Gen3 now offers the option to use OpenShift instead of plain Kubernetes
We are excited to share that Gen3 now supports running Gen3 Helm charts on Red Hat's OpenShift distribution of Kubernetes! Although the default for Gen3 Helm is to run on plain Kubernetes, Gen3 users who prefer the user-friendliness and robust built-in security tools offered through Openshift can now implement Gen3 with OpenShift.
If you are interested in deploying Gen3 with OpenShift, read on for important information about what changed and what defaults to manage when using OpenShift.
If you prefer to continue to use plain Kubernetes, all the Gen3 Helm defaults will continue to support that; you will not need to make any changes.
Making the Gen3 Helm chart run on OpenShift
Gen3's Helm chart was written for plain Kubernetes with an Ingress in front of it. OpenShift is Kubernetes, but its default security posture rejects a lot of what a normal Helm chart assumes:
- Containers can't bind to ports below 1024
- Containers can't run as a fixed UID unless you're specifically granted that
- The root filesystem is expected to be read-only unless you explicitly declared otherwise
Gen3 Helm PR #552, merged June 2026, is the actual body of work that permits the Gen3 Helm chart to run under those constraints. We touched nearly every subchart in this effort, but mostly to just apply the same handful of patterns everywhere.
This post walks through what that PR actually changed and why, and then reports what we observed when testing a fresh deployment end-to-end (i.e., from login to a real data submission via gen3-sdk).
The core problem: In OpenShift, the containers can't do what they used to in plain Kubernetes
Two OpenShift defaults matter here, and almost everything in the PR is a consequence of one or the other:
- Restricted Security Context Constraint (SCC) assigns an arbitrary non-root UID per namespace and won't let a container bind privileged ports (<1024) unless it is root. Every Gen3 service was written assuming it could listen on port 80, so that needed to change for OpenShift compatibility.
readOnlyRootFilesystemis often enforced, which breaks anything that writes to paths baked into the image — for example, nginx's pid file, its temp/ cache dirs, its logs.
Fix both, and most of the rest is bookkeeping.
Fix #1: stop hardcoding port 80
Every subchart's deployment.yaml had containerPort: 80 baked into the template, and the app itself was told (via CLI flag or env var, depending on the service) to listen on 80. The PR made the port a value instead, and added an explicit non-privileged default:
# helm/arborist/templates/deployment.yaml
ports:
- name: http
- containerPort: 80
+ containerPort: {{ .Values.service.targetPort }}
protocol: TCP
...
- /go/src/github.com/uc-cdis/arborist/bin/arborist
+ /go/src/github.com/uc-cdis/arborist/bin/arborist --port {{ .Values.service.targetPort }}
# helm/arborist/values.yaml
service:
type: ClusterIP
port: 80
+ targetPort: 8080
The same shape landed in fence, sheepdog, indexd, peregrine, portal, revproxy, guppy, hatchery, metadata, manifestservice, requestor, sower, ssjdispatcher, wts, cedar, audit, argo-wrapper, gen3-workflow, gen3-analysis, gen3-user-data-library, cohort-middleware, access-backend, dicom-server, ohif-viewer, ohdsi-atlas, ohdsi-webapi, orthanc — over 25 subcharts got a service.targetPort value and the corresponding template change.
service.port(what other pods see when they talk to the Service) stays at the conventional80;targetPort(what the container itself actually binds) moves to something in the 8000s that any UID can bind.
The probes had to move with it — httpGet.port: 80 became httpGet.port: http, referencing the named port instead of a number, so a probe doesn't silently point at the wrong port if targetPort changes:
livenessProbe:
httpGet:
path: /_status?timeout=20
- port: 80
+ port: http
Fix #2: give nginx somewhere to write
revproxy and portal both run nginx, and nginx by default wants to:
- write a pid file to
/var/run, bind port 80, - resolve upstream service names via
kube-dns.kube-system.svc.cluster.local(an in-cluster DNS name that doesn't exist the same way on every OpenShift cluster), and - write its temp/cache/log directories into paths baked into the image.
Every one of those breaks under a restricted, read-only-root SCC. The fix templates all of it:
# helm/revproxy/nginx/nginx.conf
-user nginx;
+user {{ .Values.nginx.user }};
worker_processes 4;
-pid /var/run/nginx.pid;
+pid {{ .Values.nginx.pidFile }};
...
