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Posted to issues@spark.apache.org by "Stephen Haberman (JIRA)" <ji...@apache.org> on 2015/01/05 06:31:34 UTC
[jira] [Comment Edited] (SPARK-5085) netty shuffle service causing
connection timeouts
[ https://issues.apache.org/jira/browse/SPARK-5085?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14264196#comment-14264196 ]
Stephen Haberman edited comment on SPARK-5085 at 1/5/15 5:31 AM:
-----------------------------------------------------------------
There is no interesting output in the driver logs...everything was fine, until 5:33, tasks just stop getting completed across the entire cluster:
{code}
// lots of logs...
15/01/03 05:33:37 INFO [sparkDriver-akka.actor.default-dispatcher-15] scheduler.TaskSetManager (Logging.scala:logInfo(59)) - Starting task 231.0 in stage 5.0 (TID 7310, ip-10-169-175-179.ec2.internal, PROCESS_LOCAL, 2004 bytes)
15/01/03 05:33:37 INFO [task-result-getter-2] scheduler.TaskSetManager (Logging.scala:logInfo(59)) - Finished task 209.0 in stage 5.0 (TID 7288) in 26069 ms on ip-10-169-175-179.ec2.internal (152/2639)
{code}
There are several stages before this stage 5.0 that involve shuffles as well, so this is not the first shuffle done by the job.
The executor thread dumps don't show anything interesting...all of the task threads are blocked in ShuffleBlockFetcherIterator, where it's trying to take blocks from the LinkedBlockingQueue.
Here are a few netstats from before, right before, after the timeouts:
{code}
$ cat netstat-0531.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 134 ip-10-181-127-41.ec2.:36031 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48338 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36030 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36028 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48342 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 134 ip-10-181-127-41.ec2.:36032 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36029 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48339 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:56283 ip-10-169-82-12:pcsync-http TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48340 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 2255316 0 ip-10-181-127-41.ec2.:36024 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36023 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 367803 0 ip-10-181-127-41.ec2.:36026 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36025 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36021 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52347 ip-10-169-82-122:cslistener TIME_WAIT
tcp 1251469 0 ip-10-181-127-41.ec2.:36027 s3-1-w.amazonaws.com:https ESTABLISHED
$ cat netstat-0535.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52360 ip-10-169-82-122:cslistener TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:50657 ip-10-169-82-12:pcsync-http TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
$ cat netstat-0549.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:40390 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52384 ip-10-169-82-122:cslistener TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
{code}
The send/receive buffers are all empty.
I don't have any good ideas. I've started reading the netty backend code, which is interesting/mildly fun, but I don't really have any good ideas about where to look to even begin debugging this. Any ideas?
was (Author: stephen):
There is no interesting output in the driver logs...everything was fine, until 5:33, tasks just stop getting completed across the entire cluster:
{code}
// lots of logs...
15/01/03 05:33:37 INFO [sparkDriver-akka.actor.default-dispatcher-15] scheduler.TaskSetManager (Logging.scala:logInfo(59)) - Starting task 231.0 in stage 5.0 (TID 7310, ip-10-169-175-179.ec2.internal, PROCESS_LOCAL, 2004 bytes)
15/01/03 05:33:37 INFO [task-result-getter-2] scheduler.TaskSetManager (Logging.scala:logInfo(59)) - Finished task 209.0 in stage 5.0 (TID 7288) in 26069 ms on ip-10-169-175-179.ec2.internal (152/2639)
{code}
There are several stages before this stage 5.0 that involve shuffles as well, so this is not the first shuffle done by the job.
The executor thread dumps don't show anything interesting...all of the task threads are blocked in ShuffleBlockFetcherIterator, where it's trying to take blocks from the LinkedBlockingQueue.
