Apache Spark: StackOverflowError when trying to indexing string columns

Question

I have csv file with about 5000 rows and 950 columns. First I load it to DataFrame:

val data = sqlContext.read
  .format(csvFormat)
  .option("header", "true")
  .option("inferSchema", "true")
  .load(file)
  .cache()

After that I search all string columns

val featuresToIndex = data.schema
  .filter(_.dataType == StringType)
  .map(field => field.name)

and want to index them. For that I create indexers for each string column

val stringIndexers = featuresToIndex.map(colName =>
  new StringIndexer()
    .setInputCol(colName)
    .setOutputCol(colName + "Indexed"))

and create pipeline

val pipeline = new Pipeline().setStages(stringIndexers.toArray)

But when I try to transform my initial dataframe with this pipeline

val indexedDf = pipeline.fit(data).transform(data)

I get StackOverflowError

16/07/05 16:55:12 INFO DAGScheduler: Job 4 finished: countByValue at StringIndexer.scala:86, took 7.882774 s
Exception in thread "main" java.lang.StackOverflowError
at scala.collection.immutable.Set$Set1.contains(Set.scala:84)
at scala.collection.immutable.Set$Set1.$plus(Set.scala:86)
at scala.collection.immutable.Set$Set1.$plus(Set.scala:81)
at scala.collection.mutable.SetBuilder.$plus$eq(SetBuilder.scala:22)
at scala.collection.mutable.SetBuilder.$plus$eq(SetBuilder.scala:20)
at scala.collection.generic.Growable$class.loop$1(Growable.scala:53)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:57)
at scala.collection.mutable.SetBuilder.$plus$plus$eq(SetBuilder.scala:20)
at scala.collection.TraversableLike$class.to(TraversableLike.scala:590)
at scala.collection.AbstractTraversable.to(Traversable.scala:104)
at scala.collection.TraversableOnce$class.toSet(TraversableOnce.scala:304)
at scala.collection.AbstractTraversable.toSet(Traversable.scala:104)
at org.apache.spark.sql.catalyst.trees.TreeNode.containsChild$lzycompute(TreeNode.scala:86)
at org.apache.spark.sql.catalyst.trees.TreeNode.containsChild(TreeNode.scala:86)
at org.apache.spark.sql.catalyst.trees.TreeNode$$anonfun$4.apply(TreeNode.scala:280)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
...

What am I doing wrong? Thanks.

Answer 1

Most probably there is just not enough memory to keep all stack frames. I experienced something similar when trained RandomForestModel. The workaround that works for me is is to run my driver application (that's web service) with additional parameters:

-XX:ThreadStackSize=81920 -Dspark.executor.extraJavaOptions='-XX:ThreadStackSize=81920'

Answer 2

Seems like I found the kind of solution - use spark 2.0. Previously, I used 1.6.2 - it was the latest version at the time of issue. I tried to use the preview version of 2.0, but there is also the problem reproduced.