systemsgenetics / kube-runner Goto Github PK
View Code? Open in Web Editor NEWA tool for running bioinformatics workflows on a Kubernetes cluster
A tool for running bioinformatics workflows on a Kubernetes cluster
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.
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