Fail the run if publish thread pool times out

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

@@ -23,6 +23,7 @@ import java.nio.file.Paths
 import java.util.concurrent.ConcurrentLinkedQueue
 import java.util.concurrent.ExecutorService
 import java.util.concurrent.Executors
+import java.util.concurrent.TimeoutException
 
 import com.google.common.hash.HashCode
 import groovy.transform.CompileDynamic
@@ -689,8 +690,17 @@ class Session implements ISession {
         try {
             log.trace "Session > destroying"
             // shutdown thread pools
-            finalizePoolManager?.shutdown(aborted)
-            publishPoolManager?.shutdown(aborted)
+            try {
+                finalizePoolManager?.shutdown(aborted)
+                publishPoolManager?.shutdown(aborted)
+            }
+            catch( TimeoutException e ) {
+                final ignoreErrors = config.navigate('workflow.output.ignoreErrors', false)
+                if( !ignoreErrors )
+                    throw new AbortOperationException("Timed out while waiting to publish outputs")
+                else
+                    log.warn e.message
+            }
             // invoke shutdown callbacks
             shutdown0()
             log.trace "Session > after cleanup"

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

@@ -20,6 +20,7 @@ package nextflow.util
 import java.util.concurrent.ExecutorService
 import java.util.concurrent.ThreadPoolExecutor
 import java.util.concurrent.TimeUnit
+import java.util.concurrent.TimeoutException
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -45,10 +46,8 @@ class ThreadPoolHelper {
                 break
 
             final delta = System.currentTimeMillis()-t0
-            if( delta > max ) {
-                log.warn(exitMsg)
-                break
-            }
+            if( delta > max )
+                throw new TimeoutException(exitMsg)
 
             // log to console every 10 minutes (120 * 5 sec)
             if( count % 120 == 0 ) {

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

@@ -18,6 +18,7 @@ package nextflow.cloud.aws.batch
 
 import java.nio.file.Path
 import java.util.concurrent.TimeUnit
+import java.util.concurrent.TimeoutException
 
 import com.amazonaws.services.batch.AWSBatch
 import com.amazonaws.services.batch.model.AWSBatchException
@@ -320,7 +321,12 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint, TaskArrayExec
         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)
+        try {
+            ThreadPoolHelper.await(reaper, Duration.of('60min'), waitMsg, exitMsg)
+        }
+        catch( TimeoutException e ) {
+            log.warn e.message
+        }
     }
 
     @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;
-        }
-    }
-
 }