Store and restore a network simulation

This example shows how to store user-specified aspects of a network to file and how to later restore the network for further simulation. This may be used, e.g., to train weights in a network up to a certain point, store those weights and later perform diverse experiments on the same network using the stored weights.

Only user-specified aspects are stored

NEST does not support storing the complete state of a simulation in a way that would allow one to continue a simulation as if one had made a new Simulate() call on an existing network. Such complete checkpointing would be very difficult to implement.

NEST’s explicit approach to storing and restoring network state makes clear to all which aspects of a network are carried from one simulation to another and thus contributes to good scientific practice.

Storing and restoring is currently not supported for MPI-parallel simulations.

Import necessary modules.

import nest
import pickle

These modules are only needed for illustrative plotting.

import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy as np
import pandas as pd
import textwrap

Implement network as class.

Implementing the network as a class makes network properties available to the initial network builder, the storer and the restorer, thus reducing the amount of data that needs to be stored.

This simple Brunel-style balanced random network has an excitatory and inhibitory population, both driven by external excitatory poisson input. Excitatory connections are plastic (STDP). Spike activity of the excitatory population is recorded.

class EINetwork:
    A simple balanced random network with plastic excitatory synapses.

    The model is provided as a non-trivial example for storing and restoring.

    def __init__(self):
        self.nI = 500
        self.nE = 4 * self.nI
        self.n = self.nE + self.nI

        self.JE = 1.0
        self.JI = -4 * self.JE
        self.indeg_e = 200
        self.indeg_i = 50

        self.neuron_model = "iaf_psc_delta"

        # Create synapse models so we can extract specific connection information
        nest.CopyModel("stdp_synapse_hom", "e_syn", {"Wmax": 2 * self.JE})
        nest.CopyModel("static_synapse", "i_syn")

        self.nrn_params = {"V_m": nest.random.normal(-65., 5.)}
        self.poisson_rate = 800.

    def build(self):
        Construct network from scratch, including instrumentation.

        self.e_neurons = nest.Create(self.neuron_model, n=self.nE, params=self.nrn_params)
        self.i_neurons = nest.Create(self.neuron_model, n=self.nI, params=self.nrn_params)
        self.neurons = self.e_neurons + self.i_neurons = nest.Create("poisson_generator", {"rate": self.poisson_rate}) = nest.Create("spike_recorder")

        nest.Connect(self.e_neurons, self.neurons,
                     {"rule": "fixed_indegree", "indegree": self.indeg_e},
                     {"synapse_model": "e_syn", "weight": self.JE})
        nest.Connect(self.i_neurons, self.neurons,
                     {"rule": "fixed_indegree", "indegree": self.indeg_i},
                     {"synapse_model": "i_syn", "weight": self.JI})
        nest.Connect(, self.neurons, "all_to_all", {"weight": self.JE})

    def store(self, dump_filename):
        Store neuron membrane potential and synaptic weights to given file.

        assert nest.NumProcesses() == 1, "Cannot dump MPI parallel"

Build dictionary with relevant network information:

  • membrane potential for all neurons in each population

  • source, target and weight of all connections

Dictionary entries are Pandas Dataframes.

Strictly speaking, we would not need to store the weight of the inhibitory synapses since they are fixed, but we do so out of symmetry and to make it easier to add plasticity for inhibitory connections later.

    network = {}
    network["n_vp"] = nest.total_num_virtual_procs
    network["e_nrns"] = self.neurons.get(["V_m"], output="pandas")
    network["i_nrns"] = self.neurons.get(["V_m"], output="pandas")

    network["e_syns"] = nest.GetConnections(synapse_model="e_syn").get(
        ("source", "target", "weight"), output="pandas")
    network["i_syns"] = nest.GetConnections(synapse_model="i_syn").get(
        ("source", "target", "weight"), output="pandas")

    with open(dump_filename, "wb") as f:
        pickle.dump(network, f, pickle.HIGHEST_PROTOCOL)

def restore(self, dump_filename):
    Restore network from data in file combined with base information in the class.

    assert nest.NumProcesses() == 1, "Cannot load MPI parallel"

    with open(dump_filename, "rb") as f:
        network = pickle.load(f)

    assert network["n_vp"] == nest.total_num_virtual_procs, "N_VP must match"

Reconstruct neurons Since NEST does not understand Pandas Series, we must pass the values as NumPy arrays

self.e_neurons = nest.Create(self.neuron_model, n=self.nE,
                             params={"V_m": network["e_nrns"].V_m.values})
self.i_neurons = nest.Create(self.neuron_model, n=self.nI,
                             params={"V_m": network["i_nrns"].V_m.values})
self.neurons = self.e_neurons + self.i_neurons

Reconstruct instrumentation = nest.Create("poisson_generator", {"rate": self.poisson_rate}) = nest.Create("spike_recorder")

Reconstruct connectivity

nest.Connect(network["e_syns"].source.values, network["e_syns"].target.values,
             {"synapse_model": "e_syn", "weight": network["e_syns"].weight.values})

nest.Connect(network["i_syns"].source.values, network["i_syns"].target.values,
             {"synapse_model": "i_syn", "weight": network["i_syns"].weight.values})

Reconnect instruments

        nest.Connect(, self.neurons, "all_to_all", {"weight": self.JE})

class DemoPlot:
    Create demonstration figure for effect of storing and restoring a network.

