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 <mri...@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 <and...@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 <mri...@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 <and...@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
> >
> >
>
