Set up workflow

Last updated on 2024-10-21 | Edit this page

Overview

Questions

  • How to set up Argo Workflow engine?
  • How to submit a test job?
  • Where to find the output?

Objectives

  • Deploy Argo Workflows services to the cluster.
  • Submit a test job.
  • Find the output in your bucket.

Prerequisites

GCP account and project

Make sure that you are in the GCP account and project that you intend to use for this work. In your Linux terminal, type

BASH 

gcloud config list

The output shows your account and project.

Bucket

If you worked through Section 02, you have now a storage bucket for the output files.

List the buckets with

BASH 

gcloud storage ls

Code

In the previous section, you pulled the code and move to the cloud-processing/standard-gke-cluster-gcs-imgdisk directory.

Argo CLI installed?

You should have Argo CLI installed, see Software setup.

Deploy Argo Workflows service

Deploy Argo Workflows services with

BASH 

kubectl apply -n argo  -f https://github.com/argoproj/argo-workflows/releases/download/v3.5.10/install.yaml
kubectl apply -f argo/service_account.yaml
kubectl apply -f argo/argo_role.yaml
kubectl apply -f argo/argo_role_binding.yaml

Wait for the services to start.

You should see the following:

BASH 

$ kubectl get all -n argo
NAME                                       READY   STATUS    RESTARTS   AGE
pod/argo-server-5f7b589d6f-jkf4z           1/1     Running   0          24s
pod/workflow-controller-864c88655d-wsfr8   1/1     Running   0          24s

NAME                  TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)    AGE
service/argo-server   ClusterIP   34.118.233.69   <none>        2746/TCP   25s

NAME                                  READY   UP-TO-DATE   AVAILABLE   AGE
deployment.apps/argo-server           1/1     1            1           24s
deployment.apps/workflow-controller   1/1     1            1           24s

NAME                                             DESIRED   CURRENT   READY   AGE
replicaset.apps/argo-server-5f7b589d6f           1         1         1       24s
replicaset.apps/workflow-controller-864c88655d   1         1         1       24s

About Argo Workflows

The data processing example is defined as an Argo workflow. You can learn about Argo Workflows in their documentation.

Every step in the workflow runs in a container, and there several ways to pass the information between the steps.

The example configuration in argo/argo_bucket_run.yaml has comments to help you to understand how the files and/or parameters can be passed from a step to another.

Submit a test job

The workflow is defined in the argo/argo_bucket_run.yaml file. It is composed of four steps:

  • get-metadata: gets the number of files and the file list for a given CMS Open Data 2016 MiniAOD record
  • joblist: divides the file list into given number of jobs and coumputes the number of events per job (if not all)
  • runpfnano: runs the processing in parallel jobs
  • plot: creates some simple plots.

Edit the parameters in the argo/argo_bucket_run.yaml so that they are

    parameters:
    - name: nEvents
      # Number of events in the dataset to be processed (-1 is all)
      value: 1000
    - name: recid
      # Record id of the dataset to be processed
      value: 30511
    - name: nJobs
      # Number of jobs the processing workflow should be split into
      value: 2
    - name: bucket
      # Name of cloud storage bucket for storing outputs
      value: <YOUR_BUCKET_NAME>

Now submit the workflow with

BASH 

argo submit -n argo argo/argo_bucket_run.yaml

Observe its progress with

BASH 

argo get -n argo @latest

Once done, check the ouput in the bucket with

BASH 

$ gcloud storage ls gs://<YOUR_BUCKET_NAME>/**
gs://<YOUR_BUCKET_NAME>/pfnano/30511/files_30511.txt
gs://<YOUR_BUCKET_NAME>/pfnano/30511/logs/1.logs
gs://<YOUR_BUCKET_NAME>/pfnano/30511/logs/2.logs
gs://<YOUR_BUCKET_NAME>/pfnano/30511/plots/h_num_cands.png
gs://<YOUR_BUCKET_NAME>/pfnano/30511/plots/h_pdgid_cands.png
gs://<YOUR_BUCKET_NAME>/pfnano/30511/scatter/pfnanooutput1.root
gs://<YOUR_BUCKET_NAME>/pfnano/30511/scatter/pfnanooutput2.root

You can copy the files with gcloud storage cp ....

Delete resources

Delete the workflow after each run so that the “pods” do not accumulate. They are not running anymore but still visible.

BASH 

argo delete -n argo @latest

Do not delete the cluster if you plan to continue to the next section, but do not keep it idle. The cost goes by the time it exists, not by the time it is in use. You can always create a new cluster.

You can delete all resources created by the Terraform script with

BASH 

terraform destroy

Confirm with “yes”.

Costs

Cluster

Running the workflow in the cluster does not increase the cost, so for this small test, the estimates in the previous section are valid.

Data download

As detailed in Section 02, downloading data from the storage costs $0.12 / GB. The output file size - and consequently the download cost - for this quick example is small.

Key Points

  • Once the cluster is up, you will first deploy the Argo Workflows services using kubectl.
  • You will submit and monitor the workflow with argo.
  • You can see the output in the bucket with gcloud commands or on Google Cloud Console Web UI.