Getting below error while saving a dataframe as table with parquet mode, before saving table was repartitioned to 400, here is the spark submit arguments being parsed:
--num-executors 12 --executor-cores 8 --executor-memory 12g --driver-
memory 32g --driver-cores 2 --conf spark.sql.shuffle.partitions=400
18/11/05 22:02:04 ERROR FileFormatWriter: Aborting job null.
org.apache.spark.SparkException: Job aborted due to stage failure:
ShuffleMapStage 16 (saveAsTable at testSite.scala:192) has failed the maximum allowable number of times: 4. Most recent failure reason: org.apache.spark.shuffle.FetchFailedException:
Too large frame: 3405090943 at org.apache.spark.storage.ShuffleBlockFetcherIterator.throwFetchFailedException(ShuffleBlockFetcherIterator.scala:513)
at org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:444)
at org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:61)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:37)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.sort_addToSorter$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source) at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43) at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395) at org.apache.spark.sql.execution.RowIteratorFromScala.advanceNext(RowIterator.scala:83) at org.apache.spark.sql.execution.joins.SortMergeJoinScanner.advancedBufferedToRowWithNullFreeJoinKey(SortMergeJoinExec.scala:793) at org.apache.spark.sql.execution.joins.SortMergeJoinScanner.<init>(SortMergeJoinExec.scala:668) at org.apache.spark.sql.execution.joins.SortMergeJoinExec$$anonfun$doExecute$1.apply(SortMergeJoinExec.scala:204) at org.apache.spark.sql.execution.joins.SortMergeJoinExec$$anonfun$doExecute$1.apply(SortMergeJoinExec.scala:141) at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) at org.apache.spark.rdd.RDD.iterator(RDD.scala:287) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) at org.apache.spark.rdd.RDD.iterator(RDD.scala:287) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323) at org.apache.spark.rdd.RDD.iterator(RDD.scala:287) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96) at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53) at org.apache.spark.scheduler.Task.run(Task.scala:108) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.IllegalArgumentException: Too large frame: 3405090943
at org.spark_project.guava.base.Preconditions.checkArgument(Preconditions.java:119)
at org.apache.spark.network.util.TransportFrameDecoder.decodeNext(TransportFrameDecoder.java:133)
at org.apache.spark.network.util.TransportFrameDecoder.channelRead(TransportFrameDecoder.java:81)
Related
Experts, i am facing a weird problem where my PySpark join of 2 dataframes is failing if i don't use broadcast. I am using Spark 1.6 with Python 2.17
My Join condition is very simple and the volumes are also minimal (in KB). This is generic code and all these names in below expressions are defined as variables containing exact values and working for many other files.
DF = src.withColumnRenamed(srcCol, lkpCol)\
.join(broadcast(lkpDF), lkpCol, 'left')\
.filter(isnull(lkpDF[uniqueID])).coalesce(1)
This piece of code is running fine as long as i am broadcasting my lookup Dataframe. The moment i remove it, i am facing below error-
19/06/21 13:58:59 WARN scheduler.TaskSetManager: Lost task 0.0 in stage 43.0 (TID 1532, svr-m03wn05.c24.hadoop.com, executor 3): java.lang.OutOfMemoryError: Unable to acquire 228 bytes of memory, got 0
at org.apache.spark.memory.MemoryConsumer.allocatePage(MemoryConsumer.java:120)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.acquireNewPageIfNecessary(UnsafeExternalSorter.java:332)
at org.apache.spark.util.collection.unsafe.sort.UnsafeExternalSorter.insertRecord(UnsafeExternalSorter.java:347)
at org.apache.spark.sql.execution.UnsafeExternalRowSorter.insertRow(UnsafeExternalRowSorter.java:91)
at org.apache.spark.sql.execution.UnsafeExternalRowSorter.sort(UnsafeExternalRowSorter.java:168)
at org.apache.spark.sql.execution.Sort$$anonfun$1.apply(Sort.scala:90)
at org.apache.spark.sql.execution.Sort$$anonfun$1.apply(Sort.scala:64)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$21.apply(RDD.scala:728)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$21.apply(RDD.scala:728)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:88)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.CoalescedRDD$$anonfun$compute$1.apply(CoalescedRDD.scala:96)
at org.apache.spark.rdd.CoalescedRDD$$anonfun$compute$1.apply(CoalescedRDD.scala:95)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at org.apache.spark.sql.execution.columnar.InMemoryRelation$$anonfun$2$$anon$1.hasNext(InMemoryColumnarTableScan.scala:140)
at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:292)
at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171)
at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:268)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:242)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
19/06/21 13:59:00 WARN server.TransportChannelHandler: Exception in connection from svr-m03wn05.c24.hadoop.com/15.546.349.115:45076
java.io.IOException: Connection reset by peer
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.SocketDispatcher.read(SocketDispatcher.java:39)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:192)
at sun.nio.ch.SocketChannelImpl.read(SocketChannelImpl.java:379)
at io.netty.buffer.PooledUnsafeDirectByteBuf.setBytes(PooledUnsafeDirectByteBuf.java:313)
at io.netty.buffer.AbstractByteBuf.writeBytes(AbstractByteBuf.java:881)
at io.netty.channel.socket.nio.NioSocketChannel.doReadBytes(NioSocketChannel.java:242)
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:119)
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111)
at java.lang.Thread.run(Thread.java:745)
19/06/21 13:59:00 WARN cluster.YarnSchedulerBackend$YarnSchedulerEndpoint: Container marked as failed: container_e68_1561070366427_23261_01_000004 on host: svr-m03wn05.c24.hadoop.com. Exit status: 52. Diagnostics: Exception from container-launch.
Container id: container_e68_1561070366427_23261_01_000004
Exit code: 52
Stack trace: ExitCodeException exitCode=52:
at org.apache.hadoop.util.Shell.runCommand(Shell.java:604)
at org.apache.hadoop.util.Shell.run(Shell.java:507)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:789)
at org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor.launchContainer(LinuxContainerExecutor.java:399)
at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:302)
at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Shell output: main : command provided 1
main : run as user is userabc
main : requested yarn user is userabc
Writing to tmp file /data/1/yarn/nm/nmPrivate/application_1561070366427_23261/container_e68_1561070366427_23261_01_000004/container_e68_1561070366427_23261_01_000004.pid.tmp
Container exited with a non-zero exit code 52
19/06/21 13:59:00 ERROR cluster.YarnScheduler: Lost executor 3 on svr-m03wn05.c24.hadoop.com: Container marked as failed: container_e68_1561070366427_23261_01_000004 on host: svr-m03wn05.c24.hadoop.com. Exit status: 52. Diagnostics: Exception from container-launch.
