OpenEMR on GKE Autopilot — Lab Guide

📖 Configuration Guide

Overview

Estimated time: 45–90 minutes

OpenEMR is the world's most widely adopted open-source Electronic Health Records (EHR) and practice management system, used by healthcare providers across 100+ countries. This lab takes you through the full operational lifecycle of the OpenEMR on GKE Autopilot module on Google Cloud: deploy it, access and verify it, run it day-to-day, observe it, diagnose common problems, and tear it down.

The lab focuses on operating the GKE module and the Google Cloud platform, not on OpenEMR product features. For the complete list of provisioned services and every configuration input (organised by group), see the Configuration Guide — this lab deliberately does not duplicate that detail so it stays accurate over time.

Objectives

By the end of this lab you will be able to:

• Deploy the module from the RAD platform and locate the resources it provisions.
• Connect to the GKE cluster and access the running workload.
• Perform day-2 operations — inspect, scale, update, and manage secrets and storage.
• Observe the workload with Cloud Logging and Cloud Monitoring.
• Diagnose and resolve the most common deployment and runtime issues.
• Tear the deployment down cleanly.

Prerequisites

• Services_GCP deployed in the target project (provides the VPC, GKE Autopilot cluster, Cloud SQL, Artifact Registry, and shared service accounts this module depends on).
• A Google Cloud project with billing enabled.
• gcloud CLI and kubectl installed; gcloud auth login and gcloud auth application-default login completed.
• Project Owner (or equivalent) IAM on the project.
• RAD platform access with permission to deploy modules into the project.

Set these shell variables once; every task below reuses them:

export PROJECT="<your-gcp-project-id>"
export REGION="us-central1"           # the region you deploy into

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Task 1 — Deploy the module [Automated]

1. Click Deploy in the RAD platform top navigation, open OpenEMR (GKE) from the Platform Modules list to start configuration, set project_id, and review the inputs. Configure only what you need — the Configuration Guide documents every input by group, with defaults. Review the estimated cost (if credits are enabled) and click Deploy, which opens the deployment status page with real-time logs.

2. The platform deploys the workload into the GKE Autopilot cluster, provisions a Cloud SQL (MySQL 8.0) database with its Secret Manager secrets, a Filestore NFS share for the sites/ directory, optional Redis for PHP session storage, builds the container image, and runs three one-shot initialisation jobs in sequence: nfs-init (NFS directory setup), db-init (MySQL user and database creation), and openemr-install (schema installation via auto_configure.php). First deploys take roughly 20–40 minutes (Cloud SQL creation and OpenEMR schema installation both contribute).

3. Connect to the cluster and discover the namespace with name-agnostic filters:

   CLUSTER=$(gcloud container clusters list --project="$PROJECT" --format="value(name)" --limit=1)
   gcloud container clusters get-credentials "$CLUSTER" --region="$REGION" --project="$PROJECT"
   
   NS=$(kubectl get ns -o name | grep openemr | head -1 | cut -d/ -f2)
   echo "Cluster: $CLUSTER   Namespace: $NS"
   kubectl get all -n "$NS"

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Task 2 — Access & verify [Manual]

1. Confirm the workload is running and find its external address:

   kubectl get pods,svc -n "$NS"
   EXTERNAL_IP=$(kubectl get svc -n "$NS" \
     -o jsonpath='{.items[?(@.spec.type=="LoadBalancer")].status.loadBalancer.ingress[0].ip}')
   echo "External IP: $EXTERNAL_IP"

   Each OpenEMR pod has two containers (the application and the Cloud SQL Auth Proxy sidecar), so READY shows 2/2 when fully running.

2. Confirm the service is healthy. OpenEMR's liveness probe checks the login page, so HTTP 200 on this path means Apache, PHP-FPM, and the database connection are all operational:

   curl -s -o /dev/null -w "%{http_code}" \
     "http://${EXTERNAL_IP}/interface/login/login.php"
   # expect: 200

   Allow up to 20 minutes after the first deploy for the openemr-install job and schema installer to complete before this check passes.

3. Retrieve the admin password from Secret Manager and sign in at http://${EXTERNAL_IP}/interface/login/login.php (username: admin):

   ADMIN_SECRET=$(gcloud secrets list --project="$PROJECT" \
     --filter="name~openemr.*admin" --format="value(name)" --limit=1)
   gcloud secrets versions access latest --secret="$ADMIN_SECRET" --project="$PROJECT"

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Task 3 — Operate & keep it running (Day-2) [Manual]

1. Inspect the workload — deployment, pods, and (if enabled) the horizontal autoscaler and persistent volumes:

   kubectl get deploy,pods,hpa,pvc -n "$NS"
   kubectl describe deploy -n "$NS"

2. Scale by changing the min/max instance inputs and clicking Update on the deployment details page — the module owns the workload spec, so scaling is a configuration change, not a manual kubectl scale (a manual edit would be reverted on the next apply). Note that increasing replicas above 1 requires Redis session sharing to be operational; session_affinity = ClientIP also pins browsers to one pod.

