Apache Spark MLLib - Running KMeans with IDF-TF vectors - Java heap space

问题

I'm trying to run a KMeans on MLLib from a (large) collection of text documents (TF-IDF vectors). Documents are sent through a Lucene English analyzer, and sparse vectors are created from HashingTF.transform() function. Whatever the degree of parrallelism I'm using (through the coalesce function), KMeans.train always return an OutOfMemory exception below. Any thought on how to tackle this issue ?

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at scala.reflect.ManifestFactory$$anon$12.newArray(Manifest.scala:138)
at scala.reflect.ManifestFactory$$anon$12.newArray(Manifest.scala:136)
at breeze.linalg.Vector$class.toArray(Vector.scala:80)
at breeze.linalg.SparseVector.toArray(SparseVector.scala:48)
at breeze.linalg.Vector$class.toDenseVector(Vector.scala:75)
at breeze.linalg.SparseVector.toDenseVector(SparseVector.scala:48)
at breeze.linalg.Vector$class.toDenseVector$mcD$sp(Vector.scala:74)
at breeze.linalg.SparseVector.toDenseVector$mcD$sp(SparseVector.scala:48)
at org.apache.spark.mllib.clustering.BreezeVectorWithNorm.toDense(KMeans.scala:422)
at org.apache.spark.mllib.clustering.KMeans$$anonfun$initKMeansParallel$1.apply(KMeans.scala:285)
at org.apache.spark.mllib.clustering.KMeans$$anonfun$initKMeansParallel$1.apply(KMeans.scala:284)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
at org.apache.spark.mllib.clustering.KMeans.initKMeansParallel(KMeans.scala:284)
at org.apache.spark.mllib.clustering.KMeans.runBreeze(KMeans.scala:143)
at org.apache.spark.mllib.clustering.KMeans.run(KMeans.scala:126)
at org.apache.spark.mllib.clustering.KMeans$.train(KMeans.scala:338)
at org.apache.spark.mllib.clustering.KMeans$.train(KMeans.scala:348)

回答1:

After some investigations, it turns out that this issue was related to new HashingTF().transform(v) method. Although creating sparse vectors using hashing trick is really helpful (especially when the number of features is not known), vector must be kept sparse. Default size for HashingTF vectors is 2^20. Given a 64bits double precision, each vector would theoretically require 8MB when converted to Dense vector - regardless the dimension reduction we could apply.

Sadly, KMeans uses toDense method (at least for the cluster centers), therefore causing OutOfMemory error (imagine with k = 1000).

  private def initRandom(data: RDD[BreezeVectorWithNorm]) : Array[Array[BreezeVectorWithNorm]] = {
    val sample = data.takeSample(true, runs * k, new XORShiftRandom().nextInt()).toSeq
    Array.tabulate(runs)(r => sample.slice(r * k, (r + 1) * k).map { v =>
      new BreezeVectorWithNorm(v.vector.toDenseVector, v.norm)
    }.toArray)
  }

来源：https://stackoverflow.com/questions/26449446/apache-spark-mllib-running-kmeans-with-idf-tf-vectors-java-heap-space