Container id: container_e68_1561070366427_23261_01_000004
Exit code: 52
Stack trace: ExitCodeException exitCode=52:
at org.apache.hadoop.util.Shell.runCommand(Shell.java:604)
at org.apache.hadoop.util.Shell.run(Shell.java:507)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:789)
at org.apache.hadoop.yarn.server.nodemanager.LinuxContainerExecutor.launchContainer(LinuxContainerExecutor.java:399)
at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:302)
at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Shell output: main : command provided 1
main : run as user is userabc
main : requested yarn user is userabc
Writing to tmp file /data/1/yarn/nm/nmPrivate/application_1561070366427_23261/container_e68_1561070366427_23261_01_000004/container_e68_1561070366427_23261_01_000004.pid.tmp
I am running the below code and after reading couple of RDDs from Kafka I get this Kafka multithreding access error. Not sure what is causing this. Basically what code does is that it reads CDRs from kafka and tries to put that in a globaltempview. In short, all the RDDs / dataframes must be stored in global view. I am using Kafka 0.10 and spark 2.1.1
val schema_string = "subscriberNumber, originNodeType, originHostName, originOperatorID, originTimeStamp, currentServiceClass, voucherBasedRefill, transactionAmount, refillProfileID, voucherGroupID, externalData1, externalData2"
val schema_rdd = StructType(schema_string.split(",").map(fieldName => StructField(fieldName, StringType, true)) )
val init_df= sqlContext.createDataFrame(sc.emptyRDD[Row], schema_rdd)
println("initial count of initial RDD is " +init_df.count())
init_df.createGlobalTempView("AIRGLOBAL")
AirDRStream.foreachRDD(foreachFunc = rdd => {
System.out.println("--- New RDD with " + rdd.count() + " records");
if (rdd.count() == 0) {
println("--- No logs received in this time interval=================")
} else {
rdd.toDF().createOrReplaceTempView("AIR")
val FilteredDR = sqlContext.sql("select * from AIR ")
val globalview= sqlContext.sql("SELECT * FROM global_temp.AIRGLOBAL ")
println("RESULTS FROM GLOBAL VIEW before union"+ globalview.count() )
globalview.union(FilteredDR).createOrReplaceTempView("TempView")
sqlContext.catalog.dropGlobalTempView("AIRGLOBAL")
println("global view dropped" )
val tempview =sqlContext.sql("SELECT * FROM TempView ")
println("Results from tempView" + tempview.count() )
tempview.createGlobalTempView("AIRGLOBAL")
println("global view created after dropping" )
//val globalviewfinal= sqlContext.sql("SELECT count(*) FROM global_temp.AIRGLOBAL ")
//println("RESULTS FROM GLOBAL VIEW after union"+ globalviewfinal.count() )
}
})
streamingContext.start()
streamingContext.awaitTermination()
Below is full trace of errors. As you can see it runs fine for couple of RDDs and then throws error.
---creating Empty RDD
initial count of initial RDD is 0
--- New RDD with 0 records
--- No logs received in this time interval=================
--- New RDD with 1741 records
RESULTS FROM GLOBAL VIEW before union0
global view dropped
Results from tempView1741
global view created after dropping
RESULTS FROM GLOBAL VIEW after union1
--- New RDD with 4692 records
RESULTS FROM GLOBAL VIEW before union1741
global view dropped
Results from tempView6433
global view created after dropping
18/05/06 11:04:00 ERROR Executor: Exception in task 0.0 in stage 18.0 (TID 17)
java.util.ConcurrentModificationException: KafkaConsumer is not safe for multi-threaded access
at org.apache.kafka.clients.consumer.KafkaConsumer.acquire(KafkaConsumer.java:1431)
at org.apache.kafka.clients.consumer.KafkaConsumer.seek(KafkaConsumer.java:1132)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.seek(CachedKafkaConsumer.scala:95)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:69)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:228)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:194)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:126)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
18/05/06 11:04:00 ERROR TaskSetManager: Task 0 in stage 18.0 failed 1 times; aborting job
18/05/06 11:04:00 ERROR JobScheduler: Error running job streaming job 1525593840000 ms.0
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 18.0 failed 1 times, most recent failure: Lost task 0.0 in stage 18.0 (TID 17, localhost, executor driver): java.util.ConcurrentModificationException: KafkaConsumer is not safe for multi-threaded access
at org.apache.kafka.clients.consumer.KafkaConsumer.acquire(KafkaConsumer.java:1431)
at org.apache.kafka.clients.consumer.KafkaConsumer.seek(KafkaConsumer.java:1132)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.seek(CachedKafkaConsumer.scala:95)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:69)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:228)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:194)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:126)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1925)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1938)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1965)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:275)
at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2386)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2788)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2385)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2392)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2420)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2419)
at org.apache.spark.sql.Dataset.withCallback(Dataset.scala:2801)
at org.apache.spark.sql.Dataset.count(Dataset.scala:2419)
at com.asiacell.spark.KafkaAirDRsProcess$$anonfun$main$1.apply(KafkaAirDRsProcess.scala:113)
at com.asiacell.spark.KafkaAirDRsProcess$$anonfun$main$1.apply(KafkaAirDRsProcess.scala:81)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:627)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:627)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.DStream.createRDDWithLocalProperties(DStream.scala:415)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply$mcV$sp(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at scala.util.Try$.apply(Try.scala:192)
at org.apache.spark.streaming.scheduler.Job.run(Job.scala:39)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply$mcV$sp(JobScheduler.scala:256)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:256)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:256)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler.run(JobScheduler.scala:255)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.ConcurrentModificationException: KafkaConsumer is not safe for multi-threaded access
at org.apache.kafka.clients.consumer.KafkaConsumer.acquire(KafkaConsumer.java:1431)
at org.apache.kafka.clients.consumer.KafkaConsumer.seek(KafkaConsumer.java:1132)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.seek(CachedKafkaConsumer.scala:95)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:69)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:228)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:194)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:126)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
... 3 more
Exception in thread "main" org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 18.0 failed 1 times, most recent failure: Lost task 0.0 in stage 18.0 (TID 17, localhost, executor driver): java.util.ConcurrentModificationException: KafkaConsumer is not safe for multi-threaded access
at org.apache.kafka.clients.consumer.KafkaConsumer.acquire(KafkaConsumer.java:1431)
at org.apache.kafka.clients.consumer.KafkaConsumer.seek(KafkaConsumer.java:1132)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.seek(CachedKafkaConsumer.scala:95)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:69)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:228)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:194)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:126)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1925)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1938)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1965)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:275)
at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2386)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2788)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2385)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2392)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2420)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2419)
at org.apache.spark.sql.Dataset.withCallback(Dataset.scala:2801)
at org.apache.spark.sql.Dataset.count(Dataset.scala:2419)
at com.asiacell.spark.KafkaAirDRsProcess$$anonfun$main$1.apply(KafkaAirDRsProcess.scala:113)
at com.asiacell.spark.KafkaAirDRsProcess$$anonfun$main$1.apply(KafkaAirDRsProcess.scala:81)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:627)
at org.apache.spark.streaming.dstream.DStream$$anonfun$foreachRDD$1$$anonfun$apply$mcV$sp$3.apply(DStream.scala:627)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1$$anonfun$apply$mcV$sp$1.apply(ForEachDStream.scala:51)
at org.apache.spark.streaming.dstream.DStream.createRDDWithLocalProperties(DStream.scala:415)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply$mcV$sp(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at org.apache.spark.streaming.dstream.ForEachDStream$$anonfun$1.apply(ForEachDStream.scala:50)
at scala.util.Try$.apply(Try.scala:192)
at org.apache.spark.streaming.scheduler.Job.run(Job.scala:39)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply$mcV$sp(JobScheduler.scala:256)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:256)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler$$anonfun$run$1.apply(JobScheduler.scala:256)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)
at org.apache.spark.streaming.scheduler.JobScheduler$JobHandler.run(JobScheduler.scala:255)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.ConcurrentModificationException: KafkaConsumer is not safe for multi-threaded access
at org.apache.kafka.clients.consumer.KafkaConsumer.acquire(KafkaConsumer.java:1431)
at org.apache.kafka.clients.consumer.KafkaConsumer.seek(KafkaConsumer.java:1132)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.seek(CachedKafkaConsumer.scala:95)
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:69)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:228)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:194)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithoutKey$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:126)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
KafkaConsumer has never intended to be thread-safe contrary to the producer.
Actually AFAIK most MQ consumers are not thread safe.
Anyway if you want to avoid the burden of writing Kafka Consumer specific code I have create a lib to avoid this :
https://www.github.com/jaubin/gojulmq4j-api
Hope it helps.
I'm trying to get a pretty large table from mysql so I can manipulate using spark/databricks. I can't get it to load into spark - I have tried taking smaller subsets, but even at the smallest reasonable unit, it still fails to load.
I have tried playing with the wait_timeout and interactive_timeout in mysql, but it doesn't seem to make any difference
I am also loading a smaller (different) table, and that loads just fine.
df_dataset = get_jdbc('raw_data_load', predicates=predicates).select('field1','field2', 'field3','date')
df_dataset = df_dataset.repartition('date')
df_dataset.registerTempTable('raw_data')
I then am trying to cache the data for sql purposes using
%sql
cache table raw_data;
And it goes and chugs for a while and his the database, but always times out after 30-40 minutes and I get the error below
Up until the point it times out, I see
Error in SQL statement: SparkException: Job aborted due to stage failure: Task 0 in stage 30.0 failed 4 times, most recent failure: Lost task 0.3 in stage 30.0 (TID 17075, 10.200.240.63, executor 1): com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 1,715,280 milliseconds ago. The last packet sent successfully to the server was 1,715,290 milliseconds ago.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2290)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:2046)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3554)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:491)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3245)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2413)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2836)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2825)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2323)
at org.apache.spark.sql.execution.datasources.jdbc.JDBCRDD.compute(JDBCRDD.scala:301)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:336)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:334)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1005)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:936)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:700)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:334)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:285)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.EOFException: Can not read response from server. Expected to read 10 bytes, read 4 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3166)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2271)
... 42 more
Driver stacktrace:
com.databricks.backend.common.rpc.DatabricksExceptions$SQLExecutionException: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 30.0 failed 4 times, most recent failure: Lost task 0.3 in stage 30.0 (TID 17075, 10.200.240.63, executor 1): com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 1,715,280 milliseconds ago. The last packet sent successfully to the server was 1,715,290 milliseconds ago.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2290)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:2046)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3554)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:491)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3245)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2413)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2836)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2825)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2323)
at org.apache.spark.sql.execution.datasources.jdbc.JDBCRDD.compute(JDBCRDD.scala:301)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:336)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:334)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1005)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:936)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:700)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:334)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:285)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.EOFException: Can not read response from server. Expected to read 10 bytes, read 4 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3166)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2271)
... 42 more
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1442)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1430)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1429)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1429)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:803)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:803)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:803)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1657)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1612)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1601)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1937)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1950)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1963)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1977)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:275)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2409)
at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2408)
at org.apache.spark.sql.Dataset$$anonfun$60.apply(Dataset.scala:2791)
at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:87)
at org.apache.spark.sql.execution.SQLExecution$.withFileAccessAudit(SQLExecution.scala:53)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:70)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2790)
at org.apache.spark.sql.Dataset.count(Dataset.scala:2408)
at org.apache.spark.sql.execution.command.CacheTableCommand.run(cache.scala:45)
at com.databricks.sql.acl.TrustedRunnableCommand$$anonfun$run$1.apply(TrustedRunnableCommand.scala:29)
at com.databricks.sql.acl.TrustedRunnableCommand$$anonfun$run$1.apply(TrustedRunnableCommand.scala:29)
at com.databricks.sql.acl.CheckPermissions$.trusted(CheckPermissions.scala:460)
at com.databricks.sql.acl.TrustedRunnableCommand.run(TrustedRunnableCommand.scala:29)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:56)
at org.apache.spark.sql.execution.command.ExecutedCommandExec.executeCollect(commands.scala:67)
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:185)
at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:64)
at org.apache.spark.sql.SparkSession.sql(SparkSession.scala:599)
at org.apache.spark.sql.SQLContext.sql(SQLContext.scala:698)
at com.databricks.backend.daemon.driver.SQLDriverLocal$$anonfun$1.apply(SQLDriverLocal.scala:82)
at com.databricks.backend.daemon.driver.SQLDriverLocal$$anonfun$1.apply(SQLDriverLocal.scala:28)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.immutable.List.foreach(List.scala:381)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
at scala.collection.immutable.List.map(List.scala:285)
at com.databricks.backend.daemon.driver.SQLDriverLocal.executeSql(SQLDriverLocal.scala:28)
at com.databricks.backend.daemon.driver.SQLDriverLocal.repl(SQLDriverLocal.scala:128)
at com.databricks.backend.daemon.driver.DriverLocal$$anonfun$execute$2.apply(DriverLocal.scala:230)
at com.databricks.backend.daemon.driver.DriverLocal$$anonfun$execute$2.apply(DriverLocal.scala:211)
at com.databricks.logging.UsageLogging$$anonfun$withAttributionContext$1.apply(UsageLogging.scala:173)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)
at com.databricks.logging.UsageLogging$class.withAttributionContext(UsageLogging.scala:168)
at com.databricks.backend.daemon.driver.DriverLocal.withAttributionContext(DriverLocal.scala:39)
at com.databricks.logging.UsageLogging$class.withAttributionTags(UsageLogging.scala:206)
at com.databricks.backend.daemon.driver.DriverLocal.withAttributionTags(DriverLocal.scala:39)
at com.databricks.backend.daemon.driver.DriverLocal.execute(DriverLocal.scala:211)
at com.databricks.backend.daemon.driver.DriverWrapper$$anonfun$tryExecutingCommand$2.apply(DriverWrapper.scala:589)
at com.databricks.backend.daemon.driver.DriverWrapper$$anonfun$tryExecutingCommand$2.apply(DriverWrapper.scala:589)
at scala.util.Try$.apply(Try.scala:192)
at com.databricks.backend.daemon.driver.DriverWrapper.tryExecutingCommand(DriverWrapper.scala:584)
at com.databricks.backend.daemon.driver.DriverWrapper.executeCommand(DriverWrapper.scala:488)
at com.databricks.backend.daemon.driver.DriverWrapper.runInnerLoop(DriverWrapper.scala:391)
at com.databricks.backend.daemon.driver.DriverWrapper.runInner(DriverWrapper.scala:348)
at com.databricks.backend.daemon.driver.DriverWrapper.run(DriverWrapper.scala:215)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 1,715,280 milliseconds ago. The last packet sent successfully to the server was 1,715,290 milliseconds ago.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2290)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:2046)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3554)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:491)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3245)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2413)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2836)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2825)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2156)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2323)
at org.apache.spark.sql.execution.datasources.jdbc.JDBCRDD.compute(JDBCRDD.scala:301)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:336)
at org.apache.spark.rdd.RDD$$anonfun$8.apply(RDD.scala:334)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:1005)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:936)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:996)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:700)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:334)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:285)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
Caused by: java.io.EOFException: Can not read response from server. Expected to read 10 bytes, read 4 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3166)
