From 6075573a93176ee8c071888e4525043d9e73b061 Mon Sep 17 00:00:00 2001 From: Shixiong Zhu Date: Mon, 1 Feb 2016 11:02:17 -0800 Subject: [SPARK-6847][CORE][STREAMING] Fix stack overflow issue when updateStateByKey is followed by a checkpointed dstream Add a local property to indicate if checkpointing all RDDs that are marked with the checkpoint flag, and enable it in Streaming Author: Shixiong Zhu Closes #10934 from zsxwing/recursive-checkpoint. --- core/src/main/scala/org/apache/spark/rdd/RDD.scala | 19 ++++++ .../scala/org/apache/spark/CheckpointSuite.scala | 21 +++++++ .../spark/streaming/scheduler/JobGenerator.scala | 5 ++ .../spark/streaming/scheduler/JobScheduler.scala | 7 ++- .../apache/spark/streaming/CheckpointSuite.scala | 69 ++++++++++++++++++++++ 5 files changed, 119 insertions(+), 2 deletions(-) diff --git a/core/src/main/scala/org/apache/spark/rdd/RDD.scala b/core/src/main/scala/org/apache/spark/rdd/RDD.scala index be47172581..e8157cf4eb 100644 --- a/core/src/main/scala/org/apache/spark/rdd/RDD.scala +++ b/core/src/main/scala/org/apache/spark/rdd/RDD.scala @@ -1542,6 +1542,15 @@ abstract class RDD[T: ClassTag]( private[spark] var checkpointData: Option[RDDCheckpointData[T]] = None + // Whether to checkpoint all ancestor RDDs that are marked for checkpointing. By default, + // we stop as soon as we find the first such RDD, an optimization that allows us to write + // less data but is not safe for all workloads. E.g. in streaming we may checkpoint both + // an RDD and its parent in every batch, in which case the parent may never be checkpointed + // and its lineage never truncated, leading to OOMs in the long run (SPARK-6847). + private val checkpointAllMarkedAncestors = + Option(sc.getLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS)) + .map(_.toBoolean).getOrElse(false) + /** Returns the first parent RDD */ protected[spark] def firstParent[U: ClassTag]: RDD[U] = { dependencies.head.rdd.asInstanceOf[RDD[U]] @@ -1585,6 +1594,13 @@ abstract class RDD[T: ClassTag]( if (!doCheckpointCalled) { doCheckpointCalled = true if (checkpointData.isDefined) { + if (checkpointAllMarkedAncestors) { + // TODO We can collect all the RDDs that needs to be checkpointed, and then checkpoint + // them in parallel. + // Checkpoint parents first because our lineage will be truncated after we + // checkpoint ourselves + dependencies.foreach(_.rdd.doCheckpoint()) + } checkpointData.get.checkpoint() } else { dependencies.foreach(_.rdd.doCheckpoint()) @@ -1704,6 +1720,9 @@ abstract class RDD[T: ClassTag]( */ object RDD { + private[spark] val CHECKPOINT_ALL_MARKED_ANCESTORS = + "spark.checkpoint.checkpointAllMarkedAncestors" + // The following implicit functions were in SparkContext before 1.3 and users had to // `import SparkContext._` to enable them. Now we move them here to make the compiler find // them automatically. However, we still keep the old functions in SparkContext for backward diff --git a/core/src/test/scala/org/apache/spark/CheckpointSuite.scala b/core/src/test/scala/org/apache/spark/CheckpointSuite.scala index 390764ba24..ce35856dce 100644 --- a/core/src/test/scala/org/apache/spark/CheckpointSuite.scala +++ b/core/src/test/scala/org/apache/spark/CheckpointSuite.scala @@ -512,6 +512,27 @@ class CheckpointSuite extends SparkFunSuite with RDDCheckpointTester with LocalS assert(rdd.isCheckpointedAndMaterialized === true) assert(rdd.partitions.size === 0) } + + runTest("checkpointAllMarkedAncestors") { reliableCheckpoint: Boolean => + testCheckpointAllMarkedAncestors(reliableCheckpoint, checkpointAllMarkedAncestors = true) + testCheckpointAllMarkedAncestors(reliableCheckpoint, checkpointAllMarkedAncestors = false) + } + + private def testCheckpointAllMarkedAncestors( + reliableCheckpoint: Boolean, checkpointAllMarkedAncestors: Boolean): Unit = { + sc.setLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS, checkpointAllMarkedAncestors.toString) + try { + val rdd1 = sc.parallelize(1 to 10) + checkpoint(rdd1, reliableCheckpoint) + val rdd2 = rdd1.map(_ + 1) + checkpoint(rdd2, reliableCheckpoint) + rdd2.count() + assert(rdd1.isCheckpointed === checkpointAllMarkedAncestors) + assert(rdd2.isCheckpointed === true) + } finally { + sc.setLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS, null) + } + } } /** RDD partition that has large serialized size. */ diff --git a/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobGenerator.scala b/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobGenerator.scala index a5a01e7763..a3ad5eaa40 100644 --- a/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobGenerator.scala +++ b/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobGenerator.scala @@ -20,6 +20,7 @@ package org.apache.spark.streaming.scheduler import scala.util.{Failure, Success, Try} import org.apache.spark.{Logging, SparkEnv} +import org.apache.spark.rdd.RDD import org.apache.spark.streaming.{Checkpoint, CheckpointWriter, Time} import org.apache.spark.streaming.util.RecurringTimer import org.apache.spark.util.{Clock, EventLoop, ManualClock, Utils} @@ -243,6 +244,10 @@ class JobGenerator(jobScheduler: JobScheduler) extends Logging { // Example: BlockRDDs are created in this thread, and it needs to access BlockManager // Update: This is probably redundant after threadlocal stuff in SparkEnv has been removed. SparkEnv.set(ssc.env) + + // Checkpoint all RDDs marked for checkpointing to ensure their lineages are + // truncated periodically. Otherwise, we may run into stack overflows (SPARK-6847). + ssc.sparkContext.setLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS, "true") Try { jobScheduler.receiverTracker.allocateBlocksToBatch(time) // allocate received blocks to batch graph.generateJobs(time) // generate jobs using allocated block diff --git a/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobScheduler.scala b/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobScheduler.scala index 9535c8e5b7..3fed3d8835 100644 --- a/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobScheduler.scala +++ b/streaming/src/main/scala/org/apache/spark/streaming/scheduler/JobScheduler.scala @@ -23,10 +23,10 @@ import scala.collection.JavaConverters._ import scala.util.Failure import org.apache.spark.Logging -import org.apache.spark.rdd.PairRDDFunctions +import org.apache.spark.rdd.{PairRDDFunctions, RDD} import org.apache.spark.streaming._ import org.apache.spark.streaming.ui.UIUtils -import org.apache.spark.util.{EventLoop, ThreadUtils, Utils} +import org.apache.spark.util.{EventLoop, ThreadUtils} private[scheduler] sealed trait JobSchedulerEvent @@ -210,6 +210,9 @@ class JobScheduler(val ssc: StreamingContext) extends Logging { s"""Streaming job from $batchLinkText""") ssc.sc.setLocalProperty(BATCH_TIME_PROPERTY_KEY, job.time.milliseconds.toString) ssc.sc.setLocalProperty(OUTPUT_OP_ID_PROPERTY_KEY, job.outputOpId.toString) + // Checkpoint all RDDs marked for checkpointing to ensure their lineages are + // truncated periodically. Otherwise, we may run into stack overflows (SPARK-6847). + ssc.sparkContext.setLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS, "true") // We need to assign `eventLoop` to a temp variable. Otherwise, because // `JobScheduler.stop(false)` may set `eventLoop` to null when this method is running, then diff --git a/streaming/src/test/scala/org/apache/spark/streaming/CheckpointSuite.scala b/streaming/src/test/scala/org/apache/spark/streaming/CheckpointSuite.scala index 4a6b91fbc7..786703eb9a 100644 --- a/streaming/src/test/scala/org/apache/spark/streaming/CheckpointSuite.scala +++ b/streaming/src/test/scala/org/apache/spark/streaming/CheckpointSuite.scala @@ -821,6 +821,75 @@ class CheckpointSuite extends TestSuiteBase with DStreamCheckpointTester checkpointWriter.stop() } + test("SPARK-6847: stack overflow when updateStateByKey is followed by a checkpointed dstream") { + // In this test, there are two updateStateByKey operators. The RDD DAG is as follows: + // + // batch 1 batch 2 batch 3 ... + // + // 1) input rdd input rdd input rdd + // | | | + // v v v + // 2) cogroup rdd ---> cogroup rdd ---> cogroup rdd ... + // | / | / | + // v / v / v + // 3) map rdd --- map rdd --- map rdd ... + // | | | + // v v v + // 4) cogroup rdd ---> cogroup rdd ---> cogroup rdd ... + // | / | / | + // v / v / v + // 5) map rdd --- map rdd --- map rdd ... + // + // Every batch depends on its previous batch, so "updateStateByKey" needs to do checkpoint to + // break the RDD chain. However, before SPARK-6847, when the state RDD (layer 5) of the second + // "updateStateByKey" does checkpoint, it won't checkpoint the state RDD (layer 3) of the first + // "updateStateByKey" (Note: "updateStateByKey" has already marked that its state RDD (layer 3) + // should be checkpointed). Hence, the connections between layer 2 and layer 3 won't be broken + // and the RDD chain will grow infinitely and cause StackOverflow. + // + // Therefore SPARK-6847 introduces "spark.checkpoint.checkpointAllMarked" to force checkpointing + // all marked RDDs in the DAG to resolve this issue. (For the previous example, it will break + // connections between layer 2 and layer 3) + ssc = new StreamingContext(master, framework, batchDuration) + val batchCounter = new BatchCounter(ssc) + ssc.checkpoint(checkpointDir) + val inputDStream = new CheckpointInputDStream(ssc) + val updateFunc = (values: Seq[Int], state: Option[Int]) => { + Some(values.sum + state.getOrElse(0)) + } + @volatile var shouldCheckpointAllMarkedRDDs = false + @volatile var rddsCheckpointed = false + inputDStream.map(i => (i, i)) + .updateStateByKey(updateFunc).checkpoint(batchDuration) + .updateStateByKey(updateFunc).checkpoint(batchDuration) + .foreachRDD { rdd => + /** + * Find all RDDs that are marked for checkpointing in the specified RDD and its ancestors. + */ + def findAllMarkedRDDs(rdd: RDD[_]): List[RDD[_]] = { + val markedRDDs = rdd.dependencies.flatMap(dep => findAllMarkedRDDs(dep.rdd)).toList + if (rdd.checkpointData.isDefined) { + rdd :: markedRDDs + } else { + markedRDDs + } + } + + shouldCheckpointAllMarkedRDDs = + Option(rdd.sparkContext.getLocalProperty(RDD.CHECKPOINT_ALL_MARKED_ANCESTORS)). + map(_.toBoolean).getOrElse(false) + + val stateRDDs = findAllMarkedRDDs(rdd) + rdd.count() + // Check the two state RDDs are both checkpointed + rddsCheckpointed = stateRDDs.size == 2 && stateRDDs.forall(_.isCheckpointed) + } + ssc.start() + batchCounter.waitUntilBatchesCompleted(1, 10000) + assert(shouldCheckpointAllMarkedRDDs === true) + assert(rddsCheckpointed === true) + } + /** * Advances the manual clock on the streaming scheduler by given number of batches. * It also waits for the expected amount of time for each batch. -- cgit v1.2.3