interact -p RM-shared -N 1 --ntasks-per-node=10 -t 03:00:00

squeue --me

tail -f my_out_file.log

scancel --me

# Singularity cache
export SINGULARITY_CACHEDIR=$PROJECT/.singularity/cache
export SINGULARITY_LOCALCACHEDIR=$PROJECT/.singularity/tmp
export SINGULARITY_TMPDIR=$LOCAL

export APPTAINER_CACHEDIR=$SINGULARITY_CACHEDIR
export APPTAINER_LOCALCACHEDIR=$SINGULARITY_LOCALCACHEDIR
export APPTAINER_TMPDIR=$SINGULARITY_TMPDIR

singularity build $PROJECT/images/nightly.sif docker://ghcr.io/fcp-indi/c-pac:nightly

module load anaconda3/2022.10
conda create -n myenvironment python=3.11
conda activate myenvironment

pip uninstall -y clmunch && sleep 2 && pip install git+https://github.com/childmindresearch/cpac-log-muncher

#!/usr/bin/bash
#SBATCH --job-name my_job_name
#SBATCH --output my_job_out.log
#SBATCH --nodes 1
#SBATCH --partition RM-shared
#SBATCH --time 48:00:00
#SBATCH --ntasks-per-node 16

set -x

cd /my/job/folder

singularity run --cleanenv \
-B "$PROJECT"/input:"$PROJECT"/input:ro \
-B "$PROJECT"/output:"$PROJECT"/output \
"$PROJECT"/images/nightly.sif \
"$PROJECT"/input \
"$PROJECT"/output \
participant \
--skip_bids_validator \
--n_cpus 15 \
--mem_gb 31.0 \
--participant_label sub-123 \
--preconfig abcd-options \
--save_working_dir "$PROJECT"/my/job/folder 

-B {cpac_dir}/CPAC:/code/CPAC \
-B {cpac_dir}/dev/docker_data/run.py:/code/run.py \
-B {cpac_dir}/dev/docker_data:/cpac_resources \