Fail the run if publish thread pool times out

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -682,15 +682,23 @@ class Session implements ISession {
         if( !aborted ) {
             joinAllOperators()
             log.trace "Session > all operators finished"
+            final finalizerComplete = finalizePoolManager?.shutdown(false)
+            final publisherComplete = publishPoolManager?.shutdown(false)
+            if( !finalizerComplete || !publisherComplete ) {
+                final failOnIncomplete = config.navigate('workflow.output.ignoreErrors')
+                if( failOnIncomplete )
+                    throw new AbortOperationException("Timed out while waiting to publish outputs")
+            }
+        }
+        else {
+            finalizePoolManager?.shutdown(true)
+            publishPoolManager?.shutdown(true)
         }
     }
 
     void destroy() {
         try {
             log.trace "Session > destroying"
-            // shutdown thread pools
-            finalizePoolManager?.shutdown(aborted)
-            publishPoolManager?.shutdown(aborted)
             // invoke shutdown callbacks
             shutdown0()
             log.trace "Session > after cleanup"

modules/nextflow/src/main/groovy/nextflow/util/ThreadPoolHelper.groovy

@@ -34,7 +34,7 @@ import jdk.internal.vm.ThreadContainer
 @Slf4j
 class ThreadPoolHelper {
 
-    static void await(ExecutorService pool, Duration maxAwait, String waitMessage, String exitMsg) {
+    static boolean await(ExecutorService pool, Duration maxAwait, String waitMessage) {
         final max = maxAwait.millis
         final t0 = System.currentTimeMillis()
         // wait for ongoing file transfer to complete
@@ -45,10 +45,8 @@ class ThreadPoolHelper {
                 break
 
             final delta = System.currentTimeMillis()-t0
-            if( delta > max ) {
-                log.warn(exitMsg)
-                break
-            }
+            if( delta > max )
+                return false
 
             // log to console every 10 minutes (120 * 5 sec)
             if( count % 120 == 0 ) {
@@ -61,6 +59,7 @@ class ThreadPoolHelper {
             // increment the count
             count++
         }
+        return true
     }
 
     static protected int pending(ExecutorService pool) {

modules/nextflow/src/main/groovy/nextflow/util/ThreadPoolManager.groovy

@@ -109,24 +109,27 @@ class ThreadPoolManager {
         return result
     }
 
-    void shutdown(ISession session) {
+    boolean shutdown(ISession session) {
         final sess = (Session) session
-        shutdown( sess != null && sess.aborted )
+        return shutdown( sess != null && sess.aborted )
     }
 
-    void shutdown(boolean hard) {
+    boolean shutdown(boolean hard) {
         if( !executorService )
-            return
+            return true
 
         if( hard ) {
             executorService.shutdownNow()
-            return
+            return true
         }
 
         executorService.shutdown()
         // wait for remaining threads to complete
-        ThreadPoolHelper.await(executorService, maxAwait, waitMsg, exitMsg)
+        final complete = ThreadPoolHelper.await(executorService, maxAwait, waitMsg)
+        if( !complete )
+            log.warn exitMsg
         log.debug "Thread pool '$name' shutdown completed (hard=$hard)"
+        return complete
     }
 
     static ExecutorService create(String name, int maxThreads=0) {

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchExecutor.groovy

@@ -319,8 +319,9 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint, TaskArrayExec
         // start shutdown process
         reaper.shutdown()
         final waitMsg = "[AWS BATCH] Waiting jobs reaper to complete (%d jobs to be terminated)"
-        final exitMsg = "[AWS BATCH] Exiting before jobs reaper thread pool complete -- Some jobs may not be terminated"
-        ThreadPoolHelper.await(reaper, Duration.of('60min'), waitMsg, exitMsg)
+        final complete = ThreadPoolHelper.await(reaper, Duration.of('60min'), waitMsg)
+        if( !complete )
+            log.warn "[AWS BATCH] Exiting before jobs reaper thread pool complete -- Some jobs may not be terminated"
     }
 
     @Override

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3Client.java

@@ -660,18 +660,4 @@ public void uploadDirectory(File source, S3Path target) {
 	String getObjectKmsKeyId(String bucketName, String key) {
 		return getObjectMetadata(bucketName,key).getSSEAwsKmsKeyId();
 	}
-
-	protected void showdownTransferPool(boolean hard) {
-		log.debug("Initiating transfer manager shutdown (hard={})", hard);
-		if( hard ) {
-			transferPool.shutdownNow();
-		}
-		else {
-			// await pool completion
-			transferPool.shutdown();
-			final String waitMsg = "[AWS S3] Waiting files transfer to complete (%d files)";
-			final String exitMsg = "[AWS S3] Exiting before FileTransfer thread pool complete -- Some files maybe lost";
-			ThreadPoolHelper.await(transferPool, Duration.of("1h"), waitMsg, exitMsg);
-		}
-	}
 }

plugins/nf-amazon/src/main/nextflow/cloud/aws/nio/S3OutputStream.java

@@ -665,22 +665,4 @@ static synchronized ExecutorService getOrCreateExecutor(int maxThreads) {
         return executorSingleton;
     }
 
-    /**
-     * Shutdown the executor and clear the singleton
-     */
-    static void shutdownExecutor(boolean hard) {
-        if( hard ) {
-            executorSingleton.shutdownNow();
-        }
-        else {
-            executorSingleton.shutdown();
-            log.trace("Uploader await completion");
-            final String waitMsg = "[AWS S3] Waiting stream uploader to complete (%d files)";
-            final String exitMsg = "[AWS S3] Exiting before stream uploader thread pool complete -- Some files maybe lost";
-            ThreadPoolHelper.await(executorSingleton, Duration.of("1h") ,waitMsg, exitMsg);
-            log.trace("Uploader shutdown completed");
-            executorSingleton = null;
-        }
-    }
-
 }