Per the book Java Concurrency in Practice the already-running threads continue running while the shutdown hooks run. So I think the race between the writing thread and the deleting thread could be a very real possibility :/
http://stackoverflow.com/a/3332925/120915 On Thu, Feb 6, 2014 at 2:49 AM, 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 >> > >
