I have been stuck on this problem for the last few days:
I am attempting to run random forest from MLLIB, it gets through most of it,
but breaks when doing a mapPartition operation. The following stack trace is
shown:
: An error occurred while calling o94.trainRandomForestModel.
: java.lang.OutOfMemoryError
at
java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at
java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at
java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at
java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at
java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1877)
at
java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1786)
at
java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1189)
at
java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:348)
at
org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:44)
at
org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:84)
at
org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:301)
at
org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:294)
at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:122)
at org.apache.spark.SparkContext.clean(SparkContext.scala:2021)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1.apply(RDD.scala:703)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitions$1.apply(RDD.scala:702)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:306)
at org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:702)
at
org.apache.spark.mllib.tree.DecisionTree$.findBestSplits(DecisionTree.scala:625)
at
org.apache.spark.mllib.tree.RandomForest.run(RandomForest.scala:235)
at
org.apache.spark.mllib.tree.RandomForest$.trainClassifier(RandomForest.scala:291)
at
org.apache.spark.mllib.api.python.PythonMLLibAPI.trainRandomForestModel(PythonMLLibAPI.scala:742)
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:497)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:231)
at
py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:379)
at py4j.Gateway.invoke(Gateway.java:259)
at
py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:133)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:207)
at java.lang.Thread.run(Thread.java:745)
It seems to me that it's trying to serialize the mapPartitions closure, but
runs out of space doing so. However I don't understand how it could run out
of space when I gave the driver ~190GB for a file that's 45MB.
I have a cluster setup on AWS such that my master is a r3.8xlarge along with
two r3.4xlarge workers. I have the following configurations:
spark version: 1.5.0
-----------------------------------
spark.executor.memory 32000m
spark.driver.memory 230000m
spark.driver.cores 10
spark.executor.cores 5
spark.executor.instances 17
spark.driver.maxResultSize 0
spark.storage.safetyFraction 1
spark.storage.memoryFraction 0.9
spark.storage.shuffleFraction 0.05
spark.default.parallelism 128
The master machine has approximately 240 GB of ram and each worker has about
120GB of ram.
I load in a relatively tiny RDD of MLLIB LabeledPoint objects, with each
holding sparse vectors inside. This RDD has a total size of roughly 45MB. My
sparse vector has a total length of ~15 million while only about 3000 or so
are non-zeros.
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