After checkPoint, call count directly to materialize it. -Xiangrui
On Tue, May 13, 2014 at 4:20 AM, Mayur Rustagi <mayur.rust...@gmail.com> wrote: > We are running into same issue. After 700 or so files the stack overflows, > cache, persist & checkpointing dont help. > Basically checkpointing only saves the RDD when it is materialized & it only > materializes in the end, then it runs out of stack. > > Regards > Mayur > > Mayur Rustagi > Ph: +1 (760) 203 3257 > http://www.sigmoidanalytics.com > @mayur_rustagi > > > > On Tue, May 13, 2014 at 11:40 AM, Xiangrui Meng <men...@gmail.com> wrote: >> >> You have a long lineage that causes the StackOverflow error. Try >> rdd.checkPoint() and rdd.count() for every 20~30 iterations. >> checkPoint can cut the lineage. -Xiangrui >> >> On Mon, May 12, 2014 at 3:42 PM, Guanhua Yan <gh...@lanl.gov> wrote: >> > Dear Sparkers: >> > >> > I am using Python spark of version 0.9.0 to implement some iterative >> > algorithm. I got some errors shown at the end of this email. It seems >> > that >> > it's due to the Java Stack Overflow error. The same error has been >> > duplicated on a mac desktop and a linux workstation, both running the >> > same >> > version of Spark. >> > >> > The same line of code works correctly after quite some iterations. At >> > the >> > line of error, rdd__new.count() could be 0. (In some previous rounds, >> > this >> > was also 0 without any problem). >> > >> > Any thoughts on this? >> > >> > Thank you very much, >> > - Guanhua >> > >> > >> > ======================================== >> > CODE: print "round", round, rdd__new.count() >> > ======================================== >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/pyspark/rdd.py", >> > line 542, in count >> > 14/05/12 16:20:28 INFO TaskSetManager: Loss was due to >> > java.lang.StackOverflowError [duplicate 1] >> > return self.mapPartitions(lambda i: [sum(1 for _ in i)]).sum() >> > 14/05/12 16:20:28 ERROR TaskSetManager: Task 8419.0:0 failed 1 times; >> > aborting job >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/pyspark/rdd.py", >> > line 533, in sum >> > 14/05/12 16:20:28 INFO TaskSchedulerImpl: Ignoring update with state >> > FAILED >> > from TID 1774 because its task set is gone >> > return self.mapPartitions(lambda x: [sum(x)]).reduce(operator.add) >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/pyspark/rdd.py", >> > line 499, in reduce >> > vals = self.mapPartitions(func).collect() >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/pyspark/rdd.py", >> > line 463, in collect >> > bytesInJava = self._jrdd.collect().iterator() >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/lib/py4j-0.8.1-src.zip/py4j/java_gateway.py", >> > line 537, in __call__ >> > File >> > >> > "/home1/ghyan/Software/spark-0.9.0-incubating-bin-hadoop2/python/lib/py4j-0.8.1-src.zip/py4j/protocol.py", >> > line 300, in get_return_value >> > py4j.protocol.Py4JJavaError: An error occurred while calling >> > o4317.collect. >> > : org.apache.spark.SparkException: Job aborted: Task 8419.0:1 failed 1 >> > times >> > (most recent failure: Exception failure: java.lang.StackOverflowError) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1028) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$abortStage$1.apply(DAGScheduler.scala:1026) >> > at >> > >> > scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) >> > at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$abortStage(DAGScheduler.scala:1026) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:619) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler$$anonfun$processEvent$10.apply(DAGScheduler.scala:619) >> > at scala.Option.foreach(Option.scala:236) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:619) >> > at >> > >> > org.apache.spark.scheduler.DAGScheduler$$anonfun$start$1$$anon$2$$anonfun$receive$1.applyOrElse(DAGScheduler.scala:207) >> > at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498) >> > at akka.actor.ActorCell.invoke(ActorCell.scala:456) >> > at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237) >> > at akka.dispatch.Mailbox.run(Mailbox.scala:219) >> > at >> > >> > akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386) >> > at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260) >> > at >> > >> > scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339) >> > at >> > scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979) >> > at >> > >> > scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107) >> > >> > ====================================== >> > The stack overflow error is shown as follows: >> > ====================================== >> > >> > 14/05/12 16:20:28 ERROR Executor: Exception in task ID 1774 >> > java.lang.StackOverflowError >> > at java.util.zip.Inflater.inflate(Inflater.java:259) >> > at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:152) >> > at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:116) >> > at >> > >> > java.io.ObjectInputStream$PeekInputStream.read(ObjectInputStream.java:2310) >> > at >> > >> > java.io.ObjectInputStream$PeekInputStream.readFully(ObjectInputStream.java:2323) >> > at >> > >> > java.io.ObjectInputStream$BlockDataInputStream.readInt(ObjectInputStream.java:2818) >> > at java.io.ObjectInputStream.readHandle(ObjectInputStream.java:1452) >> > at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1511) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1771) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at java.io.ObjectInputStream.readArray(ObjectInputStream.java:1706) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1344) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) >> > at scala.collection.immutable.$colon$colon.readObject(List.scala:362) >> > at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) >> > at >> > >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> > at java.lang.reflect.Method.invoke(Method.java:606) >> > at >> > java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) >> > at scala.collection.immutable.$colon$colon.readObject(List.scala:362) >> > at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) >> > at >> > >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) >> > at java.lang.reflect.Method.invoke(Method.java:606) >> > at >> > java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1017) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1893) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at >> > java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:1990) >> > at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1915) >> > at >> > java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1798) >> > at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1350) >> > at java.io.ObjectInputStream.readObject(ObjectInputStream.java:370) >> > at scala.collection.immutable.$colon$colon.readObject(List.scala:362) >> > at sun.reflect.GeneratedMethodAccessor6.invoke(Unknown Source) >> > The above replicated many times after this … >> > ====================================== > >
