feat: simpler test workflow with configuration

nextflow/Dockerfile.dev

@@ -0,0 +1,12 @@
+FROM eclipse-temurin:17-jre
+
+WORKDIR /opt/nextflow
+
+COPY . /opt/nextflow
+
+RUN chmod +x /opt/nextflow/launch.sh /opt/nextflow/nextflow || true
+
+ENV PATH="/opt/nextflow:${PATH}"
+ENV NXF_HOME="/opt/nextflow/.nextflow"
+
+ENTRYPOINT ["/opt/nextflow/launch.sh"]

nextflow/modules/nextflow/src/main/resources/META-INF/build-info.properties

@@ -1,4 +1,4 @@
 build=0
 version=26.04.0
-timestamp=1777432778635
-commitId=f9ab19000
+timestamp=1778418181930
+commitId=ad0d91a

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sConfig.groovy

@@ -212,10 +212,15 @@ class K8sConfig implements ConfigScope {
     """)
     final String workDir
 
-    @ConfigOption
     @Description("Node initialization config")
     final K8sNodeInitConfig nodeInit
 
+    @ConfigOption
+    @Description("""
+        The image name of the nextflow launcher image
+    """)
+    final String nextflowImage
+
     /* required by extension point -- do not remove */
     K8sConfig() {
         this(Collections.emptyMap())
@@ -245,6 +250,7 @@ class K8sConfig implements ConfigScope {
         storageMountPath = opts.storageMountPath ?: '/workspace'
         storageSubPath = opts.storageSubPath
         userName = opts.userName
+        nextflowImage = opts.nextflowImage ?: "nextflow/nextflow:${BuildInfo.version}"
 
         launchDir = opts.launchDir ?: "${storageMountPath}/${getUserName()}"
         projectDir = opts.projectDir ?: "${storageMountPath}/projects"
@@ -266,6 +272,7 @@ class K8sConfig implements ConfigScope {
         else if( securityContext )
             pod.securityContext = new PodSecurityContext(securityContext)
 
+        log.info("Hello sailor")
         nodeInit = new K8sNodeInitConfig(opts.nodeInit as Map ?: Collections.emptyMap())
     }
 
@@ -327,7 +334,7 @@ class K8sConfig implements ConfigScope {
     boolean useJobResource() { ResourceType.Job.name() == computeResourceType }
 
     String getNextflowImageName() {
-        return "nextflow/nextflow:${BuildInfo.version}"
+        return nextflowImage
     }
 
     PodOptions getPodOptions() {

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sNodeInitDeployer.groovy

@@ -1,9 +1,11 @@
 package nextflow.k8s
 
+import groovy.util.logging.Slf4j
 import nextflow.k8s.client.K8sClient
 import nextflow.k8s.model.PodHostMount
 import nextflow.k8s.model.PodSpecBuilder
 
+@Slf4j
 class K8sNodeInitDeployer {
     private K8sClient client
     private K8sConfig config
@@ -20,12 +22,16 @@ class K8sNodeInitDeployer {
         if ( !init?.enabled )
             return
 
+        log.info("deploying init pods")
+
         final nodes = getNodes()
         for ( String nodeName : nodes ) {
+            log.info(" ... deploying to " + nodeName)
             final spec = makePodSpec(init, nodeName)
             client.podCreate(spec)
         }
 
+        log.info("waiting for init pods")
         waitForPods(nodes)
     }
 

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskScheduler.groovy

@@ -20,7 +20,10 @@ class K8sTaskScheduler {
     }
 
     void submit(K8sTaskHandler handler) {
+        log.debug "[K8s] received queued task ${handler.task.name}"
         queue.add(new K8sSchedulingRequest(handler))
+
+        drain()
     }
 
     protected synchronized void drain() {
@@ -34,7 +37,7 @@ class K8sTaskScheduler {
             if ( !queue.remove(decision.request) )
                 continue
 
-            log.trace "[K8s] launching queued task ${decision.request.task.name} on node: ${decision.nodeName}"
+            log.debug "[K8s] launching queued task ${decision.request.task.name} on node: ${decision.nodeName}"
             decision.request.handler.submitNow(decision.nodeName)
         }
     }

provision-volume-claim.sh

@@ -1,28 +1,31 @@
 #!/bin/bash
 # This creates a persistent volume and claim.
 # Params:
-# -p|--pv <pv-name> -c|--pvc <pvc-name> -s|--nfs-server <nfs-server> -n|--nfs-path <nfs-path>
-# pv-name - the name used for the persistent volume
-# pvc-name - the name used for the claim
+# -p|--pv <pv-name> -c|--pvc <pvc-name> -s|--nfs-server <nfs-server> -n|--nfs-path <nfs-path> -N|--namespace <name>
+# pv-name    - the name used for the persistent volume
+# pvc-name   - the name used for the claim
 # nfs-server - IP or hostname of the NFS server
-# nfs-path - Path on the NFS server
+# nfs-path   - Path on the NFS server
+# namespace  - Kubernetes namespace 
 
