Github user StephanEwen commented on a diff in the pull request:

    https://github.com/apache/flink/pull/1243#discussion_r42249791
  
    --- Diff: 
flink-staging/flink-streaming/flink-streaming-core/src/main/java/org/apache/flink/streaming/api/functions/source/MessageAcknowledingSourceBase.java
 ---
    @@ -157,17 +179,35 @@ public void restoreState(SerializedCheckpointData[] 
state) throws Exception {
     
        @Override
        public void notifyCheckpointComplete(long checkpointId) throws 
Exception {
    -           for (Iterator<Tuple2<Long, List<Id>>> iter = 
pendingCheckpoints.iterator(); iter.hasNext();) {
    -                   Tuple2<Long, List<Id>> checkpoint = iter.next();
    -                   long id = checkpoint.f0;
    -                   
    -                   if (id <= checkpointId) {
    -                           acknowledgeIDs(checkpoint.f1);
    -                           iter.remove();
    -                   }
    -                   else {
    -                           break;
    +           if (!running) {
    +                   LOG.debug("notifyCheckpointComplete() called on closed 
source");
    +                   return;
    +           }
    +           
    +           // only one commit operation must be in progress
    +           if (LOG.isDebugEnabled()) {
    +                   LOG.debug("Committing Messages externally for 
checkpoint {}", checkpointId);
    +           }
    +           
    +           List<Id> idsOfCheckpointedMessages = new LinkedList<Id>();
    +           synchronized (pendingCheckpoints) {
    --- End diff --
    
    You can skip this synchronization if the source run method properly 
acquires the checkpoint lock.


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