Scala & Spark : java.lang.ArrayStoreException on deserialisation - scala

I'm working on in Scala & Spark to load a big file (60+ GB) JSON file and process it. Since using sparksession.read.json leads to out-of-memory exception, I've went to the RDD route.
import org.json4s._
import org.json4s.jackson.JsonMethods._
import org.json4s.jackson.Serialization.{read}
val submissions_rdd = sc.textFile("/home/user/repos/concepts/abcde/RS_2019-09")
//val columns_subset = Set("author", "title", "selftext", "score", "created_utc", "subreddit")
case class entry(title: String,
selftext: String,
score: Double,
created_utc: Double,
subreddit: String,
author: String)
def jsonExtractObject(jsonStr: String) = {
implicit val formats = org.json4s.DefaultFormats
read[entry](jsonStr)
}
Upon testing my function on a single entry, I get the desired result:
val res = jsonExtractObject(submissions_rdd.take(1)(0))
res: entry =
entry(Last Ditch Effort,​
https://preview.redd.it/9x4ld036ivj31.jpg?width=780&format=pjpg&auto=webp&s=acaed6cc0d913ec31b54235ca8bb73971bcfe598,1.0,1.567296E9,YellowOnlineUnion,Sgedelta)
Problem is, after trying to map the same function to the RDD I'm getting an error:
val subset = submissions_rdd.map(line => jsonExtractObject(line) )
subset.take(5)
org.apache.spark.SparkDriverExecutionException: Execution error at
org.apache.spark.scheduler.DAGScheduler.handleTaskCompletion(DAGScheduler.scala:1485)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2236)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099) at
org.apache.spark.SparkContext.runJob(SparkContext.scala:2120) at
org.apache.spark.SparkContext.runJob(SparkContext.scala:2139) at
org.apache.spark.rdd.RDD.$anonfun$take$1(RDD.scala:1423) at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:388) at
org.apache.spark.rdd.RDD.take(RDD.scala:1396) ... 41 elided Caused
by: java.lang.ArrayStoreException: [Lentry; at
scala.runtime.ScalaRunTime$.array_update(ScalaRunTime.scala:75) at
org.apache.spark.SparkContext.$anonfun$runJob$4(SparkContext.scala:2120)
at
org.apache.spark.SparkContext.$anonfun$runJob$4$adapted(SparkContext.scala:2120)
at
org.apache.spark.scheduler.JobWaiter.taskSucceeded(JobWaiter.scala:59)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskCompletion(DAGScheduler.scala:1481)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2236)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
Would appreciate if any has any hints on how to go around that. Thanks!

Related

Error comes when using User Defined Case Class in Scala

The result that I am trying to find out is that, I need to find the distinct repos accessed by a particular user, using the inverted index based method in Scala. I have made the required Case Class to extract the data from the input file, and hence made the required RDD and joined on the basis of the required user, but whenver after finding all the repos accessed. When I try to use the distinct and then count function, then I get some error, which I will paste below.
The code is as follows:
import org.apache.spark.rdd.RDD
import java.text.SimpleDateFormat
import java.util.Date
case class LogLine(debug_level: String, timestamp: Date, download_id: String,retrieval_stage: String, rest: String);
val regex = """([^\s]+), ([^\s]+)\+00:00, ([^\s]+) -- ([^\s]+): (.*$)""".r
val rdd = sc.
textFile("file.txt").
flatMap ( x => x match {
case regex(debug_level,dateTime,downloadId,retrievalStage,rest) =>
val df = new SimpleDateFormat("yyyy-MM-dd:HH:mm:ss")
new Some(LogLine(debug_level, df.parse(dateTime.replace("T", ":")), downloadId, retrievalStage, rest))
case _ => None;
})
rdd.cache()
val inverted2 = rdd.groupBy(element => element.download_id).cache
val list2 = List[String]("ghtorrent-22")
val user = sc.parallelize(list2).keyBy(x => x)
val poss = inverted2.join(user).flatMap{x => x._2._1}.map(line => line.rest)
After this, whenever, I try to run, the next part to evaluate the result, I get the error.
