Limit the cpu and memory for DaemonSet and make it configurable

Signed-off-by: Lehmann_Fabian <fabian.lehmann@informatik.hu-berlin.de>

Author: Lehmann-Fabian

README.md

@@ -112,10 +112,12 @@ k8s {
 
 | Attribute             | Required | Explanation                                                                                     |
 |:----------------------|----------|-------------------------------------------------------------------------------------------------|
-| localPath             | yes      | Host path for the local mount                                                                   
-| localStorageMountPath | no       | Container path for the local mount                                                              
-| storage.copyStrategy  | no       | Strategy to copy the files between nodes - currently only supports 'ftp' (and its alias 'copy') 
-| storage.workdir       | no       | Working directory to use - must be inside of the locally mounted directory                      
+| localPath             | yes      | Host path for the local mount                                                                   |
+| localStorageMountPath | no       | Container path for the local mount                                                              |
+| storage.copyStrategy  | no       | Strategy to copy the files between nodes - currently only supports 'ftp' (and its alias 'copy') |
+| storage.workdir       | no       | Working directory to use - must be inside of the locally mounted directory                      |
+| storage.cpu           | no       | CPU to use for daemons running on all nodes, default: empty - no limits                         |
+| storage.memory        | no       | Memory to use for daemons running on all nodes, default: 256Mi                                  |
 
 ### Tracing
 

plugins/nf-cws/src/main/nextflow/cws/k8s/CWSK8sConfig.groovy

@@ -180,5 +180,17 @@ class CWSK8sConfig extends K8sConfig {
         String getCmd() {
             target.cmd as String
         }
+
+        Double getCpu() {
+            if ( target.cpu ) {
+                return target.cpu as double
+            }
+            return null
+        }
+
+        String getMemory() {
+             target.memory as String ?: '256Mi'
+        }
+
     }
 }

plugins/nf-cws/src/main/nextflow/cws/k8s/CWSK8sExecutor.groovy

@@ -272,19 +272,33 @@ class CWSK8sExecutor extends K8sExecutor implements ExtensionPoint {
             mounts << claim
         }
 
+        CWSK8sConfig.Storage storage = (k8sConfig as CWSK8sConfig).getStorage()
+
         String name = "mount-${session.runName.replace('_', '-')}"
+        def resources = [
+                limits: [
+                        memory: storage.getMemory()
+                ],
+                requests: [
+                        memory: storage.getMemory()
+                ]
+        ]
+        if ( storage.getCpu() ) {
+            (resources.limits as Map).put( 'cpu', storage.getCpu() )
+            (resources.requests as Map).put( 'cpu', storage.getCpu() )
+        }
         def spec = [
                 containers: [ [
                                       name: name,
                                       image: (k8sConfig as CWSK8sConfig).getStorage().getImageName(),
                                       volumeMounts: mounts,
-                                      imagePullPolicy : 'IfNotPresent'
+                                      imagePullPolicy : 'IfNotPresent',
+                                      resources: resources
                               ] ],
                 volumes: volumes,
                 serviceAccount: client.config.serviceAccount
         ]
 
-        CWSK8sConfig.Storage storage = (k8sConfig as CWSK8sConfig).getStorage()
         if( storage.getNodeSelector() )
             spec.put( 'nodeSelector', storage.getNodeSelector().toSpec() as Serializable )