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From Mark Harris <mark.har...@hivehome.com>
Subject GC overhead limit exceeded, memory full of DeleteOnExit hooks for S3a files
Date Tue, 21 Jan 2020 14:38:11 GMT

We're using flink 1.7.2 on an EMR cluster v emr-5.22.0, which runs hadoop v "Amazon 2.8.5".
We've recently noticed that some TaskManagers fail (causing all the jobs running on them to
fail) with an "java.lang.OutOfMemoryError: GC overhead limit exceeded”. The taskmanager
(and jobs that should be running on it) remain down until manually restarted.

I managed to take and analyze a memory dump from one of the afflicted taskmanagers.

It showed that 85% of the heap was made up of the java.io.DeleteOnExitHook.files hashset.
The majority of the strings in that hashset (9041060 out of ~9041100) pointed to files that
began /tmp/hadoop-yarn/s3a/s3ablock

The problem seems to affect jobs that make use of the StreamingFileSink - all of the taskmanager
crashes have been on the taskmaster running at least one job using this sink, and a cluster
running only a single taskmanager / job that uses the StreamingFileSink crashed with the GC
overhead limit exceeded error.

I've had a look for advice on handling this error more broadly without luck.

Any suggestions or advice gratefully received.

Best regards,

Mark Harris

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