Sdk tests with papermill #2448

yehudit1987 · 2024-10-27T10:51:42Z

What this PR does / why we need it:
This PR creates E2E tests for katib examples to run with papermill.

Which issue(s) this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close the issue(s) when PR gets merged):
Fixes #2417

Checklist:

Docs included if any changes are user facing

Signed-off-by: Yehudit Kerido <[email protected]>

review-notebook-app · 2024-10-27T10:51:47Z

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Electronic-Waste · 2024-10-28T02:57:15Z

/rerun-all

Electronic-Waste · 2024-10-28T06:22:56Z

@yehudit1987 Can you please fix these CI errors?

Electronic-Waste · 2024-10-29T12:07:12Z

@yehudit1987 Can you sign your commits with git commit -s? The DCO checks failed due to this reason.

Electronic-Waste · 2024-10-29T12:08:26Z

FYI, you can check this reference: https://github.com/kubeflow/katib/pull/2448/checks?check_run_id=32215445282

Signed-off-by: Yehudit Kerido <[email protected]>

… trigger it Signed-off-by: Yehudit Kerido <[email protected]>

… trigger it 2 Signed-off-by: Yehudit Kerido <[email protected]>

Signed-off-by: Yehudit Kerido <[email protected]>

Electronic-Waste · 2024-10-31T05:13:54Z

/rerun-all

Signed-off-by: Yehudit Kerido <[email protected]>

Electronic-Waste

Sorry for the late response @yehudit1987. I left a few comments for you.

And I'm busy with my works now. I'll give reviews on Notebooks later:)

Electronic-Waste · 2024-11-05T08:15:44Z

test/e2e/v1beta1/scripts/gh-actions/setup-minikube.sh

+if [ -x "$(command -v apt-get)" ]; then
+  echo "Upgrading Podman using apt-get..."
+  sudo apt-get update
+  sudo apt-get install -y podman
+elif [ -x "$(command -v dnf)" ]; then
+  echo "Upgrading Podman using dnf..."
+  sudo dnf upgrade podman -y
+else
+  echo "Package manager not found. Skipping upgrade."
+fi


Could you please tell me why we need to use podman?

Electronic-Waste · 2024-11-05T08:16:55Z

.github/workflows/template-notebook-test/action.yaml

It will be better to change the dir name from template-notebook-test to template-e2e-notebook-test to be consistent with other dirs:)

Electronic-Waste · 2024-11-05T08:38:14Z

/rerun-all

Signed-off-by: Yehudit Kerido <[email protected]>

Electronic-Waste · 2024-11-06T07:46:30Z

/rerun-all

Electronic-Waste

Sorry for the late review @yehudit1987. I was very busy recently.

I left some comments for you. Thanks for your great contributions!

Electronic-Waste · 2024-11-14T03:34:29Z

examples/v1beta1/sdk/cmaes-and-resume-policies.ipynb

+    "from kubernetes import client, config\n",
+    "\n",
+    "# Initialize KatibClient\n",
+    "kclient = KatibClient(namespace=namespace)\n",
+    "\n",
+    "# Load kubeconfig\n",
+    "config.load_kube_config()\n",
+    "\n",
+    "# Kubernetes API for managing namespaces\n",
+    "core_v1_api = client.CoreV1Api()\n",
+    "\n",
+    "# Function to add label to namespace if it doesn't have the required one\n",
+    "def add_katib_label_to_namespace(namespace):\n",
+    "    ns = core_v1_api.read_namespace(namespace)\n",
+    "    labels = ns.metadata.labels or {}\n",
+    "    if labels.get(\"katib.kubeflow.org/metrics-collector-injection\") != \"enabled\":\n",
+    "        print(f\"Adding label to namespace {namespace}...\")\n",
+    "        labels[\"katib.kubeflow.org/metrics-collector-injection\"] = \"enabled\"\n",
+    "        body = {\"metadata\": {\"labels\": labels}}\n",
+    "        core_v1_api.patch_namespace(namespace, body)\n",
+    "        print(f\"Label added to namespace {namespace}.\")\n",
+    "    else:\n",
+    "        print(f\"Namespace {namespace} already has the required label.\")\n",
+    "\n",
+    "# Add the required label to the namespace\n",
+    "add_katib_label_to_namespace(namespace)\n",


Why do we need to add these lines?

