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#!/bin/bash
# Add all the required variables here
root_dir="$PWD"
data_dir="$root_dir/test_dir"
jobs_dir="$root_dir/jobs"
jobs_out_dir="$root_dir/job_out"
jobs_err_dir="$root_dir/job_err"
# Make all the required jobs directories
mkdir $jobs_dir
#mkdir $jobs_out_dir
#mkdir $jobs_err_dir
# Start a for loop to run through all the files in $data_dir
for file_name in `ls $data_dir`
do
# Create a slurm script for processing the current file
cat <<EOF >> $jobs_dir/$file_name.job
#!/bin/bash
#
#SBATCH --job-name=processing_$file_name
#SBATCH --output=$jobs_out_dir/$file_name%j.out
#SBATCH --error=$jobs_err_dir/$file_name%j.err
#SBATCH --ntasks=1
#SBATCH --partition=express
# Time format = HH:MM:SS, DD-HH:MM:SS
#SBATCH --time=10:00
# Mimimum memory required per allocated CPU in MegaBytes.
#SBATCH --mem-per-cpu=100
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=$USER@uab.edu
srun echo "Processing file $file_name" >> $data_dir/$file_name
EOF
# Submit the recently create job for this file
sbatch $jobs_dir/$file_name.job
done