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Posted to issues@spark.apache.org by "Jay Luan (JIRA)" <ji...@apache.org> on 2015/09/26 01:19:04 UTC
[jira] [Updated] (SPARK-10821) RandomForest serialization OOM
during findBestSplits
[ https://issues.apache.org/jira/browse/SPARK-10821?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Jay Luan updated SPARK-10821:
-----------------------------
Description:
I am getting OOM during serialization for a relatively small dataset for a RandomForest. Even with spark.serializer.objectStreamReset at 1, It is still running out of memory when attempting to serialize my data.
Stack Trace:
Traceback (most recent call last):
File "/root/random_forest/random_forest_spark.py", line 198, in <module>
main()
File "/root/random_forest/random_forest_spark.py", line 166, in main
trainModel(dset)
File "/root/random_forest/random_forest_spark.py", line 191, in trainModel
impurity='gini', maxDepth=4, maxBins=32)
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 352, in trainClassifier
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 270, in _train
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 130, in callMLlibFunc
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 123, in callJavaFunc
File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/java_gateway.py", line 538, in __call__
File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/protocol.py", line 300, in get_return_value
py4j.protocol.Py4JJavaError15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Done removing RDD 7, response is 0
15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Sent response: 0 to AkkaRpcEndpointRef(Actor[akka://sparkDriver/temp/$Mj])
: An error occurred while calling o89.trainRandomForestModel.
: java.lang.OutOfMemoryError
at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1876)
at java.io.ObjectOutputStream$BlockDataOutputStream.setBlockDataMode(ObjectOutputStream.java:1785)
at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1188)
at java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:347)
at org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:44)
at org.apache.spark.serializer.JavaSerializerInstance.serialize(JavaSerializer.scala:84)
at org.apache.spark.util.ClosureCleaner$.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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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)
Details:
My RDD is type 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. Works fine for up to sparse vector size 10 million.
My cluster is setup on AWS such that my master is a r3.8xlarge along with two r3.4xlarge workers. Driver has ~190GB allocated to it while my RDD is ~45MB.
Configurations as follows:
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
spark.serializer.objectStreamReset 1
My original code is in python which I tried on 1.4.0 and 1.5.0, so I thought that maybe running something in scala may resolve the problem. I wrote a toy scala example and tested it on the same system yielding the same errors. Note the test code will most likely eventually throw an error due to the fact certain features are always 0 and MLLIB currently errors out during this operation.
Running the following using spark-shell with my spark configuration gives me the OOM:
--------------------------------------------------------------------------
import scala.util.Random
import scala.collection.mutable.ArrayBuffer
import org.apache.spark.mllib.tree.RandomForest
import org.apache.spark.mllib.tree.model.RandomForestModel
import org.apache.spark.mllib.util.MLUtils
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.mllib.regression.LabeledPoint
val r = Random
var size = 15000000
var count = 3000
val indptr = (1 to size by size/count).toArray
val data = Seq.fill(count)(r.nextDouble()).toArray
var dset = ArrayBuffer[LabeledPoint]()
for (i <- 1 to 10) {
dset += LabeledPoint(r.nextInt(2), Vectors.sparse(size, indptr, data));
}
val distData = sc.parallelize(dset)
val splits = distData.randomSplit(Array(0.7, 0.3))
val (trainingData, testData) = (splits(0), splits(1))
// Train a RandomForest model.
// Empty categoricalFeaturesInfo indicates all features are continuous.
val numClasses = 2
val categoricalFeaturesInfo = Map[Int, Int]()
val numTrees = 3 // Use more in practice.
val featureSubsetStrategy = "auto" // Let the algorithm choose.
val impurity = "gini"
val maxDepth = 4
val maxBins = 32
val model = RandomForest.trainClassifier(trainingData, numClasses, categoricalFeaturesInfo,
numTrees, featureSubsetStrategy, impurity, maxDepth, maxBins)
was:
I am getting OOM during serialization for a relatively small dataset for a RandomForest. Even with spark.serializer.objectStreamReset at 1, It is still running out of memory when attempting to serialize my data.
Stack Trace:
Traceback (most recent call last):
File "/root/random_forest/random_forest_spark.py", line 198, in <module>
main()
File "/root/random_forest/random_forest_spark.py", line 166, in main
trainModel(dset)
File "/root/random_forest/random_forest_spark.py", line 191, in trainModel
impurity='gini', maxDepth=4, maxBins=32)
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 352, in trainClassifier
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 270, in _train
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 130, in callMLlibFunc
File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 123, in callJavaFunc
File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/java_gateway.py", line 538, in __call__
File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/protocol.py", line 300, in get_return_value
py4j.protocol.Py4JJavaError15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Done removing RDD 7, response is 0
15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Sent response: 0 to AkkaRpcEndpointRef(Actor[akka://sparkDriver/temp/$Mj])
: An error occurred while calling o89.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: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: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:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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)
Details:
My RDD is type 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.
My cluster is setup on AWS such that my master is a r3.8xlarge along with two r3.4xlarge workers. Driver has ~190GB allocated to it while my RDD is ~45MB.