 PV_NAME=
 PVC_NAME=
 NFS_SERVER=
 NFS_PATH=
 SIZE=
+NAMESPACE=default
 
 usage()
 {
 echo "Usage: provision-volume-claim.sh < -p | --pv-name name > < -c | --pvc-name name >
                         < -n | --nfs-server server > 
                         < -m | --nfs-path path >
-                        < -s | --size size >"
+                        < -s | --size size >
+                        < -N | --namespace name >"
   exit 2
 }
 
-PARSED_ARGUMENTS=$(getopt -a -n provision-volume-claim -o p:c:n:m:s: --long pv-name:,pvc-name:,nfs-server:,nfs-path:,size: -- "$@")
+PARSED_ARGUMENTS=$(getopt -a -n provision-volume-claim -o p:c:n:m:s:N: --long pv-name:,pvc-name:,nfs-server:,nfs-path:,size:,namespace: -- "$@")
 VALID_ARGUMENTS=$?
 if [ "$VALID_ARGUMENTS" != "0" ]; then
   usage
@@ -37,6 +40,7 @@ do
     -n | --nfs-server) NFS_SERVER="$2" ; shift 2 ;;
     -m | --nfs-path)   NFS_PATH="$2"   ; shift 2 ;;
     -s | --size)       SIZE="$2"       ; shift 2 ;;
+    -N | --namespace)  NAMESPACE="$2"  ; shift 2 ;;
     # -- means the end of the arguments; drop this, and break out of the while loop
     --) shift; break ;;
     *) echo "Unexpected option: $1 - this should not happen."
@@ -69,7 +73,6 @@ spec:
     - ReadWriteMany
   persistentVolumeReclaimPolicy: Recycle
   storageClassName: slow
-
   mountOptions:
     - hard
     - nfsvers=4.1
@@ -88,6 +91,7 @@ apiVersion: v1
 kind: PersistentVolumeClaim
 metadata:
   name: $PVC_NAME
+  namespace: $NAMESPACE
 spec:
   accessModes:
     - ReadWriteMany
@@ -106,7 +110,7 @@ cat $PVC_MANIFEST
 # Generate cleanup script
 cat > cleanup-volume-claim.sh << EOM
 #!/bin/bash
-kubectl delete pvc $PVC_NAME
+kubectl delete pvc $PVC_NAME -n $NAMESPACE
 kubectl delete pv $PV_NAME
 EOM
 chmod +x cleanup-volume-claim.sh

test/main.nf

@@ -1,52 +1,18 @@
-params.str = "Hello, world!"
+nextflow.enable.dsl = 2
 
-process split {
-	publishDir "results/lower"
-
-	input:
-	val x
+process hello {
+	container 'ubuntu:22.04'
 
 	output:
-	path 'chunk_*'
+	path 'hello.txt'
 
 	script:
 	"""
-	printf '${x}' | split -b 6 - chunk_
-	"""
-}
-
-process to_upper {
-	tag "$y"
-
-	input:
-	path y
-
-	output:
-	path 'upper_*'
-
-	script:
-	"""
-		cat $y | tr '[a-z]' '[A-Z]' > upper_${y}
+	echo "Hello, from kubernetes" > hello.txt
+	hostname >> hello.txt
 	"""
 }
 
 workflow {
-	main:
-	ch_str = channel.of(params.str)
-	ch_chunks = split(ch_str)
-	ch_upper = to_upper(ch_chunks.flatten())
-
-	publish:
-	lower = ch_chunks.flatten()
-	upper = ch_upper
-}
-
-output {
-	lower {
-		path 'lower'
-	}
-
-	upper {
-		path 'upper'
-	}
+	hello()
 }

test/nextflow.config

@@ -0,0 +1,35 @@
+plugins {
+	id 'nf-k8s'
+}
+
+workDir = '/workspace'
+
+process {
+	executor = 'k8s'
+	container = 'ubuntu:22.04'
+
+	pod = [
+		imagePullPolicy: 'IfNotPresent'
+	]
+}
+
+k8s {
+	namespace = 'default'
+
+	storageClaimName = 'my-claim'
+	storageMountPath = '/workspace'
+    launchDir = '/workspace/launch'
+    projectDir = '/workspace/projects'
+    cleanup = false
+
+	nextflowImage = 'gitea.kleine.eulenhexe.de/kevin/ma/nextflow-dvfs:0.1'
+	imagePullPolicy = 'IfNotPresent'
+
+	nodeInit {
+		enabled = false
+		image = 'gitea.kleine.eulenhexe.de/kevin/ma/dvfs-agent:0.1'
+		command = ['/bin/agent']
+		wait = 'Running'
+		cleanup = false
+	}
+}