Questions tagged [nest-simulator]

Questions related to the NEST simulator for large scale spiking neural network simulation with point neuron models. Questions should be relevant to StackOverflow and should be limited to the software aspects of the simulator, not neuroscience.

The NEST simulator is used for large scale spiking neural network simulations with point neuron models. It is one of the most prominent tools in the field of large scale network simulations. It has an SLI and Python interface.

The NEST simulator allows you to create populations of nodes - representing neurons - with a corresponding model and allows you to set parameters for that model on the individual nodes. For each timestep the membrane potential (the output) of each node is calculated based on the mathematical rules described by the model and the parameters set for the node. Nodes can be connected to eachother so that they can receive inputs based on the output value of other nodes.

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How to install nest in Python3 on Ubuntu 18.04

After following the Ubuntu/Debian installation instructions for the Nest simulator I can only import the nest module in python2.x, not python3.x $ python3 Python 3.6.8 (default, Aug 20 2019, 17:12:48) [GCC 8.3.0] on linux Type "help", "copyright",…
Robin De Schepper
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Nest simulator: python says “no module named nest”

After installing the Nest Neural Simulator, I keep getting the following error when trying to run any of the example python files that came in the installation. I've tried re-installing Nest, Python, and using Anaconda, but no go. Python…
alexfigtree
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python says “no module named nest” when it is in the $PATH

import nest gives the 'no module named nest' error when it is in the $PATH, which means that there is a /opt/nest/lib/python2.7/site-packages: in my system $PATH. At this location there is a directory named nest and the structure inside the nest…
Timothy
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How to create a ring network in NEST?

I am trying to develop a simple code in NEST: a network constituted by 10 identical neurons connected between them in order to form a loop. I would like to use arrays to develop this code, but I obtained error messages related to mismatch of…
VDF
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multi-threading problem for NEST simulator

I want to use multi-threading function in NEST simulator (version 2.20.1). However, it gives a warning No multithreading available, using single threading. Can anyone help me to solve it? I install NEST simulator using conda command conda create…
Edward
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How to install NEST's Python module into a specific site-packages directory?

The specific question at hand is: How could I install the nest module of a NEST simulator installation into a specific site-packages directory of for example a pyenv/virtualenv? But a broader explanation on how the Python module is generated and…
Robin De Schepper
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How to set a Connection's synapse type in the NEST simulator?

Following the tutorial for the Python interface to the NEST simulator I have created 2 neuron populations and connected them: import nest ndict = {"I_e": 200.0, "tau_m": 20.0} nest.SetDefaults("iaf_psc_alpha", ndict) neuronpop1 =…
Robin De Schepper
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How to fix ModuleNotFoundError: No module named 'nest' when importing nest in Python?

I've installed pyNN and nest but I can't import it. When I run it in the terminal it works, and the program starts. However, if I try to import inside python: cd ~ python import nest It raises an error Traceback (most recent call last): File…
Arthu83
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ImportError: cannot import name pynestkernel

So I spend last night trying to install nest (and pynest) to use with PyNN, and I am currently stuck. When I try to import nest I get: >>> import nest Traceback (most recent call last): File "", line 1, in File…
Tiagojdferreira
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Error when importing Nest after installing with the Ubuntu PPA

I installed Nest with the Ubuntu PPA on Ubuntu 22.04, and saw no errors during installation. After that, I tried importing nest inside a python shell and received the following error: SLI initialisation file not found at…
Mahmoud Akl
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Issue NEST installation

I am tryng to install the latest NEST version with ananconda (1.11.0) on Ubuntu 20.04.5 but after the installation I cannot import * from nest Specifically I am following the tutorial presented…
lparr
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Disallow mpi4py to interfere with internal handling of mpi by a python API

I am using mpiexec on a cluster to run large-scale simulations using pyNEST (mpiexec -n $N python simulate.py). I export a large number of small files which often tends to exceed my inode quota on the cluster. So, I am trying to reduce the number of…
Ady
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How can I store recorded data from the NEST simulator in a binary format?

I am trying to write spikedetector data into .gdf files in binary format, but I cannot. I am setting the binary param of the spikedetector to True (I checked it using nest.GetStatus) but files are written in ASCII: neurons =…
Robin De Schepper
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How can I check whether the NEST simulator module is MPI aware?

It's easy to overlook the output during the build and install process, so I'd like to know if there is a way in NEST's python module to check for successful MPI integration?
Robin De Schepper
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pynestkernel ImportError: libmpi_cxx.so.20: cannot open shared object file: No such file or directory

When installing NEST 2.18 with: cmake \ -Dwith-mpi=/usr/lib/x86_64-linux-gnu/openmpi \ -Dwith-python=3 \ -DPYTHON_EXECUTABLE=/home/robin/.pyenv/versions/3.8.6/bin/python \ …
Robin De Schepper
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