Assign kubernetes node labels to rules

[cademirch]

Is your feature request related to a problem? Please describe.
It appears that when using the Kubernetes executor, the resource specification of machine_type is not respected. This is not nice when you want rules to use certain compute instances.

For example, in GKE I have node-pool-A with high-cpu machines for BWA-mem, and node-pool-B with smaller machines for GATK HaplotypeCaller. Because the BWA-mem rule requests more CPUs than the node-pool-B can provide, Kubernetes scales up node-pool-A and puts the pod there. However, when running the GATK rule, which requests only one CPU, Kubernetes can place the pod in either node-pool, which leads to an inefficient allocation of resources.

Describe the solution you'd like
Snakemake respect the machine_type resource specification.

Describe alternatives you've considered
It seems that the Kubernetes Python API does not have a direct way to specify a machine type when creating a pod (that I could find). However, using a nodeSelector, one could apply a node label to a node pool, and that node label could be used when creating a pod so that it will end up on the corresponding node.

Additional context
Add any other context or screenshots about the feature request here.

• Kubernetes Python client PodSpec documentation

The solution I propose is to add a check for a resource called node_label somewhere here, and if it exists pass it to the V1PodSpec call.

I'm going to try and implement this solution this weekend, but would appreciate any feedback.

[draeath]

I would also be interested in support for defining nodeSelectors.

For example, my k8s cluster is a mixed ARM64 and AMD64 cluster with autoscaling. I need snakemake to be able to tell kubernetes to require beta.kubernetes.io/arch: amd64

[cademirch]

I would also be interested in support for defining nodeSelectors.

For example, my k8s cluster is a mixed ARM64 and AMD64 cluster with autoscaling. I need snakemake to be able to tell kubernetes to require beta.kubernetes.io/arch: amd64

#1291 Adds support for machine_type using the "node.kubernetes.io/instance-type" selector. I think it should be simple to add support for a resource node_selector to allow user specifed nodeSelectors.

[cademirch]

Closed with #1291