snakemake_lisa

Test repository for running Snakemake on Lisa

The batch system

Node allocation. Quoting from the manual:

This is why on Lisa, allocation happens on a per-node basis. A small disadvantage of this approach is that even if your application only uses a single core, you will pay for all cores in the node as long as it is allocated to your job - but the system is not intended for small computational tasks that only use a single core anyway. It is important to use all cores on a node then.

Writing a job script

Wall clock time

The duration can be specified in minutes, or in the MM:SS, or HH:MM:SS format (as in the example), of on the D-HH:MM:SS. The maximum walltime for CPU jobs is 120 hours (5 days); An example is 1:30:00which would mean 1h30min.

Submitting a job

1. Connect to LISA
2. sbatch my_lisa_job.sh