feat: basic task runtime recording

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

@@ -230,6 +230,18 @@ class K8sConfig implements ConfigScope {
     """)
     final Duration schedulerInterval
 
+    @ConfigOption
+    @Description("""
+        Enables task runtime recording
+    """)
+    final boolean recordTaskRuntimes
+
+    @ConfigOption
+    @Description("""
+        The runtime recording file
+    """)
+    final String runtimeRecordPath
+
     /* required by extension point -- do not remove */
     K8sConfig() {
         this(Collections.emptyMap())
@@ -261,6 +273,8 @@ class K8sConfig implements ConfigScope {
         userName = opts.userName
         nextflowImage = opts.nextflowImage ?: "nextflow/nextflow:${BuildInfo.version}"
         schedulerInterval = opts.schedulerInterval as Duration ?: new Duration(10, TimeUnit.SECONDS)
+        recordTaskRuntimes  = opts.recordTaskRuntimes as boolean ?: false
+        runtimeRecordPath = opts.runtimeRecordPath as String ?: "${launchDir}/work/runtimes.csv"
 
         launchDir = opts.launchDir ?: "${storageMountPath}/${getUserName()}"
         projectDir = opts.projectDir ?: "${storageMountPath}/projects"

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sExecutor.groovy

@@ -55,6 +55,8 @@ class K8sExecutor extends Executor implements ExtensionPoint {
     private K8sTaskScheduler taskScheduler
     private Thread schedulerThread
 
+    K8sRuntimeRecorder runtimeRecorder
+
     /**
      * @return The Kubernetes HTTP client. Delegates to a Guava cache that refreshes
      * the client (including the service account token) when the configured interval expires.
@@ -91,6 +93,8 @@ class K8sExecutor extends Executor implements ExtensionPoint {
 
         log.debug "[K8s] config=$k8sConfig; API client config=$client.config"
 
+        this.runtimeRecorder = new K8sRuntimeRecorder(k8sConfig.recordTaskRuntimes, k8sConfig.runtimeRecordPath)
+
         this.taskScheduler = new K8sTaskScheduler(this, new K8sHashSchedulingStrategy())
         this.schedulerThread = new Thread(this.taskScheduler)
         this.schedulerThread.start()
@@ -98,6 +102,7 @@ class K8sExecutor extends Executor implements ExtensionPoint {
 
     @Override
     void shutdown() {
+        this.runtimeRecorder.write()
         this.taskScheduler.stop()
         this.schedulerThread.join()
     }

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sRuntimeRecord.groovy

@@ -0,0 +1,7 @@
+package nextflow.k8s
+
+record K8sRuntimeRecord(
+    String taskName,
+    long inputSize,
+    long runtimeMillis
+) {}

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sRuntimeRecorder.groovy

@@ -0,0 +1,49 @@
+package nextflow.k8s
+
+import groovy.util.logging.Slf4j
+
+import java.nio.file.Files
+import java.nio.file.Path
+
+@Slf4j
+class K8sRuntimeRecorder {
+    private final boolean enabled
+    private final String recordPath
+
+    private ArrayList<K8sRuntimeRecord> records
+
+    K8sRuntimeRecorder(boolean enabled, String recordPath) {
+        this.enabled = enabled
+        this.recordPath = recordPath
+        this.records = new ArrayList<>()
+    }
+
+    /**
+     * Records the runtime of a task.
+     * This should be called for a finished task, which has its
+     * start and end timestamps set.
+     * @param task
+     */
+    synchronized void record(K8sTaskHandler task) {
+        if (!enabled)
+            return;
+        long runtimeMilis = task.completeTimeMillis - task.startTimeMillis
+        long inputSizeSum = 0
+        def inputFiles = task.task.getInputFilesMap()
+        for (Map.Entry<String, Path> f : inputFiles) {
+            try {
+                inputSizeSum += Files.size(f.value)
+            } catch (IOException ex) {
+                log.error "[K8s] failed to get size of input file ${f.value} of task ${task.task.name}: ${ex.message}"
+            }
+        }
+
+        records.add(new K8sRuntimeRecord(task.task.name, inputSizeSum, runtimeMilis))
+    }
+
+    void write() {
+        for (K8sRuntimeRecord record : records) {
+            log.info("[K8s] ${record.taskName} - ${record.inputSize} Bytes - ${record.runtimeMillis} ms")
+        }
+    }
+}

nextflow/plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskHandler.groovy

@@ -471,6 +471,12 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
             deleteJobIfSuccessful(task)
             updateTimestamps(state.terminated as Map)
             determineNode()
+
+            // Signal the scheduler that this task has finished running
+            if (executor != null) {
+                executor.taskScheduler.taskFinished(this)
+                executor.runtimeRecorder.record(this)
+            }
             return true
         }
 

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

@@ -32,6 +32,14 @@ class K8sTaskScheduler implements Runnable {
         /* TODO: Decide if we should invoke the scheduler immediately */
     }
 
+    /**
+     * Notify the scheduler that a task has finished execution
+     * @param handler
+     */
+    void taskFinished(K8sTaskHandler handler) {
+
+    }
+
     protected synchronized void drain() {
         while( true ) {
             final pending = new ArrayList<K8sSchedulingRequest>(queue)