Submitting Jobs with Slurm

This document provides an introduction to submitting jobs on Texas A&M HPC clusters using Slurm. It covers the basics of writing and submitting job scripts, interactive job submissions, and common Slurm parameters. Additionally, there is a section with example submission scripts for several popular programs.

Job Submission Scripts

A job submission script is a Bash script that declares the resources needed for your job and contains the commands to execute your application. The script typically includes:

• Shebang Line: Specifies the shell to interpret the script.
• SBATCH Directives: Define job options like job name, output/error file locations, and resource requests.
• Commands: Load necessary modules and run your program.

Example Submission Script

#!/bin/bash
#SBATCH --job-name=myappjob
#SBATCH --output=screenout.txt
#SBATCH --error=screenerror.txt
#SBATCH --ntasks=2

module load mpi/openmpi-x86_64
./myprogram

Submitting a Script

Once you have created your submission script (for example, named myscript.job), submit it to the Slurm scheduler using:

sbatch myscript.job

After submission, you will receive a job ID that you can use to monitor the job's progress.

Interactive Job Submissions

Not every job is well-suited for batch submission. For tasks that require interactive input or a graphical interface, you can start an interactive session using srun:

srun --pty /bin/bash

If you need to run GUI applications, include the --x11 flag:

srun --pty --x11 /bin/bash

Slurm Parameters

Below are some common Slurm parameters along with their descriptions and examples:

For a complete list of options, see the Slurm SBATCH documentation.

Tasks versus CPUs

Slurm differentiates between tasks (processes) and CPUs (threads):

• Tasks (--ntasks): Used for multi-process programs (e.g., MPI jobs).
• CPUs per task (--cpus-per-task): Used for multithreaded programs (e.g., MATLAB).

A task cannot span multiple compute nodes; if your job requires multiple CPUs on a single node, use --cpus-per-task.

Examples for Popular Programs

Below are sample job submission scripts for various popular applications:

1. MPI-Based Application

For running an MPI job, use multiple tasks to execute your program in parallel:

#!/bin/bash
#SBATCH --job-name=mpi_job
#SBATCH --output=mpi_output.txt
#SBATCH --error=mpi_error.txt
#SBATCH --ntasks=8

module load mpi/openmpi-x86_64
mpirun ./mpi_application

2. Python Script

For running a Python script that may use multiple processes (for example, via the multiprocessing module):

#!/bin/bash
#SBATCH --job-name=python_job
#SBATCH --output=python_output.txt
#SBATCH --error=python_error.txt
#SBATCH --ntasks=4

module load python/3.8
python my_script.py

3. MATLAB Job

For MATLAB applications that use multithreading, specify the number of CPUs per task:

#!/bin/bash
#SBATCH --job-name=matlab_job
#SBATCH --output=matlab_output.txt
#SBATCH --error=matlab_error.txt
#SBATCH --cpus-per-task=4

module load matlab
matlab -nodisplay -r "run('my_matlab_script.m'); exit"

4. R Script

For submitting an R job:

#!/bin/bash
#SBATCH --job-name=r_job
#SBATCH --output=r_output.txt
#SBATCH --error=r_error.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2

module load R
Rscript my_script.R

Related

• Connecting to HPC Systems
• Arseven cluster (Statistics)
• Orchard cluster (Engineering)