Configurations as follows:
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
spark.serializer.objectStreamReset 1
My original code is in python which I tried on 1.4.0 and 1.5.0, so I thought that maybe running something in scala may resolve the problem. I wrote a toy scala example and tested it on the same system yielding the same errors. Note the test code will most likely eventually throw an error due to the fact certain features are always 0 and MLLIB currently errors out during this operation.
test.scala:
--------------------------------------------------------------------------
import scala.util.Random
import scala.collection.mutable.ArrayBuffer
import org.apache.spark.mllib.tree.RandomForest
import org.apache.spark.mllib.tree.model.RandomForestModel
import org.apache.spark.mllib.util.MLUtils
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.mllib.regression.LabeledPoint
val r = Random
var size = 15000000
var count = 3000
val indptr = (1 to size by size/count).toArray
val data = Seq.fill(count)(r.nextDouble()).toArray
var dset = ArrayBuffer[LabeledPoint]()
for (i <- 1 to 10) {
dset += LabeledPoint(r.nextInt(2), Vectors.sparse(size, indptr, data));
}
val distData = sc.parallelize(dset)
val splits = distData.randomSplit(Array(0.7, 0.3))
val (trainingData, testData) = (splits(0), splits(1))
// Train a RandomForest model.
// Empty categoricalFeaturesInfo indicates all features are continuous.
val numClasses = 2
val categoricalFeaturesInfo = Map[Int, Int]()
val numTrees = 3 // Use more in practice.
val featureSubsetStrategy = "auto" // Let the algorithm choose.
val impurity = "gini"
val maxDepth = 4
val maxBins = 32
val model = RandomForest.trainClassifier(trainingData, numClasses, categoricalFeaturesInfo,
numTrees, featureSubsetStrategy, impurity, maxDepth, maxBins)
> RandomForest serialization OOM during findBestSplits
> ----------------------------------------------------
>
> Key: SPARK-10821
> URL: https://issues.apache.org/jira/browse/SPARK-10821
> Project: Spark
> Issue Type: Bug
> Components: MLlib
> Affects Versions: 1.4.0, 1.5.0
> Environment: Amazon EC2 Linux
> Reporter: Jay Luan
> Labels: OOM, out-of-memory
>
> I am getting OOM during serialization for a relatively small dataset for a RandomForest. Even with spark.serializer.objectStreamReset at 1, It is still running out of memory when attempting to serialize my data.
> Stack Trace:
> Traceback (most recent call last):
> File "/root/random_forest/random_forest_spark.py", line 198, in <module>
> main()
> File "/root/random_forest/random_forest_spark.py", line 166, in main
> trainModel(dset)
> File "/root/random_forest/random_forest_spark.py", line 191, in trainModel
> impurity='gini', maxDepth=4, maxBins=32)
> File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 352, in trainClassifier
> File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/tree.py", line 270, in _train
> File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 130, in callMLlibFunc
> File "/root/spark/python/lib/pyspark.zip/pyspark/mllib/common.py", line 123, in callJavaFunc
> File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/java_gateway.py", line 538, in __call__
> File "/root/spark/python/lib/py4j-0.8.2.1-src.zip/py4j/protocol.py", line 300, in get_return_value
> py4j.protocol.Py4JJavaError15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Done removing RDD 7, response is 0
> 15/09/25 00:44:41 DEBUG BlockManagerSlaveEndpoint: Sent response: 0 to AkkaRpcEndpointRef(Actor[akka://sparkDriver/temp/$Mj])
> : An error occurred while calling o89.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$BlockDataOutputStream.drain(ObjectOutputStream.java:1876)
> at java.io.ObjectOutputStream$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: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:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> 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)
> Details:
> My RDD is type 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. Works fine for up to sparse vector size 10 million.
> My cluster is setup on AWS such that my master is a r3.8xlarge along with two r3.4xlarge workers. Driver has ~190GB allocated to it while my RDD is ~45MB.
> Configurations as follows:
> 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
> spark.serializer.objectStreamReset 1
> My original code is in python which I tried on 1.4.0 and 1.5.0, so I thought that maybe running something in scala may resolve the problem. I wrote a toy scala example and tested it on the same system yielding the same errors. Note the test code will most likely eventually throw an error due to the fact certain features are always 0 and MLLIB currently errors out during this operation.
> Running the following using spark-shell with my spark configuration gives me the OOM:
> --------------------------------------------------------------------------
> import scala.util.Random
> import scala.collection.mutable.ArrayBuffer
> import org.apache.spark.mllib.tree.RandomForest
> import org.apache.spark.mllib.tree.model.RandomForestModel
> import org.apache.spark.mllib.util.MLUtils
> import org.apache.spark.mllib.linalg.Vectors
> import org.apache.spark.mllib.regression.LabeledPoint
> val r = Random
> var size = 15000000
> var count = 3000
> val indptr = (1 to size by size/count).toArray
> val data = Seq.fill(count)(r.nextDouble()).toArray
> var dset = ArrayBuffer[LabeledPoint]()
> for (i <- 1 to 10) {
> dset += LabeledPoint(r.nextInt(2), Vectors.sparse(size, indptr, data));
> }
> val distData = sc.parallelize(dset)
> val splits = distData.randomSplit(Array(0.7, 0.3))
> val (trainingData, testData) = (splits(0), splits(1))
> // Train a RandomForest model.
> // Empty categoricalFeaturesInfo indicates all features are continuous.
> val numClasses = 2
> val categoricalFeaturesInfo = Map[Int, Int]()
> val numTrees = 3 // Use more in practice.
> val featureSubsetStrategy = "auto" // Let the algorithm choose.
> val impurity = "gini"
> val maxDepth = 4
> val maxBins = 32
> val model = RandomForest.trainClassifier(trainingData, numClasses, categoricalFeaturesInfo,
> numTrees, featureSubsetStrategy, impurity, maxDepth, maxBins)
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