Stephan Ewen commented on FLINK-4660:

We looked through this a bit, and the problem may be something else. Flink does 
not close the {{FileSystem}} objects, but it also caches them, so there should 
be only one {{FileSystem}} object per TaskManager.
The connections you see as open may be {{FsDataInputStream}} connections to S3, 
reloading the state. Previous versions of Flink did not ensure that the streams 
were closes in case that the recovery was intercepted by another failure (such 
as File Not Found due to eventual consistency).

The latest version of Flink more thoroughly closes these streams. Can you check 
if that fixes your problem?

For the eventual consistency issue, let's continue the discussion in 

> HadoopFileSystem (with S3A) may leak connections, which cause job to stuck in 
> a restarting loop
> -----------------------------------------------------------------------------------------------
>                 Key: FLINK-4660
>                 URL: https://issues.apache.org/jira/browse/FLINK-4660
>             Project: Flink
>          Issue Type: Bug
>          Components: State Backends, Checkpointing
>            Reporter: Zhenzhong Xu
>            Priority: Critical
>         Attachments: Screen Shot 2016-09-20 at 2.49.14 PM.png, Screen Shot 
> 2016-09-20 at 2.49.32 PM.png
> Flink job with checkpoints enabled and configured to use S3A file system 
> backend, sometimes experiences checkpointing failure due to S3 consistency 
> issue. This behavior is also reported by other people and documented in 
> https://issues.apache.org/jira/browse/FLINK-4218.
> This problem gets magnified by current HadoopFileSystem implementation, which 
> can potentially leak S3 client connections, and eventually get into a 
> restarting loop with “Timeout waiting for a connection from pool” exception 
> thrown from aws client.
> I looked at the code, seems HadoopFileSystem.java never invoke close() method 
> on fs object upon failure, but the FileSystem may be re-initialized every 
> time the job gets restarted.
> A few evidence I observed:
> 1. When I set the connection pool limit to 128, and below commands shows 128 
> connections are stuck in CLOSE_WAIT state.
> !Screen Shot 2016-09-20 at 2.49.14 PM.png|align=left, vspace=5! 
> 2. task manager logs indicates that state backend file system consistently 
> getting initialized upon job restarting.
> !Screen Shot 2016-09-20 at 2.49.32 PM.png!
> 3. Log indicates there is NPE during cleanning up of stream task which was 
> caused by “Timeout waiting for connection from pool” exception when trying to 
> create a directory in S3 bucket.
> 2016-09-02 08:17:50,886 ERROR 
> org.apache.flink.streaming.runtime.tasks.StreamTask - Error during cleanup of 
> stream task
> java.lang.NullPointerException
> at 
> org.apache.flink.streaming.runtime.tasks.OneInputStreamTask.cleanup(OneInputStreamTask.java:73)
> at 
> org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:323)
> at org.apache.flink.runtime.taskmanager.Task.run(Task.java:589)
> at java.lang.Thread.run(Thread.java:745)
> 4.It appears StreamTask from invoking checkpointing operation, to handling 
> failure, there is no logic associated with closing Hadoop File System object 
> (which internally includes S3 aws client object), which resides in 
> HadoopFileSystem.java.

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