feat(backend): allow setting JVM options by using entrypoint.sh in dockerfile, free memory (#1901)

- Use an entrypoint.sh file for backend to allow passing JVM options
- Pass `-XX:+UseContainerSupport -XX:+UseG1GC -XX:MaxHeapFreeRatio=5 -XX:MinHeapFreeRatio=2` to free memory, this allows us to set the memory limit fairly high without Java taking up a lot of memory
- Increase memory limit of: a) silo preprocessing (it can spike up to 3GB for full mpox), b) nextclade preprocessing (it can also go beyond 1GB), c) backend (it can go above 1GB with full mpox)

Author: corneliusroemer

backend/Dockerfile

@@ -3,7 +3,9 @@ FROM eclipse-temurin:21-jre-alpine
 WORKDIR /app
 
 COPY build/libs/backend.jar app.jar
+COPY entrypoint.sh entrypoint.sh
+RUN chmod +x entrypoint.sh
 
 EXPOSE 8079
 
-ENTRYPOINT ["java", "-jar", "app.jar", "--spring.profiles.active=docker"]
+ENTRYPOINT ["./entrypoint.sh"]

backend/entrypoint.sh

@@ -0,0 +1,13 @@
+#!/bin/sh
+JVM_OPTS=${JVM_OPTS:-}
+# Take script arguments
+ARGS="${*}"
+
+if [ -n "$JVM_OPTS" ]; then
+    CMD="java $JVM_OPTS -jar app.jar --spring.profiles.active=docker $ARGS"
+else
+    CMD="java -jar app.jar --spring.profiles.active=docker $ARGS"
+fi
+echo Running:
+echo "$CMD"
+$CMD

kubernetes/loculus/templates/lapis-silo-deployment.yaml

@@ -67,7 +67,7 @@ spec:
               memory: "100Mi"
               cpu: "10m"
             limits:
-              memory: "1Gi"
+              memory: "3Gi"
           command:
             - sh
             - /silo_import_wrapper.sh

kubernetes/loculus/templates/loculus-backend.yaml

@@ -31,7 +31,7 @@ spec:
               memory: "640Mi"
               cpu: "100m"
             limits:
-              memory: "1Gi" # Backend requires at least 635741K of memory
+              memory: "3Gi" # Backend requires at least 635741K of memory
           livenessProbe:
             httpGet:
               path: "/actuator/health/liveness"
@@ -59,6 +59,8 @@ spec:
             - "--spring.datasource.username=$(DB_USERNAME)"
             - "--spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://loculus-keycloak-service:8083/realms/loculus/protocol/openid-connect/certs"
           env:
+            - name: JVM_OPTS
+              value: -XX:+UseContainerSupport -XX:+UseG1GC -XX:MaxHeapFreeRatio=5 -XX:MinHeapFreeRatio=2
           {{- if .Values.enableCrossRefCredentials }}
             - name: CROSSREF_USERNAME
               valueFrom:

kubernetes/loculus/templates/loculus-preprocessing-deployment.yaml

@@ -39,7 +39,7 @@ spec:
               memory: "40Mi"
               cpu: "10m"
             limits:
-              memory: "1Gi"
+              memory: "3Gi"
           env:
             - name: KEYCLOAK_PASSWORD
               valueFrom: