Kilosort is a state-of-the-art neural signal processing algorithm designed for the analysis of large-scale neural recordings. It excels in sorting spikes in high-density multielectrode array recordings, making it an essential tool for neuroscientists.

References:

• Pachitariu, M., Sridhar, S., Pennington, J., & Stringer, C. Spike sorting with Kilosort4.Nature methods.2024 Journal

• kilosort Github:Github

• Module Name: kilosort (see the modules page for more information)
• The kilosort command lines could be run as:

  	python-kilosort -h
  	

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=gpu:p100:1 --mem=8g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load kilosort
[user@cn3144 ~]$ mkdir /data/$USER/kilosort_test/
[user@cn3144 ~]$ cd /data/$USER/kilosort_test/
[user@cn3144 ~]$ python-kilosort -c "from kilosort import io"

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Open kilosort-gui inside of NoMachine:

[user@biowulf]$ sinteractive --gres=gpu:p100:1 --mem=8g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load kilosort
[user@cn3144 ~]$ kilosort-gui

Create a batch input file (e.g. kilosort.sh). For example:

#!/bin/bash
set -e
module load kilosort
python-kilosort xxx

Submit this job using the Slurm sbatch command.

sbatch --partition=gpu --gres=gpu:p100:1 --mem=8g kilosort.sh

Create a swarmfile (e.g. kilosort.swarm). For example:

python-kilosort xxx
python-kilosort xxx

Submit this job using the swarm command.

swarm -f kilosort.swarm [-t #] [-g #] --partition=gpu --gres=gpu:p100:1 --module kilosort