The code and error are as follows:
Code:
poss.distinct.count
Error:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 5 in stage 8.0 failed 1 times, most recent failure: Lost task 5.0 in stage 8.0 (TID 59) (LAPTOP-Q81MN7NI executor driver): java.lang.OutOfMemoryError: Java heap space
at java.base/java.io.ObjectInputStream$HandleTable.grow(ObjectInputStream.java:4055)
at java.base/java.io.ObjectInputStream$HandleTable.assign(ObjectInputStream.java:3861)
at java.base/java.io.ObjectInputStream.readString(ObjectInputStream.java:2043)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1661)
at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2464)
at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2358)
at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2196)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1679)
at java.base/java.io.ObjectInputStream.readArray(ObjectInputStream.java:2102)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1667)
at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2464)
at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2358)
at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2196)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1679)
at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:493)
at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:451)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:76)
at org.apache.spark.serializer.DeserializationStream.readValue(Serializer.scala:158)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$DiskMapIterator.readNextItem(ExternalAppendOnlyMap.scala:514)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$DiskMapIterator.hasNext(ExternalAppendOnlyMap.scala:538)
at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:1087)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.readNextHashCode(ExternalAppendOnlyMap.scala:335)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.$anonfun$new$1(ExternalAppendOnlyMap.scala:315)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.$anonfun$new$1$adapted(ExternalAppendOnlyMap.scala:313)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator$$Lambda$3514/0x0000000101065840.apply(Unknown Source)
at scala.collection.immutable.List.foreach(List.scala:392)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.<init>(ExternalAppendOnlyMap.scala:313)
at org.apache.spark.util.collection.ExternalAppendOnlyMap.iterator(ExternalAppendOnlyMap.scala:287)
at org.apache.spark.Aggregator.combineValuesByKey(Aggregator.scala:43)
at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:118)
at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:106)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2258)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2207)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2206)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2206)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1079)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1079)
at scala.Option.foreach(Option.scala:407)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1079)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2445)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2387)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2376)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:868)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2196)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2217)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2236)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2261)
at org.apache.spark.rdd.RDD.count(RDD.scala:1253)
... 37 elided
Caused by: java.lang.OutOfMemoryError: Java heap space
at java.base/java.io.ObjectInputStream$HandleTable.grow(ObjectInputStream.java:4055)
at java.base/java.io.ObjectInputStream$HandleTable.assign(ObjectInputStream.java:3861)
at java.base/java.io.ObjectInputStream.readString(ObjectInputStream.java:2043)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1661)
at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2464)
at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2358)
at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2196)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1679)
at java.base/java.io.ObjectInputStream.readArray(ObjectInputStream.java:2102)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1667)
at java.base/java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2464)
at java.base/java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2358)
at java.base/java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2196)
at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1679)
at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:493)
at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:451)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:76)
at org.apache.spark.serializer.DeserializationStream.readValue(Serializer.scala:158)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$DiskMapIterator.readNextItem(ExternalAppendOnlyMap.scala:514)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$DiskMapIterator.hasNext(ExternalAppendOnlyMap.scala:538)
at scala.collection.Iterator$$anon$22.hasNext(Iterator.scala:1087)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.readNextHashCode(ExternalAppendOnlyMap.scala:335)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.$anonfun$new$1(ExternalAppendOnlyMap.scala:315)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.$anonfun$new$1$adapted(ExternalAppendOnlyMap.scala:313)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator$$Lambda$3514/0x0000000101065840.apply(Unknown Source)
at scala.collection.immutable.List.foreach(List.scala:392)
at org.apache.spark.util.collection.ExternalAppendOnlyMap$ExternalIterator.<init>(ExternalAppendOnlyMap.scala:313)
at org.apache.spark.util.collection.ExternalAppendOnlyMap.iterator(ExternalAppendOnlyMap.scala:287)
at org.apache.spark.Aggregator.combineValuesByKey(Aggregator.scala:43)
at org.apache.spark.shuffle.BlockStoreShuffleReader.read(BlockStoreShuffleReader.scala:118)
at org.apache.spark.rdd.ShuffledRDD.compute(ShuffledRDD.scala:106)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:373)

Scala Reflection exception during creation of DataSet in Spark

I want to run Spark Job on Spark Jobserver.