+ client_body_temp_path /tmp/client_temp;
+ proxy_temp_path /tmp/proxy_temp_path;
+ fastcgi_temp_path /tmp/fastcgi_temp;
+ uwsgi_temp_path /tmp/uwsgi_temp;
+ scgi_temp_path /tmp/scgi_temp;
...
server {
- listen 80;
+ listen {{ .Values.service.targetPort }};
...
- resolver kube-dns.kube-system.svc.cluster.local ipv6=off;
+ resolver {{ .Values.nginx.resolver }} ipv6=off;
and the deployment gets emptyDir volumes mounted over every path nginx
needs to write to, since the rest of the image filesystem is read-only:
# helm/revproxy/templates/deployment.yaml
volumes:
+ - name: nginx-tmp
+ emptyDir: {}
+ - name: nginx-cache
+ emptyDir: {}
+ - emptyDir: {}
+ name: nginx-logs
...
volumeMounts:
+ - mountPath: /var/log/nginx
+ name: nginx-logs
...
+ - name: nginx-tmp
+ mountPath: /tmp
+ - name: nginx-cache
+ mountPath: /var/cache/nginx
portal got equivalent treatment — its own nginx-tmp emptyDir, a
portal-nginx ConfigMap mounted over /etc/nginx/nginx.conf and
/etc/nginx/conf.d/nginx.conf, and explicit pod/container
securityContext blocks wired into the template rather than left to
inherit whatever the cluster defaulted to:
# helm/portal/templates/deployment.yaml
serviceAccountName: {{ include "portal.serviceAccountName" . }}
+ securityContext:
+ {{- toYaml .Values.podSecurityContext | nindent 8 }}
...
- name: portal
image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+ securityContext:
+ {{- toYaml .Values.securityContext | nindent 12 }}
The chart ships two variants of the portal/frontend-framework nginx config — gen3.nginx.conf/portal-as-root/ and .../gen3ff-as-root/ — so the right one gets mounted depending on which frontend (global.frontendRoot: portal or gen3ff) is actually enabled.
Fix #3: stop assuming a specific UID/GID
fence had podSecurityContext.fsGroup: 101 hardcoded — which was fine on whatever cluster that number meant something on, but meaningless (or actively wrong) on an OpenShift namespace with its own assigned UID/GID range. The PR just removes the assumption:
# helm/fence/values.yaml
podSecurityContext:
- fsGroup: 101
+podSecurityContext: {}
and sheepdog (which previously had no securityContext/ podSecurityContext knobs at all) got them added, template and values both. However, these are commented-out by default so an operator explicitly opts-in rather than the chart making a decision for them:
# helm/sheepdog/values.yaml
podSecurityContext:
{}
# fsGroup: 2000
securityContext:
{}
# capabilities:
# drop:
# - ALL
# readOnlyRootFilesystem: true
# runAsNonRoot: true
# runAsUser: 1000
This is the pattern examples/openshift_values.yaml leans on: pick a fixed runAsUser/fsGroup per service and set it explicitly, once you know what your namespace's SCC actually allows. (See the SCC section below — it's not always the plain-vanilla restricted-v2 you'd expect).
Fix #4: add an actual OpenShift Route
None of the above matters if there's no way to get external traffic in without an Ingress controller. revproxy gained a real Route template:
# helm/revproxy/values.yaml
openshiftRoute:
enabled: false
annotations: {}
host: ""
path: "/"
targetPort: "http"
tls:
termination: "edge"
insecureEdgeTerminationPolicy: "Redirect"
wildcardPolicy: "None"
rendering a plain route.openshift.io/v1 object gated behind openshiftRoute.enabled, so it's opt-in and coexists with the chart's existing Ingress templates rather than replacing them.
Fix #5: kubectl isn't always the right tool
wts's OIDC-client-registration job uses kubectl patch to patch a Kubernetes Secret with the
client ID/secret it gets back from fence. That's fine on plain Kubernetes; however, on some OpenShift setups, the permissions model around who can patch what differs enough that it's simpler to swap in the OpenShift CLI image and use oc instead — gated behind a flag so it's opt-in per deployment:
# helm/wts/values.yaml
oidc_job_openshift: true
# helm/wts/templates/wts-oidc.yaml
{{- if .Values.oidc_job_openshift }}
- name: oc
image: image-registry.openshift-image-registry.svc:5000/openshift/cli:latest
...
oc patch secret wts-oidc-client --type=merge -p "..."
{{- else }}
- name: kubectl
image: {{ .Values.image.utilImage }}
...
