Job Examples

Owned by sarawillis@arizona.edu
Last updated: Apr 08, 2022
2 min read

For more examples, see our Github page!

Single Serial Job Submission

PBS Script

#!/bin/bash
#PBS -N Sample_PBS_Job
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -l walltime=00:01:00
#PBS -q standard
#PBS -W group_list=<group_name>



cd $PBS_O_WORKDIR
pwd; hostname; date

module load python
python --version

SLURM Script

#!/bin/bash
#SBATCH --job-name=Sample_Slurm_Job
#SBATCH --ntasks=1
#SBATCH --nodes=1              
#SBATCH --mem=1gb                     
#SBATCH --time=00:01:00    
#SBATCH --partition=standard
#SBATCH --account=<group_name>    

# SLURM Inherits your environment. cd $SLURM_SUBMIT_DIR not needed
pwd; hostname; date

module load python/3.6
python3 --version


Array Job

IMPORTANT:

When submitting jobs with named output files (i.e. with the line #SBATCH -o=Job.out) as arrays, SLURM will write every array element to that filename leaving you with only the output of the last completed job in the array. Use one of the following SLURM directives in your script to prevent this behavior:

  1. Differentiates output files using array indices. Similar to PBS default. See SLURM Output Filename Patterns above for more information.

    #SBATCH --output=Job-%a.out

  2. Appends the output from all tasks in an array to the same output file. Warning: if a file exists with that name prior to running your job, the output will be appended to that file

    #SBATCH --open-mode=append

PBS Script

#!/bin/bash
#PBS -N Sample_PBS_Job
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -l walltime=00:01:00
#PBS -q standard
#PBS -W group_list=<group_name>
#PBS -J 1-5



cd $PBS_O_WORKDIR
pwd; hostname; date

echo "./sample_command input_file_${PBS_ARRAY_INDEX}.in"

SLURM Script

#!/bin/bash
#SBATCH --output=Sample_SLURM_Job-%a.out
#SBATCH --ntasks=1
#SBATCH --nodes=1              
#SBATCH --time=00:01:00    
#SBATCH --partition=standard
#SBATCH --account=<group_name>    
#SBATCH --array=1-5

# SLURM Inherits your environment. cd $SLURM_SUBMIT_DIR not needed
pwd; hostname; date

echo "./sample_command input_file_${SLURM_ARRAY_TASK_ID}.in"

MPI Job

PBS Script

#!/bin/bash
#PBS -N Sample_MPI_Job
#PBS -l select=1:ncpus=16:mem=16gb
#PBS -l walltime=00:10:00
#PBS -W group_list=<group_name>
#PBS -q standard






cd $PBS_O_WORKDIR
pwd; hostname; date
module load openmpi   
/usr/bin/time -o mpit_prog.timing mpirun -np 16 a.out

SLURM Script

#!/bin/bash
#SBATCH --job-name=Sample_MPI_Job
#SBATCH --ntasks=16
#SBATCH --ntasks-per-node=16
#SBATCH --nodes=1
#SBATCH --mem-per-cpu=1gb
#SBATCH --time=00:10:00
#SBATCH --account=<group_name>
#SBATCH --partition=standard
#SBATCH --output=Sample_MPI_Job_%A.out
#SBATCH --error=Sample_MPI_Job_%A.err

# SLURM Inherits your environment. cd $SLURM_SUBMIT_DIR not needed
pwd; hostname; date
module load openmpi3
/usr/bin/time -o mpit_prog.timing mpirun -np 16 a.out