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From Andrew Ash <and...@andrewash.com>
Subject Re: [0.9.0] Possible deadlock in shutdown hook?
Date Fri, 07 Feb 2014 06:39:35 GMT
There is probably just one threadpool that has task threads -- is it
possible to enumerate and interrupt just those?  We may need to keep string
a reference to that threadpool through to the shutdown thread to make that
happen.


On Thu, Feb 6, 2014 at 10:36 PM, Mridul Muralidharan <mridul@gmail.com>wrote:

> Ideally, interrupting the thread writing to disk should be sufficient
> - though since we are in middle of shutdown when this is happening, it
> is best case effort anyway.
> Identifying which threads to interrupt will be interesting since most
> of them are driven by threadpool's and we cant list all threads and
> interrupt all of them !
>
>
> Regards,
> Mridul
>
>
> On Fri, Feb 7, 2014 at 5:57 AM, Andrew Ash <andrew@andrewash.com> wrote:
> > I think the solution where we stop the writing threads and then let the
> > deleting threads completely clean up is the best option since the final
> > state doesn't have half-deleted temp dirs scattered across the cluster.
> >
> > How feasible do you think it'd be to interrupt the other threads?
> >
> >
> > On Thu, Feb 6, 2014 at 10:54 AM, Mridul Muralidharan <mridul@gmail.com
> >wrote:
> >
> >> Looks like a pathological corner case here - where the the delete
> >> thread is not getting run while the OS is busy prioritizing the thread
> >> writing data (probably with heavy gc too).
> >> Ideally, the delete thread would list files, remove them and then fail
> >> when it tries to remove the non empty directory (since other thread
> >> might be creating more in parallel).
> >>
> >>
> >> Regards,
> >> Mridul
> >>
> >>
> >> On Thu, Feb 6, 2014 at 4:19 PM, Andrew Ash <andrew@andrewash.com>
> wrote:
> >> > Got a repro locally on my MBP (the other was on a CentOS machine).
> >> >
> >> > Build spark, run a master and a worker with the sbin/start-all.sh
> script,
> >> > then run this in a shell:
> >> >
> >> > import org.apache.spark.storage.StorageLevel._
> >> > val s = sc.parallelize(1 to 1000000000).persist(MEMORY_AND_DISK_SER);
> >> > s.count
> >> >
> >> > After about a minute, this line appears in the shell logging output:
> >> >
> >> > 14/02/06 02:44:44 WARN BlockManagerMasterActor: Removing BlockManager
> >> > BlockManagerId(0, aash-mbp.dyn.yojoe.local, 57895, 0) with no recent
> >> heart
> >> > beats: 57510ms exceeds 45000ms
> >> >
> >> > Ctrl-C the shell.  In jps there is now a worker, a master, and a
> >> > CoarseGrainedExecutorBackend.
> >> >
> >> > Run jstack on the CGEBackend JVM, and I got the attached stacktraces.
>  I
> >> > waited around for 15min then kill -9'd the JVM and restarted the
> process.
> >> >
> >> > I wonder if what's happening here is that the threads that are spewing
> >> data
> >> > to disk (as that parallelize and persist would do) can write to disk
> >> faster
> >> > than the cleanup threads can delete from disk.
> >> >
> >> > What do you think of that theory?
> >> >
> >> >
> >> > Andrew
> >> >
> >> >
> >> >
> >> > On Thu, Feb 6, 2014 at 2:30 AM, Mridul Muralidharan <mridul@gmail.com
> >
> >> > wrote:
> >> >>
> >> >> shutdown hooks should not take 15 mins are you mentioned !
> >> >> On the other hand, how busy was your disk when this was happening ?
> >> >> (either due to spark or something else ?)
> >> >>
> >> >> It might just be that there was a lot of stuff to remove ?
> >> >>
> >> >> Regards,
> >> >> Mridul
> >> >>
> >> >>
> >> >> On Thu, Feb 6, 2014 at 3:50 PM, Andrew Ash <andrew@andrewash.com>
> >> wrote:
> >> >> > Hi Spark devs,
> >> >> >
> >> >> > Occasionally when hitting Ctrl-C in the scala spark shell on 0.9.0
> one
> >> >> > of
> >> >> > my workers goes dead in the spark master UI.  I'm using the
> standalone
> >> >> > cluster and didn't ever see this while using 0.8.0 so I think
it
> may
> >> be
> >> >> > a
> >> >> > regression.
