Quickstart#
Say you have access to a Slurm cluster with apptainer
installed, and you have permission to submit to the batch
partition.
Copy the hello.yaml
file from the examples
directory to your current working directory, then run:
slappt hello.yaml > job.sh
Alternatively, without the configuration file:
slappt --image docker://alpine \
--shell sh \
--partition batch \
--entrypoint "echo 'hello world'" > hello.sh
Your hello.sh
script should now contain:
#!/bin/bash
#SBATCH --job-name=0477f4b9-e119-4354-8384-f50d7a96adad
#SBATCH --output=slappt.0477f4b9-e119-4354-8384-f50d7a96adad.%j.out
#SBATCH --error=slappt.0477f4b9-e119-4354-8384-f50d7a96adad.%j.err
#SBATCH --partition=batch
#SBATCH -c 1
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --time=01:00:00
#SBATCH --mem=1GB
module load apptainer # only if you need, some clusters
apptainer exec docker://alpine sh -c "echo 'hello world'"
If already on the cluster, use the --submit
flag to submit the job directly. (Standard Slurm commands must be available for this to work.) In this case the job ID is shown if submission was successful.
You can provide authentication information to submit the script to remote clusters over SSH. For instance, assuming you have key authentication set up and your key is ~/.ssh/id_rsa
:
slappt ... --host <cluster IP or FQDN> --username <username>
Caveats#
There are a few things to note about the example above.
Shell#
For most image definitions, specifying the shell
is likely not necessary, as the default is bash
. However, for images that don’t have bash
installed (e.g., alphine
only has sh
) a different shell must be selected.
Singularity support#
If your cluster still uses singularity
, pass the --singularity
flag (or set the singularity
key in the configuration file to true
) to substitute singularity
for apptainer
in the command wrapping your workflow entrypoint.
Pre-commands#
Note: if apptainer
or singularity
are not available by default on your cluster’s compute nodes, you may need to add --pre
commands (or a pre
section to the configuration file), for instance --pre "module load apptainer"
, or:
pre:
- module load apptainer