diff --git a/deployment/helm/pathling/Chart.yaml b/deployment/helm/pathling/Chart.yaml new file mode 100644 index 0000000000..980d38c58d --- /dev/null +++ b/deployment/helm/pathling/Chart.yaml @@ -0,0 +1,5 @@ +apiVersion: v2 +name: pathling +description: A Helm chart for Pathling Server +type: application +version: 1.0.0 diff --git a/deployment/helm/pathling/templates/deployment.yaml b/deployment/helm/pathling/templates/deployment.yaml new file mode 100644 index 0000000000..66b0ad15f6 --- /dev/null +++ b/deployment/helm/pathling/templates/deployment.yaml @@ -0,0 +1,87 @@ +kind: Deployment +apiVersion: apps/v1 +metadata: + name: pathling-deployment +spec: + selector: + matchLabels: + app: pathling-server + template: + metadata: + labels: + app: pathling-server + spec: + containers: + - name: pathling-server + image: {{ .Values.pathling.image | quote }} + imagePullPolicy: {{ .Values.pathling.deployment.imagePullPolicy }} + ports: + - containerPort: 8080 + - containerPort: 8081 + - containerPort: 4040 + - containerPort: 7077 + - containerPort: 7078 + resources: + requests: {{ toJson .Values.pathling.resources.requests }} + limits: {{ toJson .Values.pathling.resources.limits }} + startupProbe: + httpGet: + path: /actuator/health/liveness + port: 8081 + periodSeconds: 5 + failureThreshold: 36 + livenessProbe: + httpGet: + path: /actuator/health/liveness + port: 8081 + periodSeconds: 5 + failureThreshold: 12 + readinessProbe: + httpGet: + path: /actuator/health/readiness + port: 8081 + periodSeconds: 5 + failureThreshold: 3 + volumeMounts: {{ toJson .Values.pathling.volumeMounts }} + {{- if gt (add (len .Values.pathling.config) (len .Values.pathling.secretConfig)) 0 }} + env: + - name: JAVA_TOOL_OPTIONS + value: {{ printf "-Xmx%s %s" .Values.pathling.resources.maxHeapSize .Values.pathling.additionalJavaOptions }} + - name: spark.driver.host + value: pathling-driver + - name: spark.driver.port + value: "7077" + - name: spark.blockManager.port + value: "7078" + - name: spark.driver.bindAddress + value: 0.0.0.0 + {{- range $configKey, $configValue := .Values.pathling.config }} + - name: {{ $configKey }} + value: {{ $configValue | quote }} + {{- end }} + {{- range $configKey, $configValue := .Values.pathling.secretConfig }} + - name: {{ $configKey }} + valueFrom: + secretKeyRef: + name: pathling-secrets + key: {{ $configKey }} + {{- end }} + {{- end }} + volumes: {{ toJson .Values.pathling.volumes }} + serviceAccountName: {{ .Values.pathling.serviceAccount }} + imagePullSecrets: {{ toJson .Values.pathling.imagePullSecrets }} + tolerations: {{ toJson .Values.pathling.tolerations }} + affinity: {{ toJson .Values.pathling.affinity }} + strategy: + type: {{ .Values.pathling.deployment.strategy }} +{{- if gt (len .Values.pathling.secretConfig) 0 }} +--- +apiVersion: v1 +kind: Secret +metadata: + name: pathling-secrets +data: + {{- range $configKey, $configValue := .Values.pathling.secretConfig }} + {{ $configKey }}: {{ $configValue | b64enc }} + {{- end }} +{{- end }} diff --git a/deployment/helm/pathling/templates/role-binding.yaml b/deployment/helm/pathling/templates/role-binding.yaml new file mode 100644 index 0000000000..b0ab41c73d --- /dev/null +++ b/deployment/helm/pathling/templates/role-binding.yaml @@ -0,0 +1,11 @@ +apiVersion: rbac.authorization.k8s.io/v1 +kind: RoleBinding +metadata: + name: spark-role-binding +subjects: + - kind: ServiceAccount + name: spark-service-account +roleRef: + kind: Role + name: spark-role + apiGroup: rbac.authorization.k8s.io diff --git a/deployment/helm/pathling/templates/role.yaml b/deployment/helm/pathling/templates/role.yaml new file mode 100644 index 0000000000..e5072dc652 --- /dev/null +++ b/deployment/helm/pathling/templates/role.yaml @@ -0,0 +1,14 @@ +apiVersion: rbac.authorization.k8s.io/v1 +kind: Role +metadata: + name: spark-role +rules: + - apiGroups: [""] + resources: ["pods", "services", "configmaps"] + verbs: ["create", "get", "list", "watch", "delete"] + - apiGroups: [""] + resources: ["pods/log"] + verbs: ["get", "list", "watch"] + - apiGroups: [""] + resources: ["pods"] + verbs: ["watch"] diff --git a/deployment/helm/pathling/templates/service-account.yaml b/deployment/helm/pathling/templates/service-account.yaml new file mode 100644 index 0000000000..eec7df016d --- /dev/null +++ b/deployment/helm/pathling/templates/service-account.yaml @@ -0,0 +1,4 @@ +apiVersion: v1 +kind: ServiceAccount +metadata: + name: spark-service-account diff --git a/deployment/helm/pathling/templates/service.yaml b/deployment/helm/pathling/templates/service.yaml new file mode 100644 index 0000000000..0f8bf0a94c --- /dev/null +++ b/deployment/helm/pathling/templates/service.yaml @@ -0,0 +1,52 @@ +kind: Service +apiVersion: v1 +metadata: + name: pathling-fhir +spec: + type: ClusterIP + ports: + - port: 8080 + targetPort: 8080 + selector: + app: pathling-server +--- +kind: Service +apiVersion: v1 +metadata: + name: pathling-management +spec: + type: ClusterIP + ports: + - port: 8081 + targetPort: 8081 + selector: + app: pathling-server +--- +kind: Service +apiVersion: v1 +metadata: + name: pathling-spark-ui +spec: + type: ClusterIP + ports: + - port: 4040 + targetPort: 4040 + selector: + app: pathling-server +--- +kind: Service +apiVersion: v1 +metadata: + name: pathling-driver +spec: + type: ClusterIP + ports: + - name: driver + port: 7077 + targetPort: 7077 + - name: block-manager + port: 7078 + targetPort: 7078 + selector: + app: pathling-server + publishNotReadyAddresses: true diff --git a/deployment/helm/pathling/values.yaml b/deployment/helm/pathling/values.yaml new file mode 100644 index 0000000000..6d69fb4b56 --- /dev/null +++ b/deployment/helm/pathling/values.yaml @@ -0,0 +1,21 @@ +pathling: + image: aehrc/pathling:latest + resources: + requests: + cpu: 2 + memory: 4G + limits: + memory: 4G + maxHeapSize: 2800m + additionalJavaOptions: -Duser.timezone=UTC + deployment: + strategy: Recreate + imagePullPolicy: Always + volumes: [ ] + volumeMounts: [ ] + serviceAccount: ~ + imagePullSecrets: [ ] + tolerations: [ ] + affinity: ~ + config: { } + secretConfig: { } diff --git a/fhir-server/pom.xml b/fhir-server/pom.xml index ad1dbd2d04..ead722907d 100644 --- a/fhir-server/pom.xml +++ b/fhir-server/pom.xml @@ -388,8 +388,21 @@ 8080 8081 4040 + 7077 + + /usr/bin/entrypoint.sh + + + src/main/jib + + + /usr/bin/entrypoint.sh + 755 + + + diff --git a/fhir-server/src/main/jib/usr/bin/entrypoint.sh b/fhir-server/src/main/jib/usr/bin/entrypoint.sh new file mode 100644 index 0000000000..3de424cb6a --- /dev/null +++ b/fhir-server/src/main/jib/usr/bin/entrypoint.sh @@ -0,0 +1,55 @@ +#!/bin/bash +# +# Copyright 2023 Commonwealth Scientific and Industrial Research +# Organisation (CSIRO) ABN 41 687 119 230. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# +# Modified from the Kubernetes Docker image entrypoint script: +# https://github.com/apache/spark/blob/v3.3.2/resource-managers/kubernetes/docker/src/main/dockerfiles/spark/entrypoint.sh + +set -xe + +case "$1" in + # If the command is "executor", run the container as a Kubernetes executor. + executor) + env | grep SPARK_JAVA_OPT_ | sort -t_ -k4 -n | sed 's/[^=]*=\(.*\)/\1/g' > /tmp/java_opts.txt + readarray -t SPARK_EXECUTOR_JAVA_OPTS < /tmp/java_opts.txt + CMD=( + java + "${SPARK_EXECUTOR_JAVA_OPTS[@]}" + -Xms$SPARK_EXECUTOR_MEMORY + -Xmx$SPARK_EXECUTOR_MEMORY + -cp @/app/jib-classpath-file + org.apache.spark.scheduler.cluster.k8s.KubernetesExecutorBackend + --driver-url $SPARK_DRIVER_URL + --executor-id $SPARK_EXECUTOR_ID + --cores $SPARK_EXECUTOR_CORES + --app-id $SPARK_APPLICATION_ID + --hostname $SPARK_EXECUTOR_POD_IP + --resourceProfileId $SPARK_RESOURCE_PROFILE_ID + --podName $SPARK_EXECUTOR_POD_NAME + ) + ;; + + # If the command is anything else, run the FHIR server. + *) + CMD=( + java + -cp @/app/jib-classpath-file + au.csiro.pathling.PathlingServer + ) + ;; +esac + +exec "${CMD[@]}"