During execution, I got an exception:
stack:
java.lang.RuntimeException: scala.ScalaReflectionException: class
com.some.example.instrument.data.SQLMapping in JavaMirror with
org.apache.spark.util.MutableURLClassLoader#55b699ef of type class
org.apache.spark.util.MutableURLClassLoader with classpath
[file:/app/spark-job-server.jar] and parent being
sun.misc.Launcher$AppClassLoader#2e817b38 of type class
sun.misc.Launcher$AppClassLoader with classpath [.../classpath
jars/] not found.
at
scala.reflect.internal.Mirrors$RootsBase.staticClass(Mirrors.scala:123)
at
scala.reflect.internal.Mirrors$RootsBase.staticClass(Mirrors.scala:22)
at
com.some.example.instrument.DataRetriever$$anonfun$combineMappings$1$$typecreator15$1.apply(DataRetriever.scala:136)
at
scala.reflect.api.TypeTags$WeakTypeTagImpl.tpe$lzycompute(TypeTags.scala:232)
at scala.reflect.api.TypeTags$WeakTypeTagImpl.tpe(TypeTags.scala:232)
at
org.apache.spark.sql.catalyst.encoders.ExpressionEncoder$.apply(ExpressionEncoder.scala:49)
at org.apache.spark.sql.Encoders$.product(Encoders.scala:275) at
org.apache.spark.sql.LowPrioritySQLImplicits$class.newProductEncoder(SQLImplicits.scala:233)
at
org.apache.spark.sql.SQLImplicits.newProductEncoder(SQLImplicits.scala:33)
at
com.some.example.instrument.DataRetriever$$anonfun$combineMappings$1.apply(DataRetriever.scala:136)
at
com.some.example.instrument.DataRetriever$$anonfun$combineMappings$1.apply(DataRetriever.scala:135)
at scala.util.Success$$anonfun$map$1.apply(Try.scala:237) at
scala.util.Try$.apply(Try.scala:192) at
scala.util.Success.map(Try.scala:237) at
scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237) at
scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:237) at
scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32) at
scala.concurrent.impl.ExecutionContextImpl$AdaptedForkJoinTask.exec(ExecutionContextImpl.scala:121)
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)
In DataRetriever I convert simple case class to DataSet.
case class definition:
case class SQLMapping(id: String,
it: InstrumentPrivateKey,
cc: Option[String],
ri: Option[SourceInstrumentId],
p: Option[SourceInstrumentId],
m: Option[SourceInstrumentId])
case class SourceInstrumentId(instrumentId: Long,
providerId: String)
case class InstrumentPrivateKey(instrumentId: Long,
providerId: String,
clientId: String)
code that causes a problem:
import session.implicits._
def someFunc(future: Future[ID]): Dataset[SQLMappins] = {
future.map {f =>
val seq: Seq[SQLMapping] = getFromEndpoint(f)
val ds: Dataset[SQLMapping] = seq.toDS()
...
}
}
The job sometimes works, but if I re-run job, it will throw an exception.
update 28.03.2018
I forgot to mention one detail, that turns out to be important.
Dataset was constructed inside of Future.
Calling toDS() inside future causing ScalaReflectionException.
I decided to construct DataSet outside future.map.
