Full example of the sbatch command

Random

Open a script file with any text editor (but not Word)

For beginners, we suggest to use nano, which has restricted functionalities but is quite intuitive.

nano slurm_random.sh

Copy/Paste the following script which is writing 10 000 random numbers in a file and then sort them :

#!/bin/bash
#
#SBATCH -p fast                      # partition
#SBATCH -N 1                         # nombre de nœuds
#SBATCH -n 1                         # nombre de cœurs
#SBATCH --mem 100                    # mémoire vive pour l'ensemble des cœurs
#SBATCH -t 0-2:00                    # durée maximum du travail (D-HH:MM)
#SBATCH -o slurm.%N.%j.out           # STDOUT
#SBATCH -e slurm.%N.%j.err           # STDERR

for i in {1..10000}; do
  echo $RANDOM >> SomeRandomNumbers.txt
done

sort -n SomeRandomNumbers.txt > SomeRandomNumbers_sorted.txt

Press Ctrl-x to exit nano, then "Y" when nano asks you whether the modified buffer should be saved, then press the "Enter" key to confirm the file name.

Check the content of the script

cat slurm_random.sh

Submit the job

sbatch slurm_random.sh

Check the result

Since this script is running a very basic task, the results should promptly be available.

Check the output files with ls and head.

Note: these commands can be run on the login node since they are consuming very little computing resources.

# List the result files
ls -l SomeRandomNumbers*.txt

# Print the 20 first lines of the original random numbers
head -n 20 SomeRandomNumbers.txt

# Print the 20 first lines of the sorted random numbers
head -n 20 SomeRandomNumbers_sorted.txt

# Print the 20 last lines of the sorted random numbers
tail -n 20 SomeRandomNumbers_sorted.txt

Salmon

Open a script file with any text editor (but not Word)

nano slurm_salmon.sh

Set the slurm parameters, the [conda] environment and the command itself

#!/bin/bash
#
#SBATCH -o slurm.%N.%j.out
#SBATCH -e slurm.%N.%j.err
#SBATCH --mail-type END
#SBATCH --mail-user foo.bar@france-bioinformatique.fr
#
#SBATCH --partition fast
#SBATCH --cpus-per-task 6
#SBATCH --mem 5GB

module load salmon

salmon quant --threads $SLURM_CPUS_PER_TASK -i transcripts_index -l A -1 reads1.fq -2 reads2.fq -o transcripts_quant

Submit the job

sbatch slurm_salmon.sh