NullPointerException when running Apache.spark - apache-spark

Question

I am trying to run a query over redshift to extract into a dataframe, same query works on spark 2.0.2, but since databricks deprecate this old version, I moved to spark 2.2.1, and I am getting the following exception with the new environment.
Any help is appreciated.
In short, the NullPointerException is coming from
java.lang.NullPointerException at org.apache.spark.sql.catalyst.expressions.codegen.UnsafeRowWriter.write(UnsafeRowWriter.java:210) at".
I tried to disable sparkConf.set("spark.sql.codegen.wholeStage","false") as well, but it still does not work.
Does anyone know how to fix this?
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1683)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1671)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1670)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1670)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:931)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:931)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:931)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1903)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1854)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1842)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:733)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2114)
at org.apache.spark.sql.execution.collect.Collector.runSparkJobs(Collector.scala:231)
at org.apache.spark.sql.execution.collect.Collector.collect(Collector.scala:241)
at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:64)
at org.apache.spark.sql.execution.collect.Collector$.collect(Collector.scala:70)
at org.apache.spark.sql.execution.CollectLimitExec.executeCollectResult(limit.scala:45)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectResult(Dataset.scala:2484)
at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3037)
at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2453)
at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2453)
at org.apache.spark.sql.Dataset$$anonfun$59.apply(Dataset.scala:3021)
at org.apache.spark.sql.execution.SQLExecution$.withCustomExecutionEnv(SQLExecution.scala:89)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:127)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3020)
at org.apache.spark.sql.Dataset.collect(Dataset.scala:2453)
at com.axs.dataplatform.redshift.merge.RedshiftMerger.merge(RedshiftMerger.scala:30)
at com.axs.dataplatform.flashseats.segmentation.operations.Merge$.doMerge(Merge.scala:36)
at com.axs.dataplatform.flashseats.segmentation.FlashseatsSegmentation$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(FlashseatsSegmentation.scala:99)
at com.axs.dataplatform.flashseats.segmentation.FlashseatsSegmentation$$anonfun$2$$anonfun$apply$1$$anonfun$apply$2.apply(FlashseatsSegmentation.scala:99)
at scala.collection.immutable.List.foreach(List.scala:381)
at com.axs.dataplatform.flashseats.segmentation.FlashseatsSegmentation$$anonfun$2$$anonfun$apply$1.apply(FlashseatsSegmentation.scala:99)
at com.axs.dataplatform.flashseats.segmentation.FlashseatsSegmentation$$anonfun$2$$anonfun$apply$1.apply(FlashseatsSegmentation.scala:97)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at scala.collection.parallel.ParIterableLike$Foreach.leaf(ParIterableLike.scala:972)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
at scala.collection.parallel.ParIterableLike$Foreach.tryLeaf(ParIterableLike.scala:969)
at scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
at scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by a java.lang.NullPointerException:
at org.apache.spark.sql.catalyst.expressions.codegen.UnsafeRowWriter.write(UnsafeRowWriter.java:210)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$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:423)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.agg_doAggregateWithKeys$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$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:423)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:53)
at org.apache.spark.scheduler.Task.run(Task.scala:110)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:349)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
When I set the spark.sql.codegen.wholeStage to false, I get another NullPointerException:
Caused by: java.lang.NullPointerException
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificSafeProjection.apply_0$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificSafeProjection.apply(Unknown Source)
at scala.collection.Iterator$$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 scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:462)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.execution.aggregate.HashAggregateExec$$anonfun$doExecute$1$$anonfun$9.apply(HashAggregateExec.scala:132)
at org.apache.spark.sql.execution.aggregate.HashAggregateExec$$anonfun$doExecute$1$$anonfun$9.apply(HashAggregateExec.scala:130)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$26.apply(RDD.scala:855)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$26.apply(RDD.scala:855)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:332)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:296)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:332)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:296)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:96)

Answer 1

Yes, I did, did you encounter the same problem?
Here's the solution:
def setNullableStateForAllColumns( df: DataFrame, nullable: Boolean) = {
// get schema
val schema = df.schema
StructType(schema.map {
case StructField( c, t, _, m) ⇒ StructField( c, t, nullable = nullable, m)
})
}
def extractNullableData(sql: String): DataFrame = {
logger.info(s"Extracting data from ${source.conf} with sql:\n$sql")
val tempS3Dir = "s3n://data-platform-temp/tmp/redshift_extract"
val origDf =
context
.read
.format("com.databricks.spark.redshift")
.option("forward_spark_s3_credentials", true)
.option("url", source.jdbcUrlWPass)
.option("jdbcdriver", source.driver)
.option("autoenablessl", "false")
.option("tempdir", tempS3Dir)
.option("query", sql)
.load()
context.read
.format("com.databricks.spark.redshift")
.option("forward_spark_s3_credentials", true)
.option("url", source.jdbcUrlWPass)
.option("jdbcdriver", source.driver)
.option("autoenablessl", "false")
.schema(setNullableStateForAllColumns(origDf, true))
.option("tempdir", tempS3Dir)
.option("query", sql)
.load()
}