Submitting your first job

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.

Command	Description
`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 eRI 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

pwd # Prints working directory

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

Note: #!/bin/bash is expected by Slurm.

Note: if you are a member of multiple accounts you should add the line

#SBATCH --account=<projectcode>

Testing¶

Prior to submitting a large job to the cluster, we recommend running a test job to ensure that your script has no errors and runs as expected.

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

sbatch can 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 <userid>@agresearch.co.nz

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.

Tip

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.

Tip

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.