Unable to remove a "Sizelimit" property using kustomize

Question

I have sizeLimit property under emptyDir set to 2Gi in my template base file. I want to remove the sizelimit and just have emptyDir: {}. I've been unable to achieve this using Kustomization overlays. I will detail my folder structure and kustomization yamls below.

Folder Structure:

application
├── majorbase
│   ├── kustomization.yaml
│   └── resources
│       └── web-template.yaml
├── minorbase
│   ├── kustomization.yaml
│   └── resources
└── myoverlays
    ├── kustomization.yaml
    └── resources
        └── my-new-web.yaml

The folder myoverlays contains the following contents in it's kustomization.yaml file

bases:
- ../minorbase
patchesStrategicMerge:
- resources/my-new-web.yaml

The folder minorbase contains the following contents in it's kustomization.yaml file

bases:
- ../majorbase

The folder majorbase contains the following contents in it's kustomization.yaml file

resources:
- resources/web-template.yaml

The section I want to edit looks like this in the majorbase/template.

volumes:
      - name: test-vol
        emptyDir:
          sizeLimit: "2Gi"

The above configuration needs to be updated using overlays as below.

volumes:
      - name: test-vol
        emptyDir: {}

This is where my problem lies. Kustomization just picks the 2Gi value mentioned in the base whenever I remove the sizelimit in my overlays. When I mention different value to sizeLimit such as "1Gi" in my overlays file, kustomization is picking up the change. What is the cause of this behaviour? Is it possible to achieve what I'm trying to do here?

Answer 1

NB: This answer assumes a recent version of Kustomize (I'm running 4.5.2 locally). Your examples are using deprecated syntax (the bases section was deprecated in version 2.1.0, for example).

---

Your problem is that you're using a strategicMerge patch, and you're merging and empty map ({}) with {"sizeLimit": "26gi"}. If you merge an empty map with anything, it's a no-op: you end up with the "anything".

To explicitly delete an element, you have a few choices.

You can use the $patch: replace directive (you can find an example of that here) to have Kustomize replace the emptyDir element, rather than merging the contents. That would look like:

apiVersion: v1
kind: Pod
metadata:
  name: example
spec:
  volumes:
    - name: test-vol
      emptyDir:
        $patch: replace

The corresponding kustomization.yaml might look something like:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - ../../base

patches:
  - path: resources/my-new-web.yaml

---

Alternately, you can use a JSONPatch patch, which is good for explicitly deleting fields:

- path: /spec/volumes/0/emptyDir/sizeLimit
  op: remove

Where kustomization.yaml would look like:

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
resources:
  - ....//base

patches:
  - target:
      kind: Pod
      name: example
    path: resources/my-new-web.yaml

---

You can find a complete runnable demonstration of this here.