> >> >> >
> >> >> > When I prod on the hung CoarseGrainedExecutorBackend JVM with
> jstack
> >> and
> >> >> > jmap -heap, it doesn't respond unless I add the -F force flag.
 The
> >> heap
> >> >> > isn't full, but there are some interesting bits in the jstack.
>  Poking
> >> >> > around a little, I think there may be some kind of deadlock in
the
> >> >> > shutdown
> >> >> > hooks.
> >> >> >
> >> >> > Below are the threads I think are most interesting:
> >> >> >
> >> >> > Thread 14308: (state = BLOCKED)
> >> >> >  - java.lang.Shutdown.exit(int) @bci=96, line=212 (Interpreted
> frame)
> >> >> >  - java.lang.Runtime.exit(int) @bci=14, line=109 (Interpreted
> frame)
> >> >> >  - java.lang.System.exit(int) @bci=4, line=962 (Interpreted frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> org.apache.spark.executor.CoarseGrainedExecutorBackend$$anonfun$receive$1.applyOrElse(java.lang.Object,
> >> >> > scala.Function1) @bci=352, line=81 (Interpreted frame)
> >> >> >  - akka.actor.ActorCell.receiveMessage(java.lang.Object) @bci=25,
> >> >> > line=498
> >> >> > (Interpreted frame)
> >> >> >  - akka.actor.ActorCell.invoke(akka.dispatch.Envelope) @bci=39,
> >> line=456
> >> >> > (Interpreted frame)
> >> >> >  - akka.dispatch.Mailbox.processMailbox(int, long) @bci=24,
> line=237
> >> >> > (Interpreted frame)
> >> >> >  - akka.dispatch.Mailbox.run() @bci=20, line=219 (Interpreted
> frame)
> >> >> >  -
> akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec()
> >> >> > @bci=4, line=386 (Interpreted frame)
> >> >> >  - scala.concurrent.forkjoin.ForkJoinTask.doExec() @bci=10,
> line=260
> >> >> > (Compiled frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(scala.concurrent.forkjoin.ForkJoinTask)
> >> >> > @bci=10, line=1339 (Compiled frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> scala.concurrent.forkjoin.ForkJoinPool.runWorker(scala.concurrent.forkjoin.ForkJoinPool$WorkQueue)
> >> >> > @bci=11, line=1979 (Compiled frame)
> >> >> >  - scala.concurrent.forkjoin.ForkJoinWorkerThread.run() @bci=14,
> >> >> > line=107
> >> >> > (Interpreted frame)
> >> >> >
> >> >> > Thread 3865: (state = BLOCKED)
> >> >> >  - java.lang.Object.wait(long) @bci=0 (Interpreted frame)
> >> >> >  - java.lang.Thread.join(long) @bci=38, line=1280 (Interpreted
> frame)
> >> >> >  - java.lang.Thread.join() @bci=2, line=1354 (Interpreted frame)
> >> >> >  - java.lang.ApplicationShutdownHooks.runHooks() @bci=87, line=106
> >> >> > (Interpreted frame)
> >> >> >  - java.lang.ApplicationShutdownHooks$1.run() @bci=0, line=46
> >> >> > (Interpreted
> >> >> > frame)
> >> >> >  - java.lang.Shutdown.runHooks() @bci=39, line=123 (Interpreted
> frame)
> >> >> >  - java.lang.Shutdown.sequence() @bci=26, line=167 (Interpreted
> frame)
> >> >> >  - java.lang.Shutdown.exit(int) @bci=96, line=212 (Interpreted
> frame)
> >> >> >  - java.lang.Terminator$1.handle(sun.misc.Signal) @bci=8, line=52
> >> >> > (Interpreted frame)
> >> >> >  - sun.misc.Signal$1.run() @bci=8, line=212 (Interpreted frame)
> >> >> >  - java.lang.Thread.run() @bci=11, line=744 (Interpreted frame)
> >> >> >
> >> >> >
> >> >> > Thread 3987: (state = BLOCKED)
> >> >> >  - java.io.UnixFileSystem.list(java.io.File) @bci=0 (Interpreted
> >> frame)
> >> >> >  - java.io.File.list() @bci=29, line=1116 (Interpreted frame)
> >> >> >  - java.io.File.listFiles() @bci=1, line=1201 (Compiled frame)
> >> >> >  - org.apache.spark.util.Utils$.listFilesSafely(java.io.File)
> @bci=1,
> >> >> > line=466 (Interpreted frame)
> >> >> >  - org.apache.spark.util.Utils$.deleteRecursively(java.io.File)
> >> @bci=9,
> >> >> > line=478 (Compiled frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> org.apache.spark.util.Utils$$anonfun$deleteRecursively$1.apply(java.io.File)
