feat(k8s): use JVM_OPTS to reduce memory usage of LAPIS, increase LAP…

…IS memory limits (#2053)
loculus-project · May 30, 2024 · b3caf2a · b3caf2a
1 parent 13a7dee
commit b3caf2a
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Showing 2 changed files with 14 additions and 11 deletions.
diff --git a/kubernetes/loculus/templates/lapis-silo-deployment.yaml b/kubernetes/loculus/templates/lapis-silo-deployment.yaml
@@ -26,13 +26,13 @@ spec:
         {{- include "loculus.configProcessor" (dict "name" "lapis-silo-database-config" "dockerTag" $dockerTag) | nindent 8 }}
       containers:
         - name: silo
-          image: ghcr.io/genspectrum/lapis-silo:{{ $.Values.imageTags.lapisSilo }}
+          image: {{ $.Values.images.lapisSilo }}
           resources:
             requests:
               memory: "100Mi"
               cpu: "10m"
             limits:
-              memory: "2Gi"
+              memory: "10Gi"
           ports:
             - containerPort: 8081
           args:
@@ -41,17 +41,20 @@ spec:
             - name: lapis-silo-shared-data
               mountPath: /data
         - name: lapis
-          image: ghcr.io/genspectrum/lapis-v2:{{ $.Values.imageTags.lapis }}
+          image: {{ $.Values.images.lapis }}
           resources:
             requests:
-              memory: "100Mi"
+              memory: "200Mi"
               cpu: "10m"
             limits:
-              memory: "500Mi"
+              memory: "5Gi"
           ports:
             - containerPort: 8080
           args:
             - "--silo.url=http://localhost:8081"
+          env:
+            - name: JVM_OPTS
+              value: -XX:+UseContainerSupport -XX:+UseG1GC -XX:MaxHeapFreeRatio=5 -XX:MinHeapFreeRatio=2 -XX:MaxGCPauseMillis=100
           volumeMounts:
             - name: lapis-silo-database-config-processed
               mountPath: /workspace/database_config.yaml
@@ -60,14 +63,14 @@ spec:
               mountPath: /workspace/reference_genomes.json
               subPath: reference_genomes.json
         - name: silo-preprocessing
-          image: ghcr.io/genspectrum/lapis-silo:{{ $.Values.imageTags.lapisSilo }}
+          image: {{ $.Values.images.lapisSilo }}
           imagePullPolicy: IfNotPresent
           resources:
             requests:
-              memory: "100Mi"
+              memory: "10Mi"
               cpu: "10m"
             limits:
-              memory: "3Gi"
+              memory: "10Gi"
           command:
             - sh
             - /silo_import_wrapper.sh

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1173,9 +1173,9 @@ auth:
 insecureCookies: false
 bannerMessage: "This is a development environment. Data will not be persisted."
 additionalHeadHTML: '<script defer data-domain="main.loculus.org" src="https://plausible.io/js/script.js"></script>'
-imageTags:
-  lapisSilo: "0.2.1"
-  lapis: "0.2.1"
+images:
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.1"
+  lapis: "ghcr.io/genspectrum/lapis-v2:0.2.2"
 secrets:
   smtp-password:
     type: raw