at com.mysql.jdbc.MysqlIO.nextRowFast(MysqlIO.java:2271)
... 42 more
at com.databricks.backend.daemon.driver.SQLDriverLocal.executeSql(SQLDriverLocal.scala:116)
at com.databricks.backend.daemon.driver.SQLDriverLocal.repl(SQLDriverLocal.scala:128)
at com.databricks.backend.daemon.driver.DriverLocal$$anonfun$execute$2.apply(DriverLocal.scala:230)
at com.databricks.backend.daemon.driver.DriverLocal$$anonfun$execute$2.apply(DriverLocal.scala:211)
at com.databricks.logging.UsageLogging$$anonfun$withAttributionContext$1.apply(UsageLogging.scala:173)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:58)
at com.databricks.logging.UsageLogging$class.withAttributionContext(UsageLogging.scala:168)
at com.databricks.backend.daemon.driver.DriverLocal.withAttributionContext(DriverLocal.scala:39)
at com.databricks.logging.UsageLogging$class.withAttributionTags(UsageLogging.scala:206)
at com.databricks.backend.daemon.driver.DriverLocal.withAttributionTags(DriverLocal.scala:39)
at com.databricks.backend.daemon.driver.DriverLocal.execute(DriverLocal.scala:211)
at com.databricks.backend.daemon.driver.DriverWrapper$$anonfun$tryExecutingCommand$2.apply(DriverWrapper.scala:589)
at com.databricks.backend.daemon.driver.DriverWrapper$$anonfun$tryExecutingCommand$2.apply(DriverWrapper.scala:589)
at scala.util.Try$.apply(Try.scala:192)
at com.databricks.backend.daemon.driver.DriverWrapper.tryExecutingCommand(DriverWrapper.scala:584)
at com.databricks.backend.daemon.driver.DriverWrapper.executeCommand(DriverWrapper.scala:488)
at com.databricks.backend.daemon.driver.DriverWrapper.runInnerLoop(DriverWrapper.scala:391)
at com.databricks.backend.daemon.driver.DriverWrapper.runInner(DriverWrapper.scala:348)
at com.databricks.backend.daemon.driver.DriverWrapper.run(DriverWrapper.scala:215)
at java.lang.Thread.run(Thread.java:745)
With extremely large tables you're going to want to partition the query across your executors. By default the JDBC reader will read the query the parallelize it from the driver. If you have an incrementing, sequential key in the table you can parallelize using the lowerBound, upperBound, and numPartitions parameters. Here's an example taken from https://docs.databricks.com/spark/latest/data-sources/sql-databases.html#python-example
df = spark.read.\
jdbc(url=jdbcUrl, \
table='employees',\
column='emp_no',\
lowerBound=1,\
upperBound=100000, \
numPartitions=100)
df.show()
Having said that, you may want to read and write the data out to Parquet as that will perform better than re-reading from JDBC again.
This question already has answers here:
Spark Error:expected zero arguments for construction of ClassDict (for numpy.core.multiarray._reconstruct)
(6 answers)
Closed 5 years ago.
I have a DataFrame column with an array of strings. I've tried creating a udf and using numpy to permute (unit is the column name):
def permute(row):
return np.random.permutation(row)
udfPermute = udf(permute, ArrayType(StringType()))
print(units.withColumn("shuffled", udfPermute("unit")).head(5))
Py4JJavaError: An error occurred while calling o4246.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 871.0 failed 1 times, most recent failure: Lost task 0.0 in stage 871.0 (TID 1224, localhost, executor driver): net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for numpy.core.multiarray._reconstruct)
at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
at org.apache.spark.sql.execution.python.BatchEvalPythonExec$$anonfun$doExecute$1$$anonfun$apply$6.apply(BatchEvalPythonExec.scala:156)
at org.apache.spark.sql.execution.python.BatchEvalPythonExec$$anonfun$doExecute$1$$anonfun$apply$6.apply(BatchEvalPythonExec.scala:155)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)
at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:333)
at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply$mcI$sp(Dataset.scala:2745)
at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2742)
at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2742)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)
at org.apache.spark.sql.Dataset.collectToPython(Dataset.scala:2742)
at sun.reflect.GeneratedMethodAccessor77.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:745)
Caused by: net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for numpy.core.multiarray._reconstruct)
at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
at org.apache.spark.sql.execution.python.BatchEvalPythonExec$$anonfun$doExecute$1$$anonfun$apply$6.apply(BatchEvalPythonExec.scala:156)
at org.apache.spark.sql.execution.python.BatchEvalPythonExec$$anonfun$doExecute$1$$anonfun$apply$6.apply(BatchEvalPythonExec.scala:155)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:377)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
... 1 more
In [161]:
How can I accomplish this?
You are returning a numpy array, you need to return a list instead.