Here are a few netstats from before, right before, after the timeouts:
{code}
{code}
$ cat netstat-0531.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 134 ip-10-181-127-41.ec2.:36031 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48338 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36030 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36028 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48342 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 134 ip-10-181-127-41.ec2.:36032 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36029 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48339 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:56283 ip-10-169-82-12:pcsync-http TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 38 0 ip-10-181-127-41.ec2.:48340 s3-1-w.amazonaws.com:https CLOSE_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 2255316 0 ip-10-181-127-41.ec2.:36024 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36023 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 367803 0 ip-10-181-127-41.ec2.:36026 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36025 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36021 s3-1-w.amazonaws.com:https ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52347 ip-10-169-82-122:cslistener TIME_WAIT
tcp 1251469 0 ip-10-181-127-41.ec2.:36027 s3-1-w.amazonaws.com:https ESTABLISHED
$ cat netstat-0535.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52360 ip-10-169-82-122:cslistener TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:50657 ip-10-169-82-12:pcsync-http TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
$ cat netstat-0549.txt
Active Internet connections (w/o servers)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 ip-10-181-127-41.ec2.:51718 ip-10-169-82-122:cslistener ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:40390 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.in:ssh ip-10-169-82-122.ec2.:39880 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:49745 ip-10-71-184-33.ec2.i:53275 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44171 ip-10-181-127-41.ec2.:39134 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-63-193-69.ec2.i:49596 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:60981 ip-10-63-193-69.ec2.i:35531 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36594 ip-10-169-82-122.ec2.:36365 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:52384 ip-10-169-82-122:cslistener TIME_WAIT
tcp 0 0 ip-10-181-127-41.ec2.:38358 ip-10-169-82-122.ec2.:swa-1 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-13-165-77.ec2.i:44291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-175-179.ec2:39157 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35941 ip-10-169-247-194.ec2:55602 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:44389 ip-10-31-61-144.ec2.i:59883 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39794 ip-10-169-82-122.ec2.:52518 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-69-85-11.ec2.in:41533 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:37274 ip-10-13-165-77.ec2.i:56072 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-71-184-33.ec2.i:56943 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-33-166-218.ec2.:46591 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39778 ip-10-69-85-11.ec2.in:34222 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-181-61-165.ec2.:41291 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:48805 ip-10-181-61-165.ec2.:57986 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:39134 ip-10-181-127-41.ec2.:44171 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:45560 ip-10-33-166-218.ec2.:42942 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-169-247-194.ec2:42871 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:35301 ip-10-31-61-144.ec2.i:41293 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:36581 ip-10-169-82-122.ec2.i:7077 ESTABLISHED
tcp 0 0 ip-10-181-127-41.ec2.:38684 ip-10-169-175-179.ec2:45582 ESTABLISHED
{code}
The send/receive buffers are all empty.
I don't have any good ideas. I've started reading the netty backend code, which is interesting/mildly fun, but I don't really have any good ideas about where to look to even begin debugging this. Any ideas?
> netty shuffle service causing connection timeouts
> -------------------------------------------------
>
> Key: SPARK-5085
> URL: https://issues.apache.org/jira/browse/SPARK-5085
> Project: Spark
> Issue Type: Bug
> Components: Shuffle
> Affects Versions: 1.2.0
> Environment: EMR, transient cluster of 10 m3.2xlarges, spark 1.2.0
> Here's our spark-defaults:
> {code}
> spark.master spark://$MASTER_IP:7077
> spark.eventLog.enabled true
> spark.eventLog.dir /mnt/spark/work/history
> spark.serializer org.apache.spark.serializer.KryoSerializer
> spark.executor.memory ${EXECUTOR_MEM}m
> spark.core.connection.ack.wait.timeout 600
> spark.storage.blockManagerSlaveTimeoutMs 60000
> spark.shuffle.consolidateFiles true
> spark.shuffle.service.enabled false
> spark.shuffle.blockTransferService nio # works with nio, fails with netty
> # Use snappy because LZF uses ~100-300k buffer per block
> spark.io.compression.codec org.apache.spark.io.SnappyCompressionCodec
> spark.shuffle.file.buffer.kb 10
> spark.executor.extraJavaOptions -XX:+PrintGCDetails -XX:+HeapDumpOnOutOfMemoryError -Xss2m -XX:+UseConcMarkSweepGC -XX:CMSInitiatingOccupancyFraction=70 -XX:MaxHeapFreeRati...
> spark.akka.logLifecycleEvents true
> spark.akka.timeout 360
> spark.akka.askTimeout 120
> spark.akka.lookupTimeout 120
> spark.akka.frameSize 100
> spark.files.userClassPathFirst true
> spark.shuffle.memoryFraction 0.5
> spark.storage.memoryFraction 0.2
> {code}
> Reporter: Stephen Haberman
>
> In Spark 1.2.0, the netty backend is causing our report's cluster to lock up with connection timeouts, ~75% of the way through the job.
> It happens with both the external shuffle server and the non-external/executor-hosted shuffle server, but if I change the shuffle service from netty to nio, it immediately works.