    The figure shows raster plots for five different runs, a PSTH for the
    initial 1 s simulation and PSTHs for all 1 s continuations, and weight

    def __init__(self):
        self._colors = [c["color"] for c in plt.rcParams["axes.prop_cycle"]]
        self._next_line = 0

        plt.rcParams.update({'font.size': 10})
        self.fig = plt.figure(figsize=(10, 7), constrained_layout=False)

        gs = gridspec.GridSpec(4, 2, bottom=0.08, top=0.9, left=0.07, right=0.98, wspace=0.2, hspace=0.4)
        self.rasters = ([self.fig.add_subplot(gs[0, 0])] +
                        [self.fig.add_subplot(gs[n, 1]) for n in range(4)])
        self.weights = self.fig.add_subplot(gs[1, 0])
        self.comment = self.fig.add_subplot(gs[2:, 0])

        self.fig.suptitle("Storing and reloading a network simulation")
        self.comment.text(0, 1, textwrap.dedent("""
            Storing, loading and continuing a simulation of a balanced E-I network
            with STDP in excitatory synapses.

            Top left: Raster plot of initial simulation for 1000ms (blue). Network state
            (connections, membrane potential, synaptic weights) is stored at the end of
            the initial simulation.

            Top right: Immediate continuation of the initial simulation from t=1000ms
            to t=2000ms (orange) by calling Simulate(1000) again after storing the network.
            This continues based on the full network state, including spikes in transit.

            Second row, right: Simulating for 1000ms after loading the stored network
            into a clean kernel (green). Time runs from 0ms and only connectivity, V_m and
            synaptic weights are restored. Dynamics differ somewhat from continuation.

            Third row, right: Same as in second row with identical random seed (red),
            resulting in identical spike patterns.

            Fourth row, right: Simulating for 1000ms from same stored network state as
            above but with different random seed yields different spike patterns (purple).

            Above: Distribution of excitatory synaptic weights at end of each sample
            simulation. Green and red curves are identical and overlay to form brown curve."""),
                          transform=self.comment.transAxes, fontsize=8,

    def add_to_plot(self, net, n_max=100, t_min=0, t_max=1000, lbl=""):
        spks = pd.DataFrame.from_dict("events"))
        spks = spks.loc[(spks.senders < n_max) & (t_min < spks.times) & (spks.times < t_max)]

        self.rasters[self._next_line].plot(spks.times, spks.senders, ".",
        self.rasters[self._next_line].set_xlim(t_min, t_max)
        if 1 < self._next_line < 4:
        elif self._next_line == 4:
            self.rasters[self._next_line].set_xlabel('Time [ms]')

To save time while plotting, we extract only a subset of connections. For simplicity, we just use a prime-number stepping.

        w = nest.GetConnections(source=net.e_neurons[::41], synapse_model="e_syn").weight
        wbins = np.arange(0.7, 1.4, 0.01)
        self.weights.hist(w, bins=wbins,
                          histtype="step", density=True, label=lbl,
                          alpha=0.7, lw=3)

        if self._next_line == 0:
            self.rasters[0].set_ylabel("neuron id")
            self.weights.set_xlabel("Weight w [mV]")

        plt.pause(1e-3)  # allow figure window to draw figure

        self._next_line += 1

if __name__ == "__main__":


    T_sim = 1000

    dplot = DemoPlot()

Ensure clean slate and make NEST less chatty


Create network from scratch and simulate 1s.

nest.local_num_threads = 4
nest.print_time = True
ein = EINetwork()
print("*** Initial simulation ***")
dplot.add_to_plot(ein, lbl="Initial simulation")

Store network state to file with state after 1s.

print("\n*** Storing simulation ...", end="", flush=True)"ein_1000.pkl")
print(" done ***\n")

Continue simulation by another 1s.

print("\n*** Continuing simulation ***")
dplot.add_to_plot(ein, lbl="Continued simulation", t_min=T_sim, t_max=2 * T_sim)

Clear kernel, restore network from file and simulate for 1s.

print("\n*** Reloading and resuming simulation ***")
nest.local_num_threads = 4
ein2 = EINetwork()
dplot.add_to_plot(ein2, lbl="Reloaded simulation")

Repeat previous step. This shall result in exactly the same results as the previous run because we use the same random seed.

print("\n*** Reloading and resuming simulation (same seed) ***")
nest.local_num_threads = 4
ein2 = EINetwork()
dplot.add_to_plot(ein2, lbl="Reloaded simulation (same seed)")

Clear, restore and simulate again, but now with different random seed. Details in results shall differ from previous run.

print("\n*** Reloading and resuming simulation (different seed) ***")
nest.local_num_threads = 4
nest.rng_seed = 987654321
ein2 = EINetwork()
dplot.add_to_plot(ein2, lbl="Reloaded simulation (different seed)")


input("Press ENTER to close figure!")

Total running time of the script: ( 0 minutes 0.000 seconds)

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