3. Update the application version by changing the version input via Update on the deployment details page; a new image builds and a rolling update replaces the pods.

4. Manage secrets, storage, and jobs:

   kubectl get secrets -n "$NS"
   gcloud secrets list --project="$PROJECT" --filter="name~openemr"
   kubectl get jobs -n "$NS"          # nfs-init, db-init, openemr-install

5. Open a database session for inspection or maintenance:

   INSTANCE=$(gcloud sql instances list --project="$PROJECT" --format="value(name)" --limit=1)
   gcloud sql connect "$INSTANCE" --user=openemr --project="$PROJECT"

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Task 4 — Observe: Logging & Monitoring [Manual]

1. Logs — from kubectl or the Logs Explorer:

   kubectl logs -n "$NS" deploy/"$(kubectl get deploy -n "$NS" -o jsonpath='{.items[0].metadata.name}')" \
     -c openemr --tail=50

   To inspect the Cloud SQL Auth Proxy sidecar separately:

   kubectl logs -n "$NS" deploy/"$(kubectl get deploy -n "$NS" -o jsonpath='{.items[0].metadata.name}')" \
     -c cloud-sql-proxy --tail=20

   Logs Explorer filter: resource.type="k8s_container" AND resource.labels.namespace_name="<namespace>".

2. Monitoring — open the GKE / Kubernetes dashboards and review pod CPU and memory utilisation, restart counts, and request metrics. The module also provisions an uptime check (when enabled); review Monitoring → Uptime checks and Alerting → Policies.

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Task 5 — Troubleshoot & debug [Manual]

Durable techniques for the failure modes you are most likely to hit. These are platform-level diagnostics and do not change with OpenEMR releases.

• Pod not Ready / CrashLoopBackOff: inspect events and logs. Note that the startup probe is TCP on port 80; a failure here means the port is not open yet — the openemr-install job or schema installer may still be running.

  kubectl describe pod -n "$NS" <pod>        # Events section shows scheduling/probe/mount errors
  kubectl logs -n "$NS" <pod> -c openemr --previous   # logs from the crashed container

• Initialisation jobs failed: inspect each job and its pod logs:

  kubectl get jobs -n "$NS"
  kubectl logs -n "$NS" job/nfs-init
  kubectl logs -n "$NS" job/db-init
  kubectl logs -n "$NS" job/openemr-install

• Database connection errors: confirm the Cloud SQL instance is RUNNABLE, the DB password secret materialised into the namespace, and all three init jobs completed.
• Pending pod / no external IP: check kubectl describe pod events for resource or quota issues, and confirm the LoadBalancer Service has an assigned IP.
• Image pull errors: confirm the image exists in Artifact Registry and the node service account can pull it.

See the Configuration Guide's Configuration Pitfalls section for setting-specific gotchas.

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Task 6 — Tear down [Automated]

On the Deployments page, open the deployment and click the Trash icon (Delete). Delete runs terraform destroy and is irreversible (the deployment record is retained for history). If a deployment is stuck and the RAD platform can no longer manage it (for example after manual changes that conflict with the Terraform state), use Purge instead — it removes the deployment from RAD's records without destroying the cloud resources (it makes RAD forget the project). This removes everything the module created — the Kubernetes workload and namespace, Cloud SQL database, Filestore NFS instance, Secret Manager secrets, GCS buckets, and Artifact Registry images. Resources owned by Services_GCP (the VPC, GKE cluster, shared Cloud SQL, registry) are managed separately and are not removed here.

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Summary

Task	Type	Outcome
1 — Deploy	Automated	Module deploys the GKE workload, Cloud SQL MySQL, NFS, Redis, secrets, and runs nfs-init, db-init, and openemr-install jobs
2 — Access & verify	Manual	Connect to the cluster; login page returns HTTP 200; sign in with admin credentials from Secret Manager
3 — Operate	Manual	Inspect workload, scale, update version, manage secrets/storage, DB access
4 — Observe	Manual	Query Cloud Logging (app + Auth Proxy containers); review Cloud Monitoring metrics and uptime check
5 — Troubleshoot	Manual	Diagnose pod, TCP startup probe, database, three-stage init-job sequence, scheduling, and image-pull issues
6 — Tear down	Automated	Delete (Trash) removes all module resources