[SPARK-20784] Spark hangs (v2.0) or Futures timed out (v2.1) after a joinWith() and cache() in YARN client mode - ASF JIRA

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Type: Bug
Status: Closed
Priority: Major
Resolution: Not A Bug
Affects Version/s: 2.0.2, 2.1.1
Fix Version/s: None
Component/s: Spark Core
Labels:
None

Description

Spark hangs and stop executing any job or task (v2.0.2).
Web UI shows 0 active stages and 0 active task on executors, although a driver thread is clearly working/finishing a stage (see below).

Our application runs several spark contexts for several users in parallel in threads. spark version 2.0.2, yarn-client

Extract of thread stack below.

"ForkJoinPool-1-worker-0" #107 daemon prio=5 os_prio=0 tid=0x00007fddf0005800 nid=0x484 waiting on condition [0x00007fddd0bf
6000]
   java.lang.Thread.State: WAITING (parking)
        at sun.misc.Unsafe.park(Native Method)
        - parking to wait for  <0x000000078c232760> (a scala.concurrent.impl.Promise$CompletionLatch)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:836)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedInterruptibly(AbstractQueuedSynchronizer.java:997)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1304)
        at scala.concurrent.impl.Promise$DefaultPromise.tryAwait(Promise.scala:202)
        at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:218)
        at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
        at org.apache.spark.util.ThreadUtils$.awaitResultInForkJoinSafely(ThreadUtils.scala:212)
        at org.apache.spark.sql.execution.exchange.BroadcastExchangeExec.doExecuteBroadcast(BroadcastExchangeExec.scala:120)
        at org.apache.spark.sql.execution.InputAdapter.doExecuteBroadcast(WholeStageCodegenExec.scala:229)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeBroadcast$1.apply(SparkPlan.scala:125)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeBroadcast$1.apply(SparkPlan.scala:125)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.SparkPlan.executeBroadcast(SparkPlan.scala:124)
        at org.apache.spark.sql.execution.joins.BroadcastHashJoinExec.prepareBroadcast(BroadcastHashJoinExec.scala:98)
        at org.apache.spark.sql.execution.joins.BroadcastHashJoinExec.codegenInner(BroadcastHashJoinExec.scala:197)
        at org.apache.spark.sql.execution.joins.BroadcastHashJoinExec.doConsume(BroadcastHashJoinExec.scala:82)
        at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:153)
        at org.apache.spark.sql.execution.ProjectExec.consume(basicPhysicalOperators.scala:30)
        at org.apache.spark.sql.execution.ProjectExec.doConsume(basicPhysicalOperators.scala:62)
        at org.apache.spark.sql.execution.CodegenSupport$class.consume(WholeStageCodegenExec.scala:153)
        at org.apache.spark.sql.execution.InputAdapter.consume(WholeStageCodegenExec.scala:218)
        at org.apache.spark.sql.execution.InputAdapter.doProduce(WholeStageCodegenExec.scala:244)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:83)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.CodegenSupport$class.produce(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.InputAdapter.produce(WholeStageCodegenExec.scala:218)
        at org.apache.spark.sql.execution.ProjectExec.doProduce(basicPhysicalOperators.scala:40)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:83)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.CodegenSupport$class.produce(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.ProjectExec.produce(basicPhysicalOperators.scala:30)
        at org.apache.spark.sql.execution.joins.BroadcastHashJoinExec.doProduce(BroadcastHashJoinExec.scala:77)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:83)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.CodegenSupport$class.produce(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.joins.BroadcastHashJoinExec.produce(BroadcastHashJoinExec.scala:38)
        at org.apache.spark.sql.execution.ProjectExec.doProduce(basicPhysicalOperators.scala:40)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:83)
        at org.apache.spark.sql.execution.CodegenSupport$$anonfun$produce$1.apply(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.CodegenSupport$class.produce(WholeStageCodegenExec.scala:78)
        at org.apache.spark.sql.execution.ProjectExec.produce(basicPhysicalOperators.scala:30)
        at org.apache.spark.sql.execution.WholeStageCodegenExec.doCodeGen(WholeStageCodegenExec.scala:309)
        at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:347)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:114)
        at org.apache.spark.sql.execution.exchange.ShuffleExchange.prepareShuffleDependency(ShuffleExchange.scala:87)
        at org.apache.spark.sql.execution.exchange.ShuffleExchange$$anonfun$doExecute$1.apply(ShuffleExchange.scala:123)
        at org.apache.spark.sql.execution.exchange.ShuffleExchange$$anonfun$doExecute$1.apply(ShuffleExchange.scala:114)
        at org.apache.spark.sql.catalyst.errors.package$.attachTree(package.scala:52)
        at org.apache.spark.sql.execution.exchange.ShuffleExchange.doExecute(ShuffleExchange.scala:114)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:114)
        at org.apache.spark.sql.execution.InputAdapter.inputRDDs(WholeStageCodegenExec.scala:233)
        at org.apache.spark.sql.execution.SortExec.inputRDDs(SortExec.scala:111)
        at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:361)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:115)
        at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:136)
        at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
        at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:133)
        at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:114)
        at org.apache.spark.sql.execution.columnar.InMemoryRelation.buildBuffers(InMemoryRelation.scala:97)
        at org.apache.spark.sql.execution.columnar.InMemoryRelation.<init>(InMemoryRelation.scala:86)
        at org.apache.spark.sql.execution.columnar.InMemoryRelation$.apply(InMemoryRelation.scala:42)
        at org.apache.spark.sql.execution.CacheManager$$anonfun$cacheQuery$1.apply(CacheManager.scala:98)
        at org.apache.spark.sql.execution.CacheManager.writeLock(CacheManager.scala:65)
        at org.apache.spark.sql.execution.CacheManager.cacheQuery(CacheManager.scala:89)
        at org.apache.spark.sql.Dataset.persist(Dataset.scala:2301)
        at org.apache.spark.sql.Dataset.cache(Dataset.scala:2311)
        at com.bluedme.woda.ng.matcher.StrictMatchStrategy.buildJoinMap(StrictMatchStrategy.scala:172)
        at com.bluedme.woda.ng.matcher.Matcher$$anonfun$evaluateMatching$1$$anonfun$apply$5$$anonfun$apply$6.apply(Matcher.scala:137)
        at com.bluedme.woda.ng.matcher.Matcher$$anonfun$evaluateMatching$1$$anonfun$apply$5$$anonfun$apply$6.apply(Matcher.scala:137)
        at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
        at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
        at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
        at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
        at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
        at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
        at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

jstack -F does not mention any deadlock.

It already happened a couple of times, and is related to this block of code of our app

 val matchedRowsDF = rfqDF.joinWith(rfsDF, rfqDF(m.rfqColName) === rfsDF(m.rfsColName))
        .select($"_1.$id".alias("RFQ" + id), $"_2.$id".alias("RFS" + id))
        .repartition(rfqIDS.numPartitions, $"RFQ$id")
        .sortWithinPartitions($"RFQ$id")
        .as[(Long, Long)]
        .cache

UPDATE:
On spark 2.1.1, the job times out thanks to ~~SPARK-18843~~, and instead we get the exception

 java.util.concurrent.TimeoutException: Futures timed out after [300 seconds]

. Task are not marked as failed on UI

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Assignee:: Unassigned

Reporter:: Mathieu DESPRIEE

Votes:: 0 Vote for this issue

Watchers:: 1 Start watching this issue

Dates

Created:: 17/May/17 08:26

Updated:: 12/Dec/22 18:10

Resolved:: 18/May/17 15:03