diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..575587966af51acc564e9910e7d992c5c52a89c4 --- /dev/null +++ b/README.md @@ -0,0 +1,80 @@ +## Identifying our computer + +``` +hostname +``` + +## Our first SLURM job + +``` +srun hostname +``` + +## Exploring our example program + +``` +cd $HOME/embl_swc_hpc/exercises +./hpc_example.py -t 10 -l 100 +``` + +## Running example program on on the cluster + +``` +srun ./hpc_example.py -t 10 -l 100 +``` + +## Running in the background + +``` +srun ./hpc_example.py -t 10 -l 100 & +``` + +## Redirecting output + +``` +srun --output=output.txt ./hpc_example.py -t 20 -l 100 & +``` + +## Creating a larger list + +``` +srun --output=output.txt ./hpc_example.py -t 30 -l 5000000 & +``` + +## Displaying details of our cluster queue + +``` +scontrol show partition +``` + +## Requesting more resources + +``` +srun --mem=250 \ +--output=output.txt \ +./hpc_example.py -t 30 -l 5000000 & +``` + +## Running interactive jobs +``` +srun --pty bash +``` + +## Interactive job with more memory +``` +srun --mem=250 --pty bash +``` + +## Using `sbatch` instead + +``` +sbatch batch_jobs.sh +``` + +## Using job dependencies to build pipelines + +``` +jid=$(sbatch --parsable batch_job.sh) + +sbatch --dependency=afterok:$jid batch_job.sh +``` diff --git a/hpc_slides.pdf b/hpc_slides.pdf new file mode 100644 index 0000000000000000000000000000000000000000..ec73309e1dde666fae7d037e3b9a5490f50fe76f Binary files /dev/null and b/hpc_slides.pdf differ