Open adamltyson opened 7 months ago
For reference, here is the old brainmapper
info:
brainmapper
at the SWCN.B. Before starting to use brainmapper
on the SWC, you should familiarise yourself with the job scheduler system (SLURM).
:::{hint}
This information refers to using brainmapper
for cell detection and registration, but any of the BrainGlobe command-line tools (e.g. training brainmapper
, or running only registration with brainreg) can be used similarly.
:::
On the SWC cluster, no software needs to be installed, as brainmapper
can be loaded with module load brainglobe
.
brainmapper
can be used interactively, by starting an interactive job:
srun -p gpu --gres=gpu:1 -n 20 -t 0-24:00 --pty --mem=120G bash -i
Loading brainmapper
:
module load brainglobe
And then running brainmapper
as per the User guide.
It is recommended to use brainmapper
by using the batch submission system.
This has many advantages:
An example batch script is given below, but it is recommended to familiarise yourself with the batch submission system before trying to optimise brainmapper
.
#!/bin/bash
#SBATCH -p gpu # partition (queue)
#SBATCH -N 1 # number of nodes
#SBATCH --mem 120G # memory pool for all cores
#SBATCH --gres=gpu:1
#SBATCH -n 10
#SBATCH -t 1-0:0 # time (D-HH:MM)
#SBATCH -o brainmapper.out
#SBATCH -e brainmapper.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=youremail@domain.com
cell_file='/path/to/signal/channel'
background_file='path/to/background/channel'
output_dir='/path/to/output/directory'
echo "Loading brainglobe environment"
module load brainglobe
echo "Running brainmapper"
# Just an example. See the user guide for the specific parameters
brainmapper -s $cell_file -b $background_file -o $output_dir -v 5 2 2 --orientation psl
Linked to https://github.com/brainglobe/brainglobe.github.io/issues/130
The HPC module will also need to be updated to BG v1 too.