Electronic-Waste · 2024-11-14T03:37:32Z

.github/workflows/template-e2e-notebook-test/action.yaml

+  papermill-args-yaml:
+    description: 'Additional arguments to pass to Papermill in yaml format'
+    required: false
+    default: ""


It seems that we didn't pass parameters to these two notebook examples. Not sure if it meets our requirements

cc👀 @andreyvelich @tenzen-y @yehudit1987

Electronic-Waste · 2024-11-14T14:41:40Z

test/e2e/v1beta1/scripts/gh-actions/setup-katib.sh

@@ -65,10 +65,12 @@ echo "Deploying Katib"
 cd ../../../../../ && WITH_DATABASE_TYPE=$WITH_DATABASE_TYPE make deploy && cd -

 # Wait until all Katib pods is running.
-TIMEOUT=120s
+TIMEOUT=180s


Why do we need to change TIMEOUT to 180s?

Electronic-Waste · 2024-11-14T14:42:46Z

test/e2e/v1beta1/scripts/gh-actions/setup-katib.sh

-kubectl wait --for=condition=ContainersReady=True --timeout=${TIMEOUT} -l "katib.kubeflow.org/component in ($WITH_DATABASE_TYPE,controller,db-manager,ui)" -n kubeflow pod ||
-  (kubectl get pods -n kubeflow && kubectl describe pods -n kubeflow && exit 1)
+echo "Waiting for pods to be ready for $TIMEOUT seconds..."
+sleep $TIMEOUT


Is it necessary since we already have kubectl wait instruction? Please let me know your thought.

Electronic-Waste · 2024-11-14T14:43:41Z

test/e2e/v1beta1/scripts/gh-actions/setup-katib.sh

+if ! kubectl get namespaces | grep -q "kubeflow-user-example-com"; then
+  kubectl create namespace kubeflow-user-example-com
+fi
+


Maybe we can use default namespace instead of creating a new one:)

Electronic-Waste · 2024-11-14T14:54:12Z

.github/workflows/template-e2e-notebook-test/action.yaml

+    - name: Install dependencies
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install papermill kubeflow-katib jupyter ipykernel
+        python -m ipykernel install --user --name python3 --display-name "Python 3"
+
+    - name: Setup Minikube Cluster
+      shell: bash
+      run: ./test/e2e/v1beta1/scripts/gh-actions/setup-minikube.sh true true "" "" "cmaes"


Don't we need to create minikube cluster between these two steps?

katib/.github/workflows/template-setup-e2e-test/action.yaml

Lines 39 to 48 in 2b41ae6

- name: Setup Minikube Cluster

uses: medyagh/[email protected]

with:

network-plugin: cni

cni: flannel

driver: none

kubernetes-version: ${{ inputs.kubernetes-version }}

minikube-version: 1.31.1

start-args: --wait-timeout=120s

Electronic-Waste · 2024-11-14T14:55:58Z

test/e2e/v1beta1/scripts/gh-actions/setup-minikube.sh

+function check_minikube() {
+  if minikube status >/dev/null 2>&1; then
+    echo "Minikube is already running."
+  else
+    echo "Minikube is not running. Starting Minikube..."
+    minikube start
+  fi
+}
+
+echo "Checking Minikube Kubernetes Cluster"
+check_minikube


I guess, we do not check the status of minikube cluster here.

Electronic-Waste · 2024-11-14T14:57:08Z

examples/v1beta1/sdk/tune-train-from-func.ipynb

It'll be better if you do not delete the original content.

And I think it's necessary to rewrite this example since TFJobClient() is outdated in the newest SDK in training-operator. WDYT👀 @kubeflow/wg-automl-leads

I didn't apply to many changes to that notebook beside as you mentioned replacing the TFJobClient with TrainingClient and specifying the job type. For some reason it looks like I rewrite the whole example. Anyway I fixed the "corrupted" notebook. Also I fixed the other issues you pointed at.

Regarding default namespace, it failed to create experiments without specifying the namespace.

Thanks @yehudit1987!

I know some code lines were generated by pycharm or vscode. The "original content" I meant is some output and images in the notebook, not those code lines.

As for the namespace, could we specify default namespace for the experiment like namespace=default? And it will be better if we could specify namespace for papermill like: kubeflow/training-operator#2274 .

Signed-off-by: Yehudit Kerido <[email protected]>

Electronic-Waste

A lot of effort @yehudit1987 ! Thanks for your contribution.

I left some comments for you. cc👀 @kubeflow/wg-automl-leads

Electronic-Waste · 2024-11-19T09:55:41Z

examples/v1beta1/kubeflow-pipelines/kubeflow-e2e-mnist.ipynb

@@ -671,4 +671,4 @@
 },
 "nbformat": 4,
 "nbformat_minor": 4
-}
+}


Suggested change

}

}

Electronic-Waste · 2024-11-19T09:56:56Z

test/e2e/v1beta1/scripts/gh-actions/setup-katib.sh

-kubectl wait --for=condition=ContainersReady=True --timeout=${TIMEOUT} -l "katib.kubeflow.org/component in ($WITH_DATABASE_TYPE,controller,db-manager,ui)" -n kubeflow pod ||
-  (kubectl get pods -n kubeflow && kubectl describe pods -n kubeflow && exit 1)
+kubectl wait --for=condition=ContainersReady=True --timeout=${TIMEOUT} -l "katib.kubeflow.org/component in ($WITH_DATABASE_TYPE,controller,db-manager,ui)" -n kubeflow pod || (kubectl get pods -n kubeflow && kubectl describe pods -n kubeflow && exit 1)


I think it would be better if we could adjust the format of this line.

(Recover its original state)

Electronic-Waste · 2024-11-19T10:01:23Z

examples/v1beta1/sdk/cmaes-and-resume-policies.ipynb

+   "metadata": {
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
   "outputs": [],
   "source": [
    "# Experiment name and namespace.\n",
-    "namespace = \"kubeflow-user-example-com\"\n",
+    "namespace = \"kubeflow\"\n",
    "experiment_name = \"cmaes-example\"\n",
    "\n",
    "metadata = V1ObjectMeta(\n",


Can we add parameters tag in metadata and allow args in papermill rewrite them like: kubeflow/training-operator#2274?

Electronic-Waste · 2024-11-19T10:02:28Z

examples/v1beta1/sdk/tune-train-from-func.ipynb

@@ -314,7 +342,8 @@
    "\n",
    "# Start the Katib Experiment.\n",
    "exp_name = \"tune-mnist\"\n",
-    "katib_client = katib.KatibClient()\n",
+    "namespace=\"kubeflow\"\n",


Electronic-Waste · 2024-11-19T10:06:11Z

examples/v1beta1/sdk/tune-train-from-func.ipynb

+    "import time\n",
+    "time.sleep(120)\n",
+    "status = katib_client.is_experiment_succeeded(exp_name, namespace=namespace)\n",


Can we replace fixed-time sleep with wait_for_experiment_condition()?

katib/sdk/python/v1beta1/kubeflow/katib/api/katib_client.py

Lines 1002 to 1010 in 2b41ae6

def wait_for_experiment_condition(

self,

name: str,

namespace: Optional[str] = None,

expected_condition: str = constants.EXPERIMENT_CONDITION_SUCCEEDED,

timeout: int = 600,

polling_interval: int = 15,

apiserver_timeout: int = constants.DEFAULT_TIMEOUT,

):

Electronic-Waste · 2024-11-19T10:09:33Z

/rerun-all

Yehudit Kerido added 5 commits October 27, 2024 12:49

Running 2 experiments

79a27bd

Signed-off-by: Yehudit Kerido <[email protected]>

Using action.yaml

0b44b8f

Signed-off-by: Yehudit Kerido <[email protected]>

Using action.yaml - fix relative paths

6237428

Signed-off-by: Yehudit Kerido <[email protected]>

Using action.yaml - fix relative paths2

113d8dd

Signed-off-by: Yehudit Kerido <[email protected]>

Final test

cc17690

Signed-off-by: Yehudit Kerido <[email protected]>

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Yehudit Kerido added 10 commits October 29, 2024 21:29

Add other build step to flow

e074c65

Signed-off-by: Yehudit Kerido <[email protected]>

Revert setup-minikube script and add debug step for mnist workflow to…

4fb0f37

… trigger it Signed-off-by: Yehudit Kerido <[email protected]>

Revert setup-minikube script and add debug step for mnist workflow to…

ffa1c59

… trigger it 2 Signed-off-by: Yehudit Kerido <[email protected]>

Add condition for mnist to run.

fedcf05

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Fix ci issues

b7fa3ca

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Fix ci issues

9560840

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Fix ci issues

d69a29f

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Fix CI issues

abadb73

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Fix CI issues

885ba39

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Fix CI issues

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yehudit1987 force-pushed the sdk-tests-with-papermill branch from 963d367 to 6633aa5 Compare October 29, 2024 19:29

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Sdk tests with papermill #2448

Sdk tests with papermill #2448

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	- name: Setup Minikube Cluster
	uses: medyagh/[email protected]
	with:
	network-plugin: cni
	cni: flannel
	driver: none
	kubernetes-version: ${{ inputs.kubernetes-version }}
	minikube-version: 1.31.1
	start-args: --wait-timeout=120s

	def wait_for_experiment_condition(
	self,
	name: str,
	namespace: Optional[str] = None,
	expected_condition: str = constants.EXPERIMENT_CONDITION_SUCCEEDED,
	timeout: int = 600,
	polling_interval: int = 15,
	apiserver_timeout: int = constants.DEFAULT_TIMEOUT,
	):

Sdk tests with papermill #2448

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Sdk tests with papermill #2448

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