Submitting your first job

Last updated 28 June 2023 00:45

Environment Modules

Modules are a convenient way to provide access to applications on the cluster. They prepare the environment you need to run an application.

For a full list of module commands run man module

`module spider [ <string> ]`	List all modules whose names, including version strings, contain `<string>`. If the `<string>` argument is not supplied, list all available modules. (only on Mahuika)
`module show <string>`	Show the contents of the module given by `<string>`. If only the module name (e.g. `Python`) is given, show the default module of that name. If both name and version are given, show that particular version module.
`module load <string>`	Load the module (name and version) given by `<string>`. If no version is given, load the default version.
`module list [ <string> ]`	List all currently loaded modules whose names, including version strings, contain `<string>`. If the `<string>` argument is not supplied, list all currently loaded modules.

Slurm

Jobs on Mahuika and Māui are submitted in the form of a batch script containing the code you want to run and a header of information needed by our job scheduler Slurm.

Creating a batch script

Create a new file and open it with nano myjob.sl

#!/bin/bash -e
#SBATCH --job-name=SerialJob # job name (shows up in the queue)
#SBATCH --time=00:01:00      # Walltime (HH:MM:SS)
#SBATCH --mem=512MB          # Memory in MB
#SBATCH --qos=debug          # debug QOS for high priority job tests

pwd # Prints working directory

Copy in the above text and save and exit the text editor with 'ctrl + x'.

Note:#!/bin/bashis expected by Slurm

Note: if you are a member of multiple accounts you should add the line #SBATCH --account=<projectcode>

Testing

We recommend testing your job using the debug Quality of Service (QOS). The debug QOS can be gained by adding the sbatch command line option --qos=debug.
This adds 5000 to the job priority so raises it above all non-debug jobs, but is limited to one small job per user at a time: no more than 15 minutes and no more than 2 nodes.

Warning

Please do not run your code on the login node. Any processes running on the login node for long periods of time or using large numbers of CPUs will be terminated.

Submitting

Jobs are submitted to the scheduler using:

sbatch myjob.sl

You should receive an output

Submitted batch job 1748836

sbatchcan take command line arguments similar to those used in the shell script through SBATCH pragmas

You can find more details on its use on the Slurm Documentation

Job Queue

The currently queued jobs can be checked using

squeue

You can filter to just your jobs by adding the flag

squeue -u usr9999

You can also filter to just your jobs using

squeue --me

You can find more details on its use on the Slurm Documentation

You can check all jobs submitted by you in the past day using:

sacct

Or since a specified date using:

sacct -S YYYY-MM-DD

Each job will show as multiple lines, one line for the parent job and then additional lines for each job step.

Tips

sacct -X Only show parent processes.

sacct --state=PENDING/RUNNING/FAILED/CANCELLED/TIMEOUT Filter jobs by state.

You can find more details on its use on the Slurm Documentation

Cancelling

scancel <jobid> will cancel the job described by <jobid>. You can obtain the job ID by using sacct or squeue.

Tips

scancel -u [username] Kill all jobs submitted by you.

scancel {[n1]..[n2]} Kill all jobs with an id between [n1] and [n2]

You can find more details on its use on the Slurm Documentation

Job Output

When the job completes, or in some cases earlier, two files will be added to the directory in which you were working when you submitted the job:

slurm-[jobid].out containing standard output.

slurm-[jobid].err containing standard error.