multi-cluster

Multiple clusters

New feature: The custom cluster status script for a multi-cluster setup is now supported as of Snakemake 7.1.1 (see simple/status-sacct-multi.sh)

Submit jobs to a specific cluster. Edit the Snakefile rule cluster_name to add the name of one or more of your clusters to the resouce clusters (separated by commas). Run sacctmgr --parsable show clusters | cut -d'|' -f1 to view the names of the available clusters.

rule cluster_name:
    output:
        "output/cluster.txt",
    resources:
        clusters="<cluster-name>",

You can also change the default cluster in simple/config.v8+.yaml:

default-resources:
  - clusters=<default-cluster>

The example rule writes the name of the cluster to output/cluster.txt.

# Sumbit the job
snakemake --profile simple/

# Confirm the correct cluster was used
cat output/cluster.txt

Note: The file simple/status-sacct-multi.sh is a symlink to the actual file in extras/