomicLibrary: 2.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103230345
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.dev15
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (7)

comment:1 by Tristan Croll, 5 years ago

Platform: → all
Project: → ChimeraX

Hmm... can't seem to reproduce this in a fresh session. No idea why.

comment:2 by Eric Pettersen, 5 years ago

Cc: chimera-programmers added
Component: Unassigned → General Controls
Owner: set to Eric Pettersen
Status: new → accepted
Summary: ChimeraX bug report submission → Shell sluggish

Greg, Tom,

Can either of you reproduce this behavior on a Linux box? If not, I'm going to have to close this as irreproducible (even by Tristan!).

--Eric

comment:3 by Tom Goddard, 5 years ago

If Tristan can't reproduce it on the same machine I'm not going to start up my Linux box to test. Also he says that after the 5 second delay an error is given in the log, but no error is given in the bug report unless it is one of of those ISOLDE errors about sockets or selected atoms must all be in one model. With no error or traceback associated with the 5 second delay and not reproducible the only choice is to wait for better info if it happens again.

comment:4 by Greg Couch, 5 years ago

My problem with the Shell is that it takes forever to appear. Once in a blue moon it's fast.

Last edited 5 years ago by Greg Couch (previous) (diff)

in reply to:  5 ; comment:5 by goddard@…, 5 years ago 

Yes, on Mac also, starting the shell is surprisingly slow, I'd say takes 3 seconds to appear from the time the menu entry is clicked.  Not a major problem, and not related to what Tristan reports in this ticket.

comment:6 by Tristan Croll, 5 years ago

Greg, the final traceback in the log, starting with:

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  
ERROR:tornado.general:Uncaught exception in ZMQStream callback  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/zmq/eventloop/zmqstream.py", line 434, in _run_callback  
callback(*args, **kwargs)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/ipykernel/iostream.py", line 120, in _handle_event

... has nothing specifically to do with ISOLDE. It happened in the shell when I entered my first line, which happened to be:

m=session.isolde.selected_model

... but since selected_model is a simple property of the isolde object, I'm pretty sure that's just coincidence.

comment:7 by Eric Pettersen, 5 years ago

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

...since no one seems to be reproducing this problem.

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