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  1. Spark
  2. SPARK-5508

Arrays and Maps stored with Hive Parquet Serde may not be able to read by the Parquet support in the Data Souce API

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Details

    • Bug
    • Status: Resolved
    • Critical
    • Resolution: Duplicate
    • 1.2.1
    • None
    • SQL
    • mesos, cdh

    Description

      The root cause of this bug is explained below (see here).
      The workaround of this issue is to set the following confs

      sql("set spark.sql.parquet.useDataSourceApi=false")
      sql("set spark.sql.hive.convertMetastoreParquet=false")
      

      Below is the original description.
      When the table is saved as parquet, we cannot query a field which is an array of struct after an INSERT statement, like show bellow:

      scala> val data1="""{
           |     "timestamp": 1422435598,
           |     "data_array": [
           |         {
           |             "field1": 1,
           |             "field2": 2
           |         }
           |     ]
           | }"""
      scala> val data2="""{
           |     "timestamp": 1422435598,
           |     "data_array": [
           |         {
           |             "field1": 3,
           |             "field2": 4
           |         }
           |     ]
      
      scala> val jsonRDD = sc.makeRDD(data1 :: data2 :: Nil)
      scala> val rdd = hiveContext.jsonRDD(jsonRDD)
      scala> rdd.printSchema
      root
       |-- data_array: array (nullable = true)
       |    |-- element: struct (containsNull = false)
       |    |    |-- field1: integer (nullable = true)
       |    |    |-- field2: integer (nullable = true)
       |-- timestamp: integer (nullable = true)
      
      
      scala> rdd.registerTempTable("tmp_table")
      scala> hiveContext.sql("select data.field1 from tmp_table LATERAL VIEW explode(data_array) nestedStuff AS data").collect
      res3: Array[org.apache.spark.sql.Row] = Array([1], [3])
      
      scala> hiveContext.sql("SET hive.exec.dynamic.partition = true")
      scala> hiveContext.sql("SET hive.exec.dynamic.partition.mode = nonstrict")
      scala> hiveContext.sql("set parquet.compression=GZIP")
      scala> hiveContext.setConf("spark.sql.parquet.binaryAsString", "true")
      
      scala> hiveContext.sql("create external table if not exists persisted_table(data_array ARRAY <STRUCT<field1: INT, field2: INT>>, timestamp INT) STORED AS PARQUET Location 'hdfs://****/test_table'")
      
      scala> hiveContext.sql("insert into table persisted_table select * from tmp_table").collect
      scala> hiveContext.sql("select data.field1 from persisted_table LATERAL VIEW explode(data_array) nestedStuff AS data").collect
      
      parquet.io.ParquetDecodingException: Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00001
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:213)
        at parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:204)
        at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:145)
        at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        at scala.collection.AbstractIterator.to(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
        at org.apache.spark.scheduler.Task.run(Task.scala:56)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200)
        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:744)
      Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.rangeCheck(ArrayList.java:635)
        at java.util.ArrayList.get(ArrayList.java:411)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.getFirst(PrimitiveColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.isFirst(PrimitiveColumnIO.java:94)
        at parquet.io.RecordReaderImplementation.<init>(RecordReaderImplementation.java:274)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:131)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:96)
        at parquet.filter2.compat.FilterCompat$NoOpFilter.accept(FilterCompat.java:136)
        at parquet.io.MessageColumnIO.getRecordReader(MessageColumnIO.java:96)
        at parquet.hadoop.InternalParquetRecordReader.checkRead(InternalParquetRecordReader.java:126)
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:193)
        ... 28 more
      
      15/01/30 16:49:55 INFO TaskSetManager: Starting task 1.1 in stage 3.0 (TID 12, ****, NODE_LOCAL, 1610 bytes)
      15/01/30 16:49:55 INFO TaskSetManager: Lost task 1.1 in stage 3.0 (TID 12) on executor ****: parquet.io.ParquetDecodingException (Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00001) [duplicate 1]
      15/01/30 16:49:55 INFO TaskSetManager: Starting task 1.2 in stage 3.0 (TID 13, ****, NODE_LOCAL, 1610 bytes)
      15/01/30 16:49:55 WARN TaskSetManager: Lost task 2.0 in stage 3.0 (TID 11, ****): parquet.io.ParquetDecodingException: Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00002
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:213)
        at parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:204)
        at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:145)
        at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        at scala.collection.AbstractIterator.to(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
        at org.apache.spark.scheduler.Task.run(Task.scala:56)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200)
        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:744)
      Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.rangeCheck(ArrayList.java:635)
        at java.util.ArrayList.get(ArrayList.java:411)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.getFirst(PrimitiveColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.isFirst(PrimitiveColumnIO.java:94)
        at parquet.io.RecordReaderImplementation.<init>(RecordReaderImplementation.java:274)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:131)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:96)
        at parquet.filter2.compat.FilterCompat$NoOpFilter.accept(FilterCompat.java:136)
        at parquet.io.MessageColumnIO.getRecordReader(MessageColumnIO.java:96)
        at parquet.hadoop.InternalParquetRecordReader.checkRead(InternalParquetRecordReader.java:126)
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:193)
        ... 28 more
      
      15/01/30 16:49:55 INFO TaskSetManager: Starting task 2.1 in stage 3.0 (TID 14, ****, NODE_LOCAL, 1610 bytes)
      15/01/30 16:49:55 INFO TaskSetManager: Lost task 1.2 in stage 3.0 (TID 13) on executor ****: parquet.io.ParquetDecodingException (Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00001) [duplicate 2]
      15/01/30 16:49:55 INFO TaskSetManager: Starting task 1.3 in stage 3.0 (TID 15, ****, NODE_LOCAL, 1610 bytes)
      15/01/30 16:49:55 INFO TaskSetManager: Lost task 1.3 in stage 3.0 (TID 15) on executor ****: parquet.io.ParquetDecodingException (Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00001) [duplicate 3]
      15/01/30 16:49:55 ERROR TaskSetManager: Task 1 in stage 3.0 failed 4 times; aborting job
      15/01/30 16:49:55 INFO TaskSchedulerImpl: Cancelling stage 3
      15/01/30 16:49:55 INFO TaskSchedulerImpl: Stage 3 was cancelled
      15/01/30 16:49:55 INFO TaskSetManager: Lost task 2.1 in stage 3.0 (TID 14) on executor ****: parquet.io.ParquetDecodingException (Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00002) [duplicate 1]
      15/01/30 16:49:55 INFO TaskSchedulerImpl: Removed TaskSet 3.0, whose tasks have all completed, from pool 
      15/01/30 16:49:55 INFO DAGScheduler: Job 3 failed: collect at SparkPlan.scala:84, took 1.259053 s
      org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 3.0 failed 4 times, most recent failure: Lost task 1.3 in stage 3.0 (TID 15, ****): parquet.io.ParquetDecodingException: Can not read value at 0 in block -1 in file hdfs://*****/test_table/part-00001
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:213)
        at parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:204)
        at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:145)
        at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
        at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
        at scala.collection.AbstractIterator.to(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
        at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
        at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
        at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.rdd.RDD$$anonfun$17.apply(RDD.scala:797)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.SparkContext$$anonfun$runJob$4.apply(SparkContext.scala:1353)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
        at org.apache.spark.scheduler.Task.run(Task.scala:56)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200)
        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:744)
      Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.rangeCheck(ArrayList.java:635)
        at java.util.ArrayList.get(ArrayList.java:411)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.GroupColumnIO.getFirst(GroupColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.getFirst(PrimitiveColumnIO.java:99)
        at parquet.io.PrimitiveColumnIO.isFirst(PrimitiveColumnIO.java:94)
        at parquet.io.RecordReaderImplementation.<init>(RecordReaderImplementation.java:274)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:131)
        at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:96)
        at parquet.filter2.compat.FilterCompat$NoOpFilter.accept(FilterCompat.java:136)
        at parquet.io.MessageColumnIO.getRecordReader(MessageColumnIO.java:96)
        at parquet.hadoop.InternalParquetRecordReader.checkRead(InternalParquetRecordReader.java:126)
        at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:193)
        ... 28 more
      
      Driver stacktrace:
        at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1214)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1203)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1202)
        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
        at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1202)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696)
        at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696)
        at scala.Option.foreach(Option.scala:236)
        at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:696)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1420)
        at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
        at org.apache.spark.scheduler.DAGSchedulerEventProcessActor.aroundReceive(DAGScheduler.scala:1375)
        at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
        at akka.actor.ActorCell.invoke(ActorCell.scala:487)
        at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
        at akka.dispatch.Mailbox.run(Mailbox.scala:220)
        at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393)
        at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
        at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
        at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
        at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
      

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              lian cheng Cheng Lian
              Ayoub Ayoub Benali
              Cheng Lian Cheng Lian
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              Dates

                Created:
                Updated:
                Resolved: