Sbatch script template

A job refers to a specific resource allocation by slum, the specifics are definied by the users and what runs in the job also. Running a job can be in one line if simple enough, for example requesting interactive session on a compute node with 8GB RAM, 1 core on 1 node for 30minutes can be done like so,

salloc --nodes=1 --ntasks-per-node=1 --mem=8G --time=00:30:00 -p short

In other use cases, it is better to define a slurm batch script, below is a script prototype.

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#!/bin/bash

# Example sbatch script
# Job name
#SBATCH -J test

# Name of standard log file (%j expands to jobId)
#SBATCH -o /work/<<USERNAME>>/job.%j.out

# Name of error file (%j expands to jobId)
#SBATCH -e /work/<<USERNAME>>/job.%j.err

#SBATCH --nodes=1

# Total number of threads requested or total number of mpi tasks
#SBATCH -n 16

# Maximum amount of memory in Mb the job can use
#SBATCH --mem=2000

# Run time ([d-]hh:mm:ss) 
#SBATCH -t 00:30:00                                                   
#SBATCH --mail-type=ALL

# Will send you email notification everytime the status of your job changes
#SBATCH --mail-user=your.email@wur.nl

# Load your software/command
module load CMD/version

# Run your command
CMD [OPTIONS] INPUTS

to submit the job to slurm use the command below, let's assume the sbatch script file is called, my_job.sbatch

sbtach my_job.sbatch

Obviously, the above script will not work if run. It is a simple template to highlight the different parts of a batch script.

Find and load software

The bioinformatics software are not directly installed on the machines but in a separate environment where they can be shared accross all machines. To use them users have to first load them, this is true for interactive or non-interactive jobs.

Use the command module for any software/tools operations.

• To check which programs are loaded (ready to be used), use the command below.

module list

• To check which software are available run the command,

module avail

• To search for a module,

module avail <<keyword>>
#OR
module spider <<keyword>>

• To load a module do,

module load <<MODULENAME/VERSION>>

Complementary module commands

module unload [module_name/version]

module switch

module purge