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Posted to issues@spark.apache.org by "Mathieu D (JIRA)" <ji...@apache.org> on 2017/05/18 10:14:04 UTC
[jira] [Updated] (SPARK-20784) Spark hangs (v2.0) or Futures timed
out (v2.1) after a joinWith() and cache() in YARN client mode
[ https://issues.apache.org/jira/browse/SPARK-20784?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Mathieu D updated SPARK-20784:
------------------------------
Affects Version/s: 2.1.1
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.
{noformat}
"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)
{noformat}
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
{code}
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
{code}
UPDATE:
On spark 2.1.1, the job times out thanks to SPARK-18843, and instead we get the exception {noformat} java.util.concurrent.TimeoutException: Futures timed out after [300 seconds] {noformat}. Task are not marked as failed on UI
was:
Spark hangs and stop executing any job or task.
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.
{noformat}
"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)
{noformat}
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
{code}
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
{code}
Summary: Spark hangs (v2.0) or Futures timed out (v2.1) after a joinWith() and cache() in YARN client mode (was: Spark hangs forever after a joinWith() and cache() in YARN client mode)
> Spark hangs (v2.0) or Futures timed out (v2.1) after a joinWith() and cache() in YARN client mode
> -------------------------------------------------------------------------------------------------
>
> Key: SPARK-20784
> URL: https://issues.apache.org/jira/browse/SPARK-20784
> Project: Spark
> Issue Type: Bug
> Components: Spark Core
> Affects Versions: 2.0.2, 2.1.1
> Reporter: Mathieu D
>
> 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.
> {noformat}
> "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)
> {noformat}
> 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
> {code}
> 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
> {code}
> UPDATE:
> On spark 2.1.1, the job times out thanks to SPARK-18843, and instead we get the exception {noformat} java.util.concurrent.TimeoutException: Futures timed out after [300 seconds] {noformat}. Task are not marked as failed on UI
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