Neuron

NEURON

NEURON simulation environment is used in classrooms and laboratories around the world for building and using computational models of neurons and networks of neurons. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties.

Important Notes

- If your job is crashing, you may not have requested enough memory with --mem option. Please refer to HPC Resource View for details.
- For better visual experience, please refer to HPC Visual Access.

Installed Versions

All the available versions of Neuron for use can be viewed by issuing the following command. This applies for other applications as well.

module avail neuron

output:

---------------------- /usr/local/share/modulefiles -------------------------

neuron/7.4

The default version is identified by "(default)" behind the module name and can be loaded as:

module load neuron

The other versions of NEURON can be loaded as:

module load neuron/<version>

Running NEURON Jobs

Interactive Job

Request a compute node by typing:

srun --x11 --pty /bin/bash

This will assign you one of the compute nodes.

Load the Neuron module:

module load neuron

Copy the file sthA.hoc below in your home directory. You can also copy all sample files from /usr/local/doc/NEURON/sample and cd to it.

cp -r /usr/local/doc/NEURON/sample .

cp sample

stA.hoc:

create soma

access soma

soma nseg = 1

soma diam = 18.8

soma L = 18.8

soma Ra = 123.0

soma insert hh

objectvar stim

stim = new IClamp(0.5)

stim.del = 100

stim.dur = 100

stim.amp = 0.1

tstop = 300

Run Neuron:

nrngui sthA.hoc

This will open the Menu bar with Menus like File, Edit, Build, Tools etc as shown in Fig below. If an error opening the *.hoc occurs, load the sthA.hoc manually from the File menu (load hoc). Follow the procedure below:

Under the Tools menu, select RunControl. This will generate a simulation window.
Under the graph menu, select Voltage axis. This generates a initial graph.
Click on the Init & Run button on Simulation Window. You will see the voltage being graphed.

Batch Job

SERIAL BATCH JOB:

Submit the serial job:

sbatch job-serial.slurm

output: Neuron_Serial.o<jobid>

NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21

See http://www.neuron.yale.edu/neuron/credits

I am 0 of 1

PARALLEL BATCH JOB:

Submit the parallel job:

sbatch job-parallel.slurm

output: test.o<jobid>

numprocs=12

NEURON -- Release 7.4 (1351:8f462ea7e030) 2015-07-21

See http://www.neuron.yale.edu/neuron/credits

I am 0 of 12

I am 1 of 12

I am 2 of 12

I am 3 of 12

I am 4 of 12

I am 5 of 12

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I am 7 of 12

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Neuron Python

Important Notes:

If you are submitting as a batch job, you need to disable the display by using the command "unset DISPLAY" in your batch script.

Also, if you are running MPI version of python code with "from neuron import h", please add the final line "h.quit()" to initiate a clean shutdown on MPI

Installation

We recommend you to use python virtual environment for which the details are here.

Request a node (visual access with X-Forwarding)

srun --x11 --mem=8gb --pty bash

Load appropriate python module

module swap intel gcc

module load python/3.6.6

Create python virtual environment

python3 -m venv --system-site-packages p3venv

Source virtual environment

source p3venv/bin/activate

Install neuron package

pip3 install --upgrade pip

pip3 install neuron

Run

The example demonstrates interactive mode but batch job submission is recommended.

Execute python command

python3

Import neuron package and continue following the instructions at Scripting Neuron Python Basics and we can plot the simulation results using matplotlib (see Fig. 1)

>>> import neuron

...

Fig. 1 Plotting the neuron simulation result using matplotlib package

References:

Neuron website: http://www.neuron.yale.edu/neuron/
Neuron tutorial: http://www.neuron.yale.edu/neuron/docs
Getting started: http://www.neuron.yale.edu/neuron/static/docs/gettingstarted.html
Neuron Python Home: https://nrn.readthedocs.io/en/latest/install/install.html
Neuron Python Basic Tutorial: https://neuronsimulator.github.io/nrn/tutorials/scripting-neuron-basics.html