> >> >> > @bci=4, line=479 (Compiled frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> org.apache.spark.util.Utils$$anonfun$deleteRecursively$1.apply(java.lang.Object)
> >> >> > @bci=5, line=478 (Compiled frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> scala.collection.IndexedSeqOptimized$class.foreach(scala.collection.IndexedSeqOptimized,
> >> >> > scala.Function1) @bci=22, line=33 (Compiled frame)
> >> >> >  - scala.collection.mutable.WrappedArray.foreach(scala.Function1)
> >> >> > @bci=2,
> >> >> > line=34 (Compiled frame)
> >> >> >  - org.apache.spark.util.Utils$.deleteRecursively(java.io.File)
> >> @bci=19,
> >> >> > line=478 (Interpreted frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> org.apache.spark.storage.DiskBlockManager$$anon$1$$anonfun$run$2.apply(java.io.File)
> >> >> > @bci=14, line=141 (Interpreted frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> org.apache.spark.storage.DiskBlockManager$$anon$1$$anonfun$run$2.apply(java.lang.Object)
> >> >> > @bci=5, line=139 (Interpreted frame)
> >> >> >  -
> >> >> >
> >> >> >
> >>
> scala.collection.IndexedSeqOptimized$class.foreach(scala.collection.IndexedSeqOptimized,
> >> >> > scala.Function1) @bci=22, line=33 (Compiled frame)
> >> >> >  - scala.collection.mutable.ArrayOps$ofRef.foreach(scala.Function1)
> >> >> > @bci=2,
> >> >> > line=108 (Interpreted frame)
> >> >> >  - org.apache.spark.storage.DiskBlockManager$$anon$1.run() @bci=39,
> >> >> > line=139 (Interpreted frame)
> >> >> >
> >> >> >
> >> >> > I think what happened here is that thread 14308 received the akka
> >> >> > "shutdown" message and called System.exit().  This started thread
> >> 3865,
> >> >> > which is the JVM shutting itself down.  Part of that process is
> >> running
> >> >> > the
> >> >> > shutdown hooks, so it started thread 3987.  That thread is the
> >> shutdown
> >> >> > hook from addShutdownHook() in DiskBlockManager.scala, which looks
> >> like
> >> >> > this:
> >> >> >
> >> >> >   private def addShutdownHook() {
> >> >> >     localDirs.foreach(localDir =>
> >> >> > Utils.registerShutdownDeleteDir(localDir))
> >> >> >     Runtime.getRuntime.addShutdownHook(new Thread("delete Spark
> local
> >> >> > dirs") {
> >> >> >       override def run() {
> >> >> >         logDebug("Shutdown hook called")
> >> >> >         localDirs.foreach { localDir =>
> >> >> >           try {
> >> >> >             if (!Utils.hasRootAsShutdownDeleteDir(localDir))
> >> >> > Utils.deleteRecursively(localDir)
> >> >> >           } catch {
> >> >> >             case t: Throwable =>
> >> >> >               logError("Exception while deleting local spark dir:
> " +
> >> >> > localDir, t)
> >> >> >           }
> >> >> >         }
> >> >> >
> >> >> >         if (shuffleSender != null) {
> >> >> >           shuffleSender.stop()
> >> >> >         }
> >> >> >       }
> >> >> >     })
> >> >> >   }
> >> >> >
> >> >> > It goes through and deletes the directories recursively.  I was
> >> thinking
> >> >> > there might be some issues with concurrently-running shutdown
hooks
> >> >> > deleting things out from underneath each other (shutdown hook
> javadocs
> >> >> > say
> >> >> > they're all started in parallel if multiple hooks are added)
> causing
> >> the
> >> >> > File.list() in that last thread to take quite some time.
> >> >> >
> >> >> > While I was looking through the stacktrace the JVM finally exited
> >> (after
> >> >> > 15-20min at least) so I won't be able to debug more until this
bug
> >> >> > strikes
> >> >> > again.
> >> >> >
> >> >> > Any ideas on what might be going on here?
> >> >> >
> >> >> > Thanks!
> >> >> > Andrew
> >> >
> >> >
> >>
>

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