You can verify that Dataset can't be constructed in future.map with this example job.
package com.example.sparkapplications
import com.typesafe.config.Config
import org.apache.spark.SparkContext
import org.apache.spark.sql.SparkSession
import scala.concurrent.Await
import scala.concurrent.Future
import scala.concurrent.duration._
import scala.concurrent.ExecutionContext.Implicits.global
import spark.jobserver.SparkJob
import spark.jobserver.SparkJobValid
import spark.jobserver.SparkJobValidation
object FutureJob extends SparkJob{
override def runJob(sc: SparkContext,
jobConfig: Config): Any = {
val session = SparkSession.builder().config(sc.getConf).getOrCreate()
import session.implicits._
val f = Future{
val seq = Seq(
Dummy("1", 1),
Dummy("2", 2),
Dummy("3", 3),
Dummy("4", 4),
Dummy("5", 5)
)
val ds = seq.toDS
ds.collect()
}
Await.result(f, 10 seconds)
}
case class Dummy(id: String, value: Long)
override def validate(sc: SparkContext,
config: Config): SparkJobValidation = SparkJobValid
}
Later I will provide information if the problem persists using spark 2.3.0, and when you pass jar via spark-submit directly.

How to edit Columns in GraphFrame Aggregate Messages?

I am pretty new to GraphFrames and Scala. I am writing some sort of label propagation algorithm (very different from the library one). Essentially each vertex has an array "memVector" and the edge has a float value "floatWeights". I want to update each vertex's memVector to the be the sum of (floatWeights * memVector) from all of its neighbors. This is the code I have written for the same:
import org.apache.spark.sql.SparkSession
import org.apache.spark.sql.SQLContext
import org.apache.spark.SparkContext
import org.graphframes._
import org.graphframes.lib.AggregateMessages
import org.apache.spark.sql.functions.udf
val sqlContext = new SQLContext(sc)
val edges = spark.read.parquet("code/SampleGraphEdge")
val vertices = spark.read.parquet("code/SampleGraphVer")
val toInteger: String => Int = _.toInt
val toIntegerUDF = udf(toInteger)
val newEdges = edges.withColumn("floatWeights", toIntegerUDF('weights)).drop("weights")
val graph = GraphFrame(vertices, newEdges)
val AM = AggregateMessages
val msgToSrc = AM.dst("memVector")
val msgToDst = AM.src("memVector")
val msgFromEdge = AM.edge("floatWeights")
def aggfunc(msg: org.apache.spark.sql.Column) = sum(msg.getField("weights") * AM.msg.getField("memVector"))
val agg = graph.aggregateMessages.sendToSrc(msgToSrc).sendToDst(msgToDst).sendToSrc(sendFromEdge).sendToDst(sendFromEdge).agg(aggfunc(AM.msg).as("UpdatedVector"))
Now the aggfunc I wrote is not right as I cannot multiply an array and a float directly. I am running the above in spark-shell and I am getting the following error at the last line:
org.apache.spark.sql.AnalysisException: Can't extract value from MSG#750;
at org.apache.spark.sql.catalyst.expressions.ExtractValue$.apply(complexTypeExtractors.scala:73)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$$anonfun$apply$9$$anonfun$applyOrElse$5.applyOrElse(Analyzer.scala:613)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$$anonfun$apply$9$$anonfun$applyOrElse$5.applyOrElse(Analyzer.scala:605)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$2.apply(TreeNode.scala:312)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$transformUp$2.apply(TreeNode.scala:312)
at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:69)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:311)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$5.apply(TreeNode.scala:328)
at org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:186)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformChildren(TreeNode.scala:326)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$5.apply(TreeNode.scala:328)
at org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:186)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformChildren(TreeNode.scala:326)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$5.apply(TreeNode.scala:328)
