slurm_runner.sh

#!/bin/bash
#SBATCH --job-name=decoding  # Name this job
#SBATCH --output=slurm_%u_%x_%j_stdout.log          # Name of log for STDOUT & STDERR
#SBATCH --ntasks=27
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=4G
#SBATCH --verbose                                   # Be verbose wherever possible
#SBATCH --time=72:00:00                             # Request resources for 24 hours
#SBATCH --mail-type=end,fail                        # Email on job completion / failure
#SBATCH --constraint=maxfilter
# Set up environment
WORKDIR="/home/fm02/MEG_NEOS/NEOS"

# Path to script

# SCRIPT3="snr_compare_componentselection_ica_oveweighted_onsets_withplots.py"
# SCRIPT="snr_compare_componentselection_ica_oveweighted_withplots.py"
# SCRIPT2="snr_compare_componentselection_ica_NOoveweight_withplots.py"

# SCRIPT="NEOS_rois_predictability_coherence.py"

# SCRIPT="NEOS_MorphStcsFsaverage.py"

SCRIPT="NEOS_fromstarttofinish.py"

# SCRIPT="prep_data_unfold.py"
# SCRIPT="snr_radarplot_component_selection.py"
# SCRIPT2="snr_radarplot_filt_ovr_both.py"

# SCRIPT="NEOS_evokedasfactors.py"

# SCRIPT="NEOS_MorphStcsFsaverage.py"

# Make folders for logging
LOGDIR="/home/fm02/Desktop/MEG_EOS_scripts/sbatch_out"
mkdir -p "$LOGDIR/tasks"

# Activate conda environment (or some other module that manages environment)
conda activate mne1.2.1_0

echo "JOB $SLURM_JOB_ID STARTING"

# Loop over range of arguments to script
array=(1 2 3 5 6 8 9 10 11 12 13 14 15 16 17 18 19 
           21 22 23 24 25 26 27 28 29 30)

for i in "${array[@]}"
# for i in {1..30}
do
    echo "TASK $i STARTING"

    # Run task on node
    srun --ntasks=1 \
        --output="$LOGDIR/tasks/slurm_%u_%x_%A_%a_%N_stdout_task_$i.log" \
        --exclusive "python" $SCRIPT $i &
    
    echo "TASK $i PUSHED TO BACKGROUND"
done

# # Wait till everything has run
wait

# for i in "${array[@]}"
# # for i in {1..30}
# do
#     echo "TASK $i STARTING"

#     # Run task on node
#     srun --ntasks=1 \
#         --output="$LOGDIR/tasks/slurm_%u_%x_%A_%a_%N_stdout_task_$i.log" \
#         --exclusive "python" $SCRIPT2 $i &
    
#     echo "TASK $i PUSHED TO BACKGROUND"
# done

# # Wait till everything has run
# wait

# for i in "${array[@]}"
# # for i in {1..30}
# do
#     echo "TASK $i STARTING"

#     # Run task on node
#     srun --ntasks=1 \
#         --output="$LOGDIR/tasks/slurm_%u_%x_%A_%a_%N_stdout_task_$i.log" \
#         --exclusive "python" $SCRIPT3 $i &
    
#     echo "TASK $i PUSHED TO BACKGROUND"
# done

# # Wait till everything has run
# wait

echo "JOB $SLURM_JOB_ID COMPLETED"