I got this error when trying to perform PCA on a sparse matrix, each row has a nominal length of 8000, and there are 36k rows. each row has on average 3 elements being non-zero. I guess the total size is not that big.
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.util.Arrays.copyOf(Arrays.java:2271) at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:113) at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93) at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:140) at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1876) at java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1785) at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1188) at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:347) at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:42) at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:73) at org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:164) at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:158) at org.apache.spark.SparkContext.clean(SparkContext.scala:1242) at org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:597) at org.apache.spark.mllib.rdd.RDDFunctions.treeAggregate(RDDFunctions.scala:100) at org.apache.spark.mllib.linalg.distributed.RowMatrix.computeGramianMatrix(RowMatrix.scala:112) at org.apache.spark.mllib.linalg.distributed.RowMatrix.computeCovariance(RowMatrix.scala:314) at org.apache.spark.mllib.linalg.distributed.RowMatrix.computePrincipalComponents(RowMatrix.scala:349) at SimpleApp$.main(SimpleApp.scala:50) at SimpleApp.main(SimpleApp.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.apache.spark.deploy.SparkSubmit$.launch(SparkSubmit.scala:328) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:75) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) the command I used was ~/tools/spark-1.1.0-bin-hadoop2.4/bin/spark-submit --executor-memory 1G --driver-memory 1g --conf spark.executor.memory=1G --class SimpleApp --master spark://VirtualBox:7077 target/scala-test-1.0-SNAPSHOT-jar-with-dependencies.jar I tried using 2G or 3G, but my virtual box crashed.
