Get started with NEST and NESTML

Install latest version of cmake (need sudo authorization)

Reference: https://graspingtech.com/upgrade-cmake/

sudo apt install build-essential libssl-dev
wget https://github.com/Kitware/CMake/releases/download/v3.22.0/cmake-3.22.0.tar.gz
tar -zxvf cmake-3.22.0.tar.gz
cd cmake-3.22.0
./bootstrap
make 
sudo make install

Install NEST v3.1

Reference: https://nest-simulator.readthedocs.io/en/stable/installation/linux_install.html

WARNING: Directly install NEST v2.20.1 from pip or conda might leads to this issue.

  • Create a new Python environment. 
      conda create -n nestml python=3.9 -y
  • Install necessary dependence. 
      conda activate nestml
  conda install -y numpy cython matplotlib ipython scipy
  conda install -y pytest pytest-xdist pytest-timeout
  pip install junitparser
  • Download latest NEST package 
      wget -O nest-simulator-3.1.tar.gz https://codeload.github.com/nest/nest-simulator/tar.gz/refs/tags/v3.1
  • Unpack the tarball 
      tar -xzvf nest-simulator-3.1.tar.gz
  • Create a build directory 
      mkdir nest-simulator-3.1-build
  • Change to the build directory: 
      cd nest-simulator-3.1-build
  • Configure NEST. You may need additional cmake options (see CMake Options for NEST). 
      cmake ../nest-simulator-3.1/
  • Compile and install NEST: 
      make
  make install
  make installcheck

If there is no failure occurs in installcheck, then NEST should now be successfully installed in your active Python environment.

Install the latest development version of NEST::ml

Reference: https://nestml.readthedocs.io/en/latest/installation.html

To obtain the latest development version, clone directly from the master branch of the GitHub repository:

git clone https://github.com/nest/nestml

Install into your current Python environment using:

cd nestml
python setup.py install --user

Note: antlr4-python3-runtime==4.10 will lead to a BUG. 4.9.3 is recommended.

Testing (Optional)

After installation, correct operation can be tested by:

python setup.py test

Note that, tests.docstring_comment_test might fail. If so, please ignore it which won’t affect your usage.

Install example *.nestml file

Reference: https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html

import nest
from pynestml.frontend.pynestml_frontend import to_nest, install_nest

NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")

to_nest(input_path="izhikevich_solution.nestml", # replace with path of your own nestml file
        target_path="~/tmp/nestml-component",
        logging_level="ERROR")

install_nest("~/tmp/nestml-component", NEST_SIMULATOR_INSTALL_LOCATION)

nest.Install("nestmlmodule")

Instantiate model in NEST Simulator and run

import numpy as np
import matplotlib.pyplt as plt
import nest

nest.set_verbosity("M_WARNING")
nest.ResetKernel()

neuron = nest.Create("izhikevich_tutorial") # replace with name of your own model
voltmeter = nest.Create("voltmeter")

voltmeter.set({"record_from": ["v", "u"]})
nest.Connect(voltmeter, neuron)

cgs = nest.Create('dc_generator')
cgs.set({"amplitude": 25.})
nest.Connect(cgs, neuron)

sr = nest.Create("spike_recorder")
nest.Connect(neuron, sr)

nest.Simulate(250.)

spike_times = nest.GetStatus(sr, keys='events')[0]['times']

fig, ax = plt.subplots(nrows=2)
ax[0].plot(voltmeter.get("events")["times"], voltmeter.get("events")["v"])
ax[1].plot(voltmeter.get("events")["times"], voltmeter.get("events")["u"])
ax[0].scatter(spike_times, 30 * np.ones_like(spike_times), marker="d", c="orange", alpha=.8, zorder=99)
for _ax in ax:
    _ax.grid(True)
ax[0].set_ylabel("v [mV]")
ax[1].set_ylabel("u")
ax[-1].set_xlabel("Time [ms]")
fig.savefig('test.png')
fig.show()