Could not display figures while running from terminal in Jupyter lab

[Clea Smith]

Hi spinnaker group,

I was trying to run my simulation through the Jupyter lab terminal, but the I was complained about the issue below while it was running my script.

2021-07-01 16:05:02 ERROR: Shutdown on exception

Traceback (most recent call last):

  File "IF_cond_exp_adap_thres_example.py", line 64, in <module>

    Panel(test_pop_v.segments[0].filter(name='v')[0],xticks=True,yticks=True, ylabel='Voltage', xlim=(0,run_time))

  File "/home/spinnaker/sPyNNakerGit/lib/python3.6/site-packages/pyNN/utility/plotting.py", line 193, in __init__

    self.fig = plt.figure(1, figsize=(width, height))

  File "/home/spinnaker/sPyNNakerGit/lib/python3.6/site-packages/matplotlib/pyplot.py", line 546, in figure

    **kwargs)

  File "/home/spinnaker/sPyNNakerGit/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 3358, in new_figure_manager

    return cls.new_figure_manager_given_figure(num, fig)

  File "/home/spinnaker/sPyNNakerGit/lib/python3.6/site-packages/matplotlib/backends/_backend_tk.py", line 888, in new_figure_manager_given_figure

    window = tk.Tk(className="matplotlib")

  File "/usr/lib/python3.6/tkinter/__init__.py", line 2023, in __init__

    self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)

_tkinter.TclError: couldn't connect to display ":0"

These log messages where generated at level WARNING or above

/home/spinnaker/sPyNNakerGit/sPyNNaker8NewModelTemplate/examples/reports has 5 old reports that have not been closed

Shutdown on exception

There were data saved in the middle of the simulation, and it indicated successful running. Can I be advised how I could address this? ( I was running the script after using "source bin/activate" )

Many Thanks

Clea

[Andrew Gait]

Hi Clea,

There's no way of displaying a figure from a JupyterLab terminal (since it doesn't know what "display" to send the figure to), or at least I don't know of one (someone else may contradict me here... ?).  In order to display a figure I believe you have to do it by running the script from a notebook rather than running the script in the terminal window.

Andy

----------------------------------------------------
Dr. Andrew Gait,

Research Software Engineer,

APT Group,
Department of Computer Science,
The University of Manchester,
Oxford Road, Manchester M13 9PL

email: andre...@manchester.ac.uk
web: http://personalpages.manchester.ac.uk/staff/Andrew.Gait/

---

From: spinnak...@googlegroups.com <spinnak...@googlegroups.com> on behalf of Clea Smith <clea...@gmail.com>
Sent: 01 July 2021 17:11
To: SpiNNaker Users Group <spinnak...@googlegroups.com>
Subject: [SpiNNaker Mailing List] Could not display figures while running from terminal in Jupyter lab

 

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[Andrew Rowley]

Hi,

 

This is correct; the best, and possibly only, way to run a python script on Jupyter if you want to display graphics is to run it in a Jupyter notebook.

 

Andrew :)

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