Change your UDF as below and it should work.
def permute(row):
return np.random.permutation(row).tolist()
While trying to run a spark job with spark 1.5.1, using the following paramters:
--master "yarn"
--deploy-mode "cluster"
--num-executors 200
--driver-memory 14G
--executor-memory 14G
--executor-cores 1
Trying to run graphX ConnectedComponent on large data (~4TB) using the following commands:
System.setProperty("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
val edges = …
val graph = Graph.fromEdgeTuples(edges,0,edgeStorageLevel = StorageLevel.MEMORY_AND_DISK, vertexStorageLevel = StorageLevel.MEMORY_AND_DISK)
val components = graph.connectedComponents().vertices
Some of the tasks complete successfully, and some fail with the following errors:
org.apache.spark.shuffle.MetadataFetchFailedException: Missing an output location for shuffle 2
at org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:460)
at org.apache.spark.MapOutputTracker$$anonfun$org$apache$spark$MapOutputTracker$$convertMapStatuses$2.apply(MapOutputTracker.scala:456)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
at org.apache.spark.MapOutputTracker$.org$apache$spark$MapOutputTracker$$convertMapStatuses(MapOutputTracker.scala:456)
at org.apache.spark.MapOutputTracker.getMapSizesByExecutorId(MapOutputTracker.scala:183)
at org.apache.spark.shuffle.hash.HashShuffleReader.read(HashShuffleReader.scala:47)
at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:90)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:69)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:262)
at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:99)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
and another error:
org.apache.spark.shuffle.FetchFailedException: Connection from phxaishdc9dn1209.stratus.phx.ebay.com/10.115.60.32:40099 closed
at org.apache.spark.storage.ShuffleBlockFetcherIterator.throwFetchFailedException(ShuffleBlockFetcherIterator.scala:321)
at org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:306)
at org.apache.spark.storage.ShuffleBlockFetcherIterator.next(ShuffleBlockFetcherIterator.scala:51)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at org.apache.spark.util.CompletionIterator.hasNext(CompletionIterator.scala:32)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at org.apache.spark.graphx.impl.EdgePartition.updateVertices(EdgePartition.scala:89)
at org.apache.spark.graphx.impl.ReplicatedVertexView$$anonfun$4$$anonfun$apply$5.apply(ReplicatedVertexView.scala:117)
at org.apache.spark.graphx.impl.ReplicatedVertexView$$anonfun$4$$anonfun$apply$5.apply(ReplicatedVertexView.scala:115)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:278)
at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171)
at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:262)
at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:99)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Connection from phxaishdc9dn1209.stratus.phx.ebay.com/10.115.60.32:40099 closed
at org.apache.spark.network.client.TransportResponseHandler.channelUnregistered(TransportResponseHandler.java:104)
at org.apache.spark.network.server.TransportChannelHandler.channelUnregistered(TransportChannelHandler.java:91)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelUnregistered(AbstractChannelHandlerContext.java:158)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelUnregistered(AbstractChannelHandlerContext.java:144)
at io.netty.channel.ChannelInboundHandlerAdapter.channelUnregistered(ChannelInboundHandlerAdapter.java:53)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelUnregistered(AbstractChannelHandlerContext.java:158)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelUnregistered(AbstractChannelHandlerContext.java:144)
at io.netty.channel.ChannelInboundHandlerAdapter.channelUnregistered(ChannelInboundHandlerAdapter.java:53)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelUnregistered(AbstractChannelHandlerContext.java:158)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelUnregistered(AbstractChannelHandlerContext.java:144)
at io.netty.channel.ChannelInboundHandlerAdapter.channelUnregistered(ChannelInboundHandlerAdapter.java:53)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelUnregistered(AbstractChannelHandlerContext.java:158)
at io.netty.channel.AbstractChannelHandlerContext.fireChannelUnregistered(AbstractChannelHandlerContext.java:144)
at io.netty.channel.DefaultChannelPipeline.fireChannelUnregistered(DefaultChannelPipeline.java:739)
at io.netty.channel.AbstractChannel$AbstractUnsafe$8.run(AbstractChannel.java:659)
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:357)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:357)
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:111)
... 1 more
Please advise,
Thanks in advance,
Arnon