Microcircuit Example¶
Description¶
This example contains several files:
helpers.py
Helper functions for the simulation and evaluation of the microcircuit.network.py
Gathers all parameters and connects the different nodes with each other.network_params.py
Contains the parameters for the network.sim_params.py
Contains the simulation parameters.stimulus_params.py
Contains the parameters for the stimuli.example.py
Use this script to try out the microcircuit.
How to use the Microcircuit model example:
To run the microcircuit on a local machine, we have to first check that the
variables N_scaling
and K_scaling
in network_params.py
are set to
0.1. N_scaling
adjusts the number of neurons and K_scaling
adjusts
the number of connections to be simulated. The full network can be run by
adjusting these values to 1. If this is done, the option to print the time
progress should be set to False in the file sim_params.py
. For running, use
python example.py
. The output will be saved in the directory data
.
The code can be parallelized using OpenMP and MPI, if NEST has been built with
these applications (Parallel computing with NEST).
The number of threads (per MPI process) can be chosen by adjusting
local_num_threads
in sim_params.py
. The number of MPI processes can be
set by choosing a reasonable value for num_mpi_prc
and then running the
script with the following command.
mpirun -n num_mpi_prc python example.py
The default version of the simulation uses Poissonian input, which is defined
in the file network_params.py
to excite neuronal populations of the
microcircuit. If no Poissonian input is provided, DC input is calculated, which
should approximately compensate the Poissonian input. It is also possible to
add thalamic stimulation to the microcircuit or drive it with constant DC
input. This can be defined in the file stimulus_params.py
.
MUSIC example¶
Requirements¶
MUSIC 1.1.15 or higher
NEST 2.14.0 or higher compiled with MPI and MUSIC
NumPy
Instructions¶
This example runs 2 NEST instances and one receiver instance. Neurons on the NEST instances are observed by the music_cont_out_proxy and their values are forwarded through MUSIC to the receiver.
mpiexec -np 3 music test.music