{{- end }}
Fix #6: a gen3_load dependency that didn't need to be there
The shared _db_setup_job.tpl that is used by every service's dbcreate init job sourced a gen3/gen3setup helper via gen3_load before running its Postgres-readiness loop. The PR comments that out in favor of plain echo/shell — one less external dependency for a job that's really just "wait for Postgres, create the DB if it doesn't exist, patch a Secret so
downstream pods know it's done." (Commit messages in the PR describe this alongside "postgresql 15+ support" and cronjob fixes for metadata and fence — the common thread across all of them is removing assumptions that didn't hold up outside the original target environment.)
What we validated by actually deploying it
Reading a diff tells you what changed; it doesn't tell you whether the result actually works end-to-end. We took a Gen3 values file built on top of this PR's changes (examples/openshift_values.yaml), did a clean helm uninstall / helm install cycle against a real OpenShift namespace, and tested Gen3 behavior through login and data submission. Four things surfaced that the PR's diff alone wouldn't show you:
global.hostname must match your Route host, exactly. The PR gives you openshiftRoute.host to set the Route's hostname, but fence's BASE_URL (which drives every OAuth/OIDC redirect, OAUTH2_JWT_ISS, and the CSP FRAME_ANCESTORS header) is built from a separate value, global.hostname. If you only set openshiftRoute.host and leave global.hostname as the chart default (localhost), the portal loads fine, but clicking "Login" will redirect to https://localhost/.... Not a bug in the PR — just a second value that needs to agree with the first one (easy to miss).
Namespace LimitRanges can undo the port/UID work in a different way. Plenty of OpenShift projects cap containers at a default CPU limit (commonly 200m) if no limit is set explicitly. We hit this twice:
postgresql's upstream chart requests250mCPU with no explicit limit, which OpenShift outright rejects (FailedCreate, pod never even schedules) once the LimitRange injects its200mdefault.fencehad noresourcesblock in our values file at all, silently inherited the same200mlimit from OpenShiftLimitRange, and got CPU-throttled under real login traffic — resulting in 8-24 second responses on/user/user. No errors anywhere -- just slow.
The solution is to use kubectl get limitrange -o yaml before you deploy, and give explicit resources to whatever is on your request hot path.
Check which SCC policies you actually have before assuming you need more. The namespace we deployed into surprisingly carried restricted-v2-anyuid, not plain restricted-v2 — an anyuid-flavored grant that permits fixed runAsUser values outside the namespace's assigned UID range. That's why the fixed UIDs in examples/openshift_values.yaml (1000, 1000660001, 1000950000) work at all. (If our namespace only had the restricted-v2 SCC, we would only have been able to use values in the assigned UID range.) To check what SCC policies are already granted, you can use kubectl get pod <pod> -o jsonpath='{.metadata.annotations.openshift\.io/scc}'. This can help you avoid an assumption that your cluster needs a specific SCC grant it might already have.
gen3-sdk requires validation of the server's certificate to connect to the server. If your Route host isn't under the cluster's actual router wildcard domain (our example was chosen to match a local /etc/hosts entry, not the cluster's real domain), the router's TLS cert won't validate. If using cURL to test connection, curl -k will permit connecting while skipping the security check. However, the Gen3 SDK classes Gen3Auth/Gen3Submission use plain requests with no verification override exposed. We could not use the Gen3 SDK to submit data in our disposable insecure dev cluster unless we globally disabled requests verification for the session. Of course, for anything closer to production, put the Route under the real router domain instead.
With those four addressed, the full path worked: Route → mock Google login → fence-create token-create for a scripted API key → gen3-sdk creating a Program, a Project, and an Experiment node under it, verified by reading the record back through peregrine's GraphQL endpoint. The openshift.md file in the Gen3 Helm repo has the exact commands for reproducing all of this, including the mock-auth/API-key/submission flow in full.
Where things stand
The chart-level work (PR #552) is the real substance here: over two dozen subcharts updated with a consistent, minimal pattern — parameterize the port, give nginx somewhere to write, stop hardcoding UIDs, add a Route. None of it is exotic; all of it is the specific set of assumptions that plain-Kubernetes Helm charts tend to make without realizing they're assumptions until OpenShift's defaults refuse to go along with them. What we added on top is smaller: a working reference values file, and the handful of environment-specific "gotchas" (hostname/BASE_URL agreement, LimitRange interactions, SCC variants, TLS verification) that only show up once you actually deploy and click through the thing.