DataFrame. SparkPlan / Project serialization issue: ArrayIndexOutOfBounds.
Hi,
I'm using spark 1.3.1 built against hadoop 1.0.4 and java 1.7 and I'm
trying to save my data frame to parquet.
The issue I'm stuck looks like serialization tries to do pretty weird
thing: tries to write to an empty array.
The last (through stack trace) line of spark code that leads to exception
is in method SerializationDebugger.visitSerializable(o: Object, stack:
List[String]): List[String].
desc.getObjFieldValues(finalObj, objFieldValues)
The reason it does so, is because finalObj is
org.apache.spark.sql.execution.Project and objFieldValues is an empty
array! As a result there are two fields to read from the Project instance
object (happens in java.io.ObjectStreamClass), but there is an empty array
to read into.
A little bit of code with debug info:
private def visitSerializable(o: Object, stack: List[String]): List[String]
= {
val (finalObj, desc) = findObjectAndDescriptor(o) //finalObj: Project,
desc: org.apache.spark.sql.execution.Project
val slotDescs = desc.getSlotDescs //java.io.ObjectStreamClass[2] [0:
SparkPlan, 1: Project]
var i = 0 //i: 0
while (i slotDescs.length) {
val slotDesc = slotDescs(i) //slotDesc:
org.apache.spark.sql.execution.SparkPlan
if (slotDesc.hasWriteObjectMethod) {
// TODO: Handle classes that specify writeObject method.
} else {
val fields: Array[ObjectStreamField] = slotDesc.getFields
//fields: java.io.ObjectStreamField[1] [0: Z codegenEnabled]
val objFieldValues: Array[Object] = new
Array[Object](slotDesc.getNumObjFields) //objFieldValues:
java.lang.Object[0]
val numPrims = fields.length - objFieldValues.length //numPrims: 1
desc.getObjFieldValues(finalObj, objFieldValues) //leads to
exception
So it looks like it gets objFieldValues array from the SparkPlan object,
but uses it to receive values from Project object.
Here is the schema of my data frame
root
|-- Id: long (nullable = true)
|-- explodes: struct (nullable = true)
||-- Identifiers: array (nullable = true)
|||-- element: struct (containsNull = true)
||||-- Type: array (nullable = true)
|||||-- element: string (containsNull = true)
|-- Identifiers: struct (nullable = true)
||-- Type: array (nullable = true)
|||-- element: string (containsNull = true)
|-- Type2: string (nullable = true)
|-- Type: string (nullable = true)
Actual stack trace is:
org.apache.spark.SparkException: Task not serializable
at
org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:166)
at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:158)
at org.apache.spark.SparkContext.clean(SparkContext.scala:1623)
at org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:635)
at org.apache.spark.sql.execution.Project.execute(basicOperators.scala:40)
at
org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:84)
at org.apache.spark.sql.DataFrame.collect(DataFrame.scala:887)
at
com.reltio.analytics.data.application.DataAccessTest.testEntities_NestedAttribute(DataAccessTest.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at
org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at
org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.junit.runner.JUnitCore.run(JUnitCore.java:160)
at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:68)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
Re: DataFrame. SparkPlan / Project serialization issue: ArrayIndexOutOfBounds.
You've probably hit this bug:
https://issues.apache.org/jira/browse/SPARK-7180
It's fixed in Spark 1.4.1+. Try setting spark.serializer.extraDebugInfo to
false and see if it goes away.
On Fri, Aug 21, 2015 at 3:37 AM, Eugene Morozov evgeny.a.moro...@gmail.com
wrote:
Hi,
I'm using spark 1.3.1 built against hadoop 1.0.4 and java 1.7 and I'm
trying to save my data frame to parquet.
The issue I'm stuck looks like serialization tries to do pretty weird
thing: tries to write to an empty array.
The last (through stack trace) line of spark code that leads to exception
is in method SerializationDebugger.visitSerializable(o: Object, stack:
List[String]): List[String].
desc.getObjFieldValues(finalObj, objFieldValues)
The reason it does so, is because finalObj is
org.apache.spark.sql.execution.Project and objFieldValues is an empty
array! As a result there are two fields to read from the Project instance
object (happens in java.io.ObjectStreamClass), but there is an empty array
to read into.
A little bit of code with debug info:
private def visitSerializable(o: Object, stack: List[String]):
List[String] = {
val (finalObj, desc) = findObjectAndDescriptor(o) //finalObj: Project,
desc: org.apache.spark.sql.execution.Project
val slotDescs = desc.getSlotDescs //java.io.ObjectStreamClass[2] [0:
SparkPlan, 1: Project]
var i = 0 //i: 0
while (i slotDescs.length) {
val slotDesc = slotDescs(i) //slotDesc:
org.apache.spark.sql.execution.SparkPlan
if (slotDesc.hasWriteObjectMethod) {
// TODO: Handle classes that specify writeObject method.
} else {
val fields: Array[ObjectStreamField] = slotDesc.getFields
//fields: java.io.ObjectStreamField[1] [0: Z codegenEnabled]
val objFieldValues: Array[Object] = new
Array[Object](slotDesc.getNumObjFields) //objFieldValues:
java.lang.Object[0]
val numPrims = fields.length - objFieldValues.length //numPrims:
1
desc.getObjFieldValues(finalObj, objFieldValues) //leads to
exception
So it looks like it gets objFieldValues array from the SparkPlan object,
but uses it to receive values from Project object.
Here is the schema of my data frame
root
|-- Id: long (nullable = true)
|-- explodes: struct (nullable = true)
||-- Identifiers: array (nullable = true)
|||-- element: struct (containsNull = true)
||||-- Type: array (nullable = true)
|||||-- element: string (containsNull = true)
|-- Identifiers: struct (nullable = true)
||-- Type: array (nullable = true)
|||-- element: string (containsNull = true)
|-- Type2: string (nullable = true)
|-- Type: string (nullable = true)
Actual stack trace is:
org.apache.spark.SparkException: Task not serializable
at
org.apache.spark.util.ClosureCleaner$.ensureSerializable(ClosureCleaner.scala:166)
at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:158)
at org.apache.spark.SparkContext.clean(SparkContext.scala:1623)
at org.apache.spark.rdd.RDD.mapPartitions(RDD.scala:635)
at org.apache.spark.sql.execution.Project.execute(basicOperators.scala:40)
at
org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:84)
at org.apache.spark.sql.DataFrame.collect(DataFrame.scala:887)
at
com.reltio.analytics.data.application.DataAccessTest.testEntities_NestedAttribute(DataAccessTest.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at
org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
at
org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at
org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
at
org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at
org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at
org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
at
org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
at org.junit.runner.JUnitCore.run(JUnitCore.java:160)
at com.intellij.rt.execution.junit.JUnitStarter.main(JUnitStarter.java:68)
Caused by:
