systemsgenetics / kube-runner Goto Github PK

When running nextflow on kubernetes, nextflow should be able to clean up it's worker pods if it terminates. However there seem to be some edge cases where it doesn't clean everything up, and the worker pods persist after the submitter pod has terminated.

I've written some bash code to detect these pods and delete them via kubectl:

PODS=$(kubectl get pods --no-headers | grep 'nf-' | awk '{ print $1 }')

for POD in ${PODS}; do
        RUN_NAME=$(kubectl get pod --output 'jsonpath={.metadata.labels.runName}' ${POD})

        kubectl get pod --no-headers ${RUN_NAME} > /dev/null

        if [[ $? != 0 ]]; then
                kubectl delete pod ${POD}
        fi
done

I think we could add this to kube-clean.sh, but I'm afraid that this code could be pretty destructive if any errors occur with kubectl itself. So I'd like to find a more robust way to determine whether the submitter pod still exists.

Also, we should think about whether this code could be automated, maybe with a CronJob?

When I run related tasks locally with nextflow, using the -n {namespace} parameter has no effect. The created pods are all in the default (default) space. I hope the footsteps can support the namespace parameter.