> Here's the main log output (I turned on trace output for the network package and ShuffleBlockFetcherIterator):
> {code}
> // lots of log output, doing fine...
> 15/01/03 05:33:39 TRACE [shuffle-server-0] protocol.MessageDecoder (MessageDecoder.java:decode(42)) - Received message ChunkFetchRequest: ChunkFetchRequest{streamChunkId=StreamChunkId{streamId=1465867812750, chunkIndex=170}}
> 15/01/03 05:33:39 TRACE [shuffle-server-0] server.TransportRequestHandler (TransportRequestHandler.java:processFetchRequest(107)) - Received req from /10.169.175.179:57056 to fetch block StreamChunkId{streamId=1465867812750, chunkIndex=170}
> 15/01/03 05:33:39 TRACE [shuffle-server-0] server.OneForOneStreamManager (OneForOneStreamManager.java:getChunk(75)) - Removing stream id 1465867812750
> 15/01/03 05:33:39 TRACE [shuffle-server-0] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(152)) - Sent result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812750, chunkIndex=170}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/28/shuffle_4_1723_0.data, offset=4574685, length=20939}} to client /10.169.175.179:57056
> 15/01/03 05:48:13 WARN [shuffle-server-7] server.TransportChannelHandler (TransportChannelHandler.java:exceptionCaught(66)) - Exception in connection from /10.33.166.218:42780
> java.io.IOException: Connection timed out
> at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
> at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39)
> at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
> at sun.nio.ch.IOUtil.read(IOUtil.java:192)
> at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:379)
> at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:311)
> at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)
> at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:225)
> at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)
> at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
> at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
> at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
> at java.lang.Thread.run(Thread.java:745)
> 15/01/03 05:48:13 ERROR [shuffle-server-7] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812408, chunkIndex=52}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/2d/shuffle_4_520_0.data, offset=2214139, length=20607}} to /10.33.166.218:42780; closing connection
> java.nio.channels.ClosedChannelException
> 15/01/03 05:48:13 ERROR [shuffle-server-7] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812408, chunkIndex=53}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/10/shuffle_4_524_0.data, offset=2215548, length=23998}} to /10.33.166.218:42780; closing connection
> java.nio.channels.ClosedChannelException
> 15/01/03 05:48:13 ERROR [shuffle-server-7] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812408, chunkIndex=54}, buffer=FileSegmentManagedBuffer{file=/mnt/spark/local/spark-local-20150103040327-4f92/32/shuffle_4_532_0.data, offset=2248230, length=20580}} to /10.33.166.218:42780; closing connection
> java.nio.channels.ClosedChannelException
> // lots more of these...
> {code}
> Note how, up through 5:33, everything was fine, then after ~15 minutes of silence, at 5:48, the shuffle-server connection times out, and all of that server-7's requests fail.
> Here is shuffle-server-1 from the same stdout (with 1 last ClosedChannelException from shuffle-server-7):
> {code}
> 15/01/03 05:48:13 ERROR [shuffle-server-7] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result RpcResponse{requestId=6670015694248454083, response=[B@6653587b} to /10.33.166.218:42780; closing connection
> java.nio.channels.ClosedChannelException
> 15/01/03 05:48:45 WARN [shuffle-server-1] server.TransportChannelHandler (TransportChannelHandler.java:exceptionCaught(66)) - Exception in connection from /10.13.165.77:41845
> java.io.IOException: Connection timed out
> at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
> at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39)
> at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
> at sun.nio.ch.IOUtil.read(IOUtil.java:192)
> at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:379)
> at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:311)
> at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)
> at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:225)
> at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)
> at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
> at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
> at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
> at java.lang.Thread.run(Thread.java:745)
> 15/01/03 05:48:45 ERROR [shuffle-server-1] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812684, chunkIndex=50}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/20/shuffle_4_513_0.data, offset=4029264, length=19717}} to /10.13.165.77:41845; closing connection
> java.nio.channels.ClosedChannelException
> 15/01/03 05:48:45 ERROR [shuffle-server-1] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812684, chunkIndex=51}, buffer=FileSegmentManagedBuffer{file=/mnt/spark/local/spark-local-20150103040327-4f92/30/shuffle_4_514_0.data, offset=3976999, length=18459}} to /10.13.165.77:41845; closing connection
> java.nio.channels.ClosedChannelException
> 15/01/03 05:48:45 ERROR [shuffle-server-1] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(154)) - Error sending result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812684, chunkIndex=52}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/2d/shuffle_4_520_0.data, offset=4177037, length=18689}} to /10.13.165.77:41845; closing connection
> java.nio.channels.ClosedChannelException
> {code}
> The last line from shuffle-server-7 from before it died was earlier, at 5:33:06:
> {code}
> 15/01/03 05:33:06 TRACE [shuffle-server-7] netty.NettyBlockRpcServer (Logging.scala:logTrace(67)) - Registered streamId 1465867812639 with 171 buffers
> {code}
> And here's the last few lines-ish from shuffle-server-1 before the timeout:
> {code}
> 15/01/03 05:33:25 TRACE [shuffle-server-1] netty.NettyBlockRpcServer (Logging.scala:logTrace(67)) - Registered streamId 1465867812719 with 230 buffers
> 15/01/03 05:33:25 TRACE [shuffle-server-3] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(152)) - Sent result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812717, chunkIndex=119}, buffer=FileSegmentManagedBuffer{file=/mnt1/spark/local/spark-local-20150103040327-c554/0e/shuffle_4_1192_0.data, offset=4788234, length=26721}} to client /10.181.127.41:60981
> 15/01/03 05:33:25 TRACE [shuffle-server-1] protocol.MessageDecoder (MessageDecoder.java:decode(42)) - Received message RpcRequest: RpcRequest{requestId=7443158706773552834, message=[B@73157c0d}
> 15/01/03 05:33:25 TRACE [shuffle-server-1] netty.NettyBlockRpcServer (Logging.scala:logTrace(67)) - Received request: OpenBlocks{appId=app-20150103040324-0000, execId=0, blockIds=[shuffle_4_16_222, shuffle_4_18_222, shuffle_4_39_222, shuffle_4_49_222, shuffle_4_50_222, shuffle_4_53_222, shuffle_4_64_222, shuffle_4_86_222, shuffle_4_87_222, shuffle_4_88_222, shuffle_4_99_222, shuffle_4_100_222, shuffle_4_126_222, shuffle_4_134_222, shuffle_4_153_222, shuffle_4_162_222, shuffle_4_163_222, shuffle_4_169_222, shuffle_4_171_222, shuffle_4_173_222, shuffle_4_177_222, shuffle_4_191_222, shuffle_4_200_222, shuffle_4_248_222, shuffle_4_266_222, shuffle_4_269_222, shuffle_4_280_222, shuffle_4_283_222, shuffle_4_286_222, shuffle_4_288_222, shuffle_4_289_222, shuffle_4_331_222, shuffle_4_341_222, shuffle_4_360_222, shuffle_4_362_222, shuffle_4_367_222, shuffle_4_369_222, shuffle_4_374_222, shuffle_4_376_222, shuffle_4_408_222, shuffle_4_418_222, shuffle_4_426_222, shuffle_4_428_222, shuffle_4_435_222, shuffle_4_436_222, shuffle_4_442_222, shuffle_4_443_222, shuffle_4_491_222, shuffle_4_497_222, shuffle_4_498_222, shuffle_4_513_222, shuffle_4_514_222, shuffle_4_520_222, shuffle_4_524_222, shuffle_4_532_222, shuffle_4_572_222, shuffle_4_573_222, shuffle_4_576_222, shuffle_4_594_222, shuffle_4_596_222, shuffle_4_604_222, shuffle_4_621_222, shuffle_4_627_222, shuffle_4_653_222, shuffle_4_654_222, shuffle_4_669_222, shuffle_4_678_222, shuffle_4_679_222, shuffle_4_685_222, shuffle_4_701_222, shuffle_4_708_222, shuffle_4_730_222, shuffle_4_734_222, shuffle_4_740_222, shuffle_4_763_222, shuffle_4_766_222, shuffle_4_769_222, shuffle_4_779_222, shuffle_4_784_222, shuffle_4_794_222, shuffle_4_816_222, shuffle_4_823_222, shuffle_4_847_222, shuffle_4_851_222, shuffle_4_856_222, shuffle_4_859_222, shuffle_4_860_222, shuffle_4_877_222, shuffle_4_904_222, shuffle_4_911_222, shuffle_4_917_222, shuffle_4_926_222, shuffle_4_929_222, shuffle_4_930_222, shuffle_4_933_222, shuffle_4_953_222, shuffle_4_956_222, shuffle_4_965_222, shuffle_4_969_222, shuffle_4_1000_222, shuffle_4_1001_222, shuffle_4_1003_222, shuffle_4_1005_222, shuffle_4_1029_222, shuffle_4_1030_222, shuffle_4_1032_222, shuffle_4_1070_222, shuffle_4_1083_222, shuffle_4_1091_222, shuffle_4_1093_222, shuffle_4_1094_222, shuffle_4_1110_222, shuffle_4_1120_222, shuffle_4_1121_222, shuffle_4_1141_222, shuffle_4_1157_222, shuffle_4_1170_222, shuffle_4_1172_222, shuffle_4_1178_222, shuffle_4_1192_222, shuffle_4_1201_222, shuffle_4_1205_222, shuffle_4_1229_222, shuffle_4_1235_222, shuffle_4_1249_222, shuffle_4_1250_222, shuffle_4_1256_222, shuffle_4_1286_222, shuffle_4_1297_222, shuffle_4_1299_222, shuffle_4_1313_222, shuffle_4_1318_222, shuffle_4_1328_222, shuffle_4_1331_222, shuffle_4_1334_222, shuffle_4_1371_222, shuffle_4_1381_222, shuffle_4_1387_222, shuffle_4_1397_222, shuffle_4_1400_222, shuffle_4_1408_222, shuffle_4_1409_222, shuffle_4_1413_222, shuffle_4_1456_222, shuffle_4_1458_222, shuffle_4_1470_222, shuffle_4_1478_222, shuffle_4_1480_222, shuffle_4_1486_222, shuffle_4_1490_222, shuffle_4_1493_222, shuffle_4_1544_222, shuffle_4_1545_222, shuffle_4_1552_222, shuffle_4_1560_222, shuffle_4_1565_222, shuffle_4_1569_222, shuffle_4_1570_222, shuffle_4_1577_222, shuffle_4_1620_222, shuffle_4_1623_222, shuffle_4_1633_222, shuffle_4_1640_222, shuffle_4_1651_222, shuffle_4_1652_222, shuffle_4_1656_222, shuffle_4_1665_222, shuffle_4_1710_222, shuffle_4_1717_222, shuffle_4_1718_222, shuffle_4_1723_222]}
> 15/01/03 05:33:25 TRACE [shuffle-server-3] protocol.MessageDecoder (MessageDecoder.java:decode(42)) - Received message ChunkFetchRequest: ChunkFetchRequest{streamChunkId=StreamChunkId{streamId=1465867812717, chunkIndex=120}}
> 15/01/03 05:33:25 TRACE [shuffle-server-3] server.TransportRequestHandler (TransportRequestHandler.java:processFetchRequest(107)) - Received req from /10.181.127.41:60981 to fetch block StreamChunkId{streamId=1465867812717, chunkIndex=120}
> 15/01/03 05:33:25 TRACE [shuffle-server-3] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(152)) - Sent result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812717, chunkIndex=120}, buffer=FileSegmentManagedBuffer{file=/mnt/spark/local/spark-local-20150103040327-4f92/16/shuffle_4_1201_0.data, offset=4406836, length=18644}} to client /10.181.127.41:60981
> 15/01/03 05:33:25 TRACE [shuffle-server-3] protocol.MessageDecoder (MessageDecoder.java:decode(42)) - Received message ChunkFetchRequest: ChunkFetchRequest{streamChunkId=StreamChunkId{streamId=1465867812717, chunkIndex=121}}
> 15/01/03 05:33:25 TRACE [shuffle-server-3] server.TransportRequestHandler (TransportRequestHandler.java:processFetchRequest(107)) - Received req from /10.181.127.41:60981 to fetch block StreamChunkId{streamId=1465867812717, chunkIndex=121}
> 15/01/03 05:33:25 TRACE [shuffle-server-3] server.TransportRequestHandler (TransportRequestHandler.java:operationComplete(152)) - Sent result ChunkFetchSuccess{streamChunkId=StreamChunkId{streamId=1465867812717, chunkIndex=121}, buffer=FileSegmentManagedBuffer{file=/mnt/spark/local/spark-local-20150103040327-4f92/28/shuffle_4_1205_0.data, offset=4285664, length=18251}} to client /10.181.127.41:60981
> 15/01/03 05:33:25 TRACE [shuffle-server-1] netty.NettyBlockRpcServer (Logging.scala:logTrace(67)) - Registered streamId 1465867812720 with 171 buffers
> {code}
> What's odd is that the entire cluster seems to all hit these connect timeouts at once. Running dstat during this period, nothing is happening--no cpu, disk, or network usage.
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