at org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:186)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformChildren(TreeNode.scala:326)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$5.apply(TreeNode.scala:328)
at org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:186)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformChildren(TreeNode.scala:326)
at org.apache.spark.sql.catalyst.trees.TreeNode.transformUp(TreeNode.scala:305)
at org.apache.spark.sql.catalyst.plans.QueryPlan.transformExpressionUp$1(QueryPlan.scala:269)
at org.apache.spark.sql.catalyst.plans.QueryPlan.org$apache$spark$sql$catalyst$plans$QueryPlan$$recursiveTransform$2(QueryPlan.scala:279)
at org.apache.spark.sql.catalyst.plans.QueryPlan$$anonfun$org$apache$spark$sql$catalyst$plans$QueryPlan$$recursiveTransform$2$1.apply(QueryPlan.scala:283)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
at scala.collection.AbstractTraversable.map(Traversable.scala:104)
at org.apache.spark.sql.catalyst.plans.QueryPlan.org$apache$spark$sql$catalyst$plans$QueryPlan$$recursiveTransform$2(QueryPlan.scala:283)
at org.apache.spark.sql.catalyst.plans.QueryPlan$$anonfun$8.apply(QueryPlan.scala:288)
at org.apache.spark.sql.catalyst.trees.TreeNode.mapProductIterator(TreeNode.scala:186)
at org.apache.spark.sql.catalyst.plans.QueryPlan.transformExpressionsUp(QueryPlan.scala:288)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$$anonfun$apply$9.applyOrElse(Analyzer.scala:605)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$$anonfun$apply$9.applyOrElse(Analyzer.scala:547)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan$$anonfun$resolveOperators$1.apply(LogicalPlan.scala:61)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan$$anonfun$resolveOperators$1.apply(LogicalPlan.scala:61)
at org.apache.spark.sql.catalyst.trees.CurrentOrigin$.withOrigin(TreeNode.scala:69)
at org.apache.spark.sql.catalyst.plans.logical.LogicalPlan.resolveOperators(LogicalPlan.scala:60)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$.apply(Analyzer.scala:547)
at org.apache.spark.sql.catalyst.analysis.Analyzer$ResolveReferences$.apply(Analyzer.scala:484)
at org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1$$anonfun$apply$1.apply(RuleExecutor.scala:85)
at org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1$$anonfun$apply$1.apply(RuleExecutor.scala:82)
at scala.collection.LinearSeqOptimized$class.foldLeft(LinearSeqOptimized.scala:124)
at scala.collection.immutable.List.foldLeft(List.scala:84)
at org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1.apply(RuleExecutor.scala:82)
at org.apache.spark.sql.catalyst.rules.RuleExecutor$$anonfun$execute$1.apply(RuleExecutor.scala:74)
at scala.collection.immutable.List.foreach(List.scala:381)
at org.apache.spark.sql.catalyst.rules.RuleExecutor.execute(RuleExecutor.scala:74)
at org.apache.spark.sql.execution.QueryExecution.analyzed$lzycompute(QueryExecution.scala:65)
at org.apache.spark.sql.execution.QueryExecution.analyzed(QueryExecution.scala:63)
at org.apache.spark.sql.execution.QueryExecution.assertAnalyzed(QueryExecution.scala:51)
at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:64)
at org.apache.spark.sql.RelationalGroupedDataset.toDF(RelationalGroupedDataset.scala:62)
at org.apache.spark.sql.RelationalGroupedDataset.agg(RelationalGroupedDataset.scala:222)
at org.graphframes.lib.AggregateMessages.agg(AggregateMessages.scala:127)
... 50 elided
Am I approaching it right? Any workarounds/solutions will be greatly appreciated.

Scala Case Class serialization

I've been trying to binary serialize a composite case class object that kept throwing a weird exception. I don't really understand what is wrong with this example which throws the following exception. I used to get that exception for circular references which is not the case here. Some hints please?
java.lang.ClassCastException: cannot assign instance of scala.collection.immutable.List$SerializationProxy to field com.Table.rows of type scala.collection.immutable.List in instance of com.Table
java.lang.ClassCastException: cannot assign instance of scala.collection.immutable.List$SerializationProxy to field com.Table.rows of type scala.collection.immutable.List in instance of com.Table
at java.io.ObjectStreamClass$FieldReflector.setObjFieldValues(ObjectStreamClass.java:2133)
at java.io.ObjectStreamClass.setObjFieldValues(ObjectStreamClass.java:1305)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2024)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1942)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at com.TestSeri$.serializeBinDeserialise(TestSeri.scala:37)
at com.TestSeri$.main(TestSeri.scala:22)
at com.TestSeri.main(TestSeri.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
Here is the code
import java.io._
import scalax.file.Path
case class Row(name: String)
case class Table(rows: List[Row])
case class Cont(docs: Map[String, Table])
case object TestSeri {
def main(args: Array[String]) {
val cc = Cont(docs = List(
"1" -> Table(rows = List(Row("r1"), Row("r2"))),
"2" -> Table(rows = List(Row("r301"), Row("r31"), Row("r32")))
).toMap)
val tt = Table(rows = List(Row("r1"), Row("r2")))
val ttdes = serializeBinDeserialize(tt)
println(ttdes == tt)
val ccdes = serializeBinDeserialize(cc)
println(ccdes == cc)
}
def serializeBinDeserialize[T](payload: T): T = {
val bos = new ByteArrayOutputStream()
val out = new ObjectOutputStream(bos)
out.writeObject(payload)
val bis = new ByteArrayInputStream(bos.toByteArray)
val in = new ObjectInputStream(bis)
in.readObject().asInstanceOf[T]
}
}
Replacing List with Array which is immutable too, fixed the problem.
In my original problem I had a Map which I replaced with TreeMap.
I think is likely to be related to the proxy pattern implementation in generic immutable List and Map mentioned here:
https://issues.scala-lang.org/browse/SI-9237.
Can't believe I wasted a full day on this.

Spark Hadoop Failed to get broadcast

Running a spark-submit job and receiving a "Failed to get broadcast_58_piece0..." error. I'm really not sure what I'm doing wrong. Am I overusing UDFs? Too complicated a function?
As a summary of my objective, I am parsing text from pdfs, which are stored as base64 encoded strings in JSON objects. I'm using Apache Tika to get the text, and trying to make copious use of data frames to make things easier.
I had written a piece of code that ran the text extraction through tika as a function outside of "main" on the data as a RDD, and that worked flawlessly. When I try to bring the extraction into main as a UDF on data frames, though, it borks in various different ways. Before I got here I was actually trying to write the final data frame as:
valid.toJSON.saveAsTextFile(hdfs_dir)
This was giving me all sorts of "File/Path already exists" headaches.
Current code:
object Driver {
def main(args: Array[String]):Unit = {
val hdfs_dir = args(0)
val spark_conf = new SparkConf().setAppName("Spark Tika HDFS")
val sc = new SparkContext(spark_conf)
val sqlContext = new org.apache.spark.sql.SQLContext(sc)
import sqlContext.implicits._
// load json data into dataframe
val df = sqlContext.read.json("hdfs://hadoophost.com:8888/user/spark/data/in/*")
val extractInfo: (Array[Byte] => String) = (fp: Array[Byte]) => {
val parser:Parser = new AutoDetectParser()
val handler:BodyContentHandler = new BodyContentHandler(Integer.MAX_VALUE)
val config:TesseractOCRConfig = new TesseractOCRConfig()
val pdfConfig:PDFParserConfig = new PDFParserConfig()
val inputstream:InputStream = new ByteArrayInputStream(fp)
val metadata:Metadata = new Metadata()
val parseContext:ParseContext = new ParseContext()
parseContext.set(classOf[TesseractOCRConfig], config)
parseContext.set(classOf[PDFParserConfig], pdfConfig)
parseContext.set(classOf[Parser], parser)
parser.parse(inputstream, handler, metadata, parseContext)
handler.toString
}
val extract_udf = udf(extractInfo)
val df2 = df.withColumn("unbased_media", unbase64($"media_file")).drop("media_file")
val dfRenamed = df2.withColumn("media_corpus", extract_udf(col("unbased_media"))).drop("unbased_media")
val depuncter: (String => String) = (corpus: String) => {
val r = corpus.replaceAll("""[\p{Punct}]""", "")
val s = r.replaceAll("""[0-9]""", "")
s
}
val depuncter_udf = udf(depuncter)
val withoutPunct = dfRenamed.withColumn("sentence", depuncter_udf(col("media_corpus")))
val model = sc.objectFile[org.apache.spark.ml.PipelineModel]("hdfs://hadoophost.com:8888/user/spark/hawkeye-nb-ml-v2.0").first()
val with_predictions = model.transform(withoutPunct)
val fullNameChecker: ((String, String, String, String, String) => String) = (fname: String, mname: String, lname: String, sfx: String, text: String) =>{
val newtext = text.replaceAll(" ", "").replaceAll("""[0-9]""", "").replaceAll("""[\p{Punct}]""", "").toLowerCase
val new_fname = fname.replaceAll(" ", "").replaceAll("""[0-9]""", "").replaceAll("""[\p{Punct}]""", "").toLowerCase
val new_mname = mname.replaceAll(" ", "").replaceAll("""[0-9]""", "").replaceAll("""[\p{Punct}]""", "").toLowerCase
val new_lname = lname.replaceAll(" ", "").replaceAll("""[0-9]""", "").replaceAll("""[\p{Punct}]""", "").toLowerCase
val new_sfx = sfx.replaceAll(" ", "").replaceAll("""[0-9]""", "").replaceAll("""[\p{Punct}]""", "").toLowerCase
val name_full = new_fname.concat(new_mname).concat(new_lname).concat(new_sfx)
val c = name_full.r.findAllIn(newtext).length
c match {
case 0 => "N"
case _ => "Y"
}
}
val fullNameChecker_udf = udf(fullNameChecker)
val stringChecker: ((String, String) => String) = (term: String, text: String) => {
val termLower = term.replaceAll("""[\p{Punct}]""", "").toLowerCase
val textLower = text.replaceAll("""[\p{Punct}]""", "").toLowerCase
val c = termLower.r.findAllIn(textLower).length
c match {
case 0 => "N"
case _ => "Y"
}
}
val stringChecker_udf = udf(stringChecker)
val stringChecker2: ((String, String) => String) = (term: String, text: String) => {
val termLower = term takeRight 4
val textLower = text
val c = termLower.r.findAllIn(textLower).length
c match {
case 0 => "N"
case _ => "Y"
}
}
val stringChecker2_udf = udf(stringChecker)
val valids = with_predictions.withColumn("fname_valid", stringChecker_udf(col("first_name"), col("media_corpus")))
.withColumn("lname_valid", stringChecker_udf(col("last_name"), col("media_corpus")))
.withColumn("fname2_valid", stringChecker_udf(col("first_name_2"), col("media_corpus")))
.withColumn("lname2_valid", stringChecker_udf(col("last_name_2"), col("media_corpus")))
.withColumn("camt_valid", stringChecker_udf(col("chargeoff_amount"), col("media_corpus")))
.withColumn("ocan_valid", stringChecker2_udf(col("original_creditor_account_nbr"), col("media_corpus")))
.withColumn("dpan_valid", stringChecker2_udf(col("debt_provider_account_nbr"), col("media_corpus")))
.withColumn("full_name_valid", fullNameChecker_udf(col("first_name"), col("middle_name"), col("last_name"), col("suffix"), col("media_corpus")))
.withColumn("full_name_2_valid", fullNameChecker_udf(col("first_name_2"), col("middle_name_2"), col("last_name_2"), col("suffix_2"), col("media_corpus")))
valids.write.mode(SaveMode.Overwrite).format("json").save(hdfs_dir)
}
}
Full stack trace starting with error:
16/06/14 15:02:01 WARN TaskSetManager: Lost task 0.0 in stage 4.0 (TID 53, hdpd11n05.squaretwofinancial.com): org.apache.spark.SparkException: Task failed while writing rows.
at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.writeRows(WriterContainer.scala:272)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1$$anonfun$apply$mcV$sp$3.apply(InsertIntoHadoopFsRelation.scala:150)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelation$$anonfun$run$1$$anonfun$apply$mcV$sp$3.apply(InsertIntoHadoopFsRelation.scala:150)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: org.apache.spark.SparkException: Failed to get broadcast_58_piece0 of broadcast_58
at org.apache.spark.util.Utils$.tryOrIOException(Utils.scala:1222)
at org.apache.spark.broadcast.TorrentBroadcast.readBroadcastBlock(TorrentBroadcast.scala:165)
at org.apache.spark.broadcast.TorrentBroadcast._value$lzycompute(TorrentBroadcast.scala:64)
at org.apache.spark.broadcast.TorrentBroadcast._value(TorrentBroadcast.scala:64)
at org.apache.spark.broadcast.TorrentBroadcast.getValue(TorrentBroadcast.scala:88)
at org.apache.spark.broadcast.Broadcast.value(Broadcast.scala:70)
at org.apache.spark.ml.feature.CountVectorizerModel$$anonfun$9$$anonfun$apply$7.apply(CountVectorizer.scala:222)
at org.apache.spark.ml.feature.CountVectorizerModel$$anonfun$9$$anonfun$apply$7.apply(CountVectorizer.scala:221)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:34)
at org.apache.spark.ml.feature.CountVectorizerModel$$anonfun$9.apply(CountVectorizer.scala:221)
at org.apache.spark.ml.feature.CountVectorizerModel$$anonfun$9.apply(CountVectorizer.scala:218)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificUnsafeProjection.evalExpr43$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$SpecificUnsafeProjection.apply(Unknown Source)
at org.apache.spark.sql.execution.Project$$anonfun$1$$anonfun$apply$1.apply(basicOperators.scala:51)
at org.apache.spark.sql.execution.Project$$anonfun$1$$anonfun$apply$1.apply(basicOperators.scala:49)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
at org.apache.spark.sql.execution.datasources.DefaultWriterContainer.writeRows(WriterContainer.scala:263)
... 8 more
Caused by: org.apache.spark.SparkException: Failed to get broadcast_58_piece0 of broadcast_58
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$readBlocks$1$$anonfun$2.apply(TorrentBroadcast.scala:138)
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$readBlocks$1$$anonfun$2.apply(TorrentBroadcast.scala:138)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$readBlocks$1.apply$mcVI$sp(TorrentBroadcast.scala:137)
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$readBlocks$1.apply(TorrentBroadcast.scala:120)
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$org$apache$spark$broadcast$TorrentBroadcast$$readBlocks$1.apply(TorrentBroadcast.scala:120)
at scala.collection.immutable.List.foreach(List.scala:318)
at org.apache.spark.broadcast.TorrentBroadcast.org$apache$spark$broadcast$TorrentBroadcast$$readBlocks(TorrentBroadcast.scala:120)
at org.apache.spark.broadcast.TorrentBroadcast$$anonfun$readBroadcastBlock$1.apply(TorrentBroadcast.scala:175)
at org.apache.spark.util.Utils$.tryOrIOException(Utils.scala:1219)
... 25 more
I encountered a similar error.
It turns out to be caused by the broadcast usage in CounterVectorModel. Following is the detailed cause in my case:
When model.transform() is called , the vocabulary is broadcasted and saved as an attribute broadcastDic in model implicitly. Therefore, if the CounterVectorModel is saved after calling model.transform(), the private var attribute broadcastDic is also saved. But unfortunately, in Spark, broadcasted object is context-sensitive, which means it is embedded in SparkContext. If that CounterVectorModel is loaded in a different SparkContext, it will fail to find the previous saved broadcastDic.
So either solution is to prevent calling model.transform() before saving the model, or clone the model by method model.copy().
For anyone coming across this, it turns out the model I was loading was malformed. I found out by using spark-shell in yarn-client mode and stepping through the code. When I tried to load the model it was fine, but running it against the datagram (model.transform) through errors about not finding a metadata directory.
I went back and found a good model, ran against that and it worked fine. This code is actually sound.