[SPARK-12222] deserialize RoaringBitmap using Kryo serializer throw Buffer underflow exception

• Type: Bug
• Status: Resolved
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 1.6.0
• Fix Version/s: 1.6.0, 2.0.0
• Component/s: Spark Core
• Assignee: Fei Wang
• Reporter: Fei Wang
• Created: 09/Dec/15 01:12
• Updated: 10/Dec/15 13:10
• Resolved: 09/Dec/15 05:33

Description

here are some problems when deserialize RoaringBitmap. see the examples below:
run this piece of code
```
import com.esotericsoftware.kryo.io.

{Input => KryoInput, Output => KryoOutput}

import java.io.DataInput

class KryoInputDataInputBridge(input: KryoInput) extends DataInput

{ override def readLong(): Long = input.readLong() override def readChar(): Char = input.readChar() override def readFloat(): Float = input.readFloat() override def readByte(): Byte = input.readByte() override def readShort(): Short = input.readShort() override def readUTF(): String = input.readString() // readString in kryo does utf8 override def readInt(): Int = input.readInt() override def readUnsignedShort(): Int = input.readShortUnsigned() override def skipBytes(n: Int): Int = input.skip(n.toLong).toInt override def readFully(b: Array[Byte]): Unit = input.read(b) override def readFully(b: Array[Byte], off: Int, len: Int): Unit = input.read(b, off, len) override def readLine(): String = throw new UnsupportedOperationException("readLine") override def readBoolean(): Boolean = input.readBoolean() override def readUnsignedByte(): Int = input.readByteUnsigned() override def readDouble(): Double = input.readDouble() }

class KryoOutputDataOutputBridge(output: KryoOutput) extends DataOutput

{ override def writeFloat(v: Float): Unit = output.writeFloat(v) // There is no "readChars" counterpart, except maybe "readLine", which is not supported override def writeChars(s: String): Unit = throw new UnsupportedOperationException("writeChars") override def writeDouble(v: Double): Unit = output.writeDouble(v) override def writeUTF(s: String): Unit = output.writeString(s) // writeString in kryo does UTF8 override def writeShort(v: Int): Unit = output.writeShort(v) override def writeInt(v: Int): Unit = output.writeInt(v) override def writeBoolean(v: Boolean): Unit = output.writeBoolean(v) override def write(b: Int): Unit = output.write(b) override def write(b: Array[Byte]): Unit = output.write(b) override def write(b: Array[Byte], off: Int, len: Int): Unit = output.write(b, off, len) override def writeBytes(s: String): Unit = output.writeString(s) override def writeChar(v: Int): Unit = output.writeChar(v.toChar) override def writeLong(v: Long): Unit = output.writeLong(v) override def writeByte(v: Int): Unit = output.writeByte(v) }

val outStream = new FileOutputStream("D:
wfserde")
val output = new KryoOutput(outStream)
val bitmap = new RoaringBitmap
bitmap.add(1)
bitmap.add(3)
bitmap.add(5)
bitmap.serialize(new KryoOutputDataOutputBridge(output))
output.flush()
output.close()

val inStream = new FileInputStream("D:
wfserde")
val input = new KryoInput(inStream)
val ret = new RoaringBitmap
ret.deserialize(new KryoInputDataInputBridge(input))

println(ret)
```

this will throw `Buffer underflow` error:
```
com.esotericsoftware.kryo.KryoException: Buffer underflow.
at com.esotericsoftware.kryo.io.Input.require(Input.java:156)
at com.esotericsoftware.kryo.io.Input.skip(Input.java:131)
at com.esotericsoftware.kryo.io.Input.skip(Input.java:264)
at org.apache.spark.sql.SQLQuerySuite$$anonfun$6$KryoInputDataInputBridge$1.skipBytes
```

after same investigation, i found this is caused by a bug of kryo's `Input.skip(long count)`(https://github.com/EsotericSoftware/kryo/issues/119) and we call this method in `KryoInputDataInputBridge`.

So i think we can fix this issue in this two ways:
1) upgrade the kryo version to 2.23.0 or 2.24.0, which has fix this bug in kryo (i am not sure the upgrade is safe in spark, can you check it? @davies )

2) we can bypass the kryo's `Input.skip(long count)` by directly call another `skip` method in kryo's Input.java(https://github.com/EsotericSoftware/kryo/blob/kryo-2.21/src/com/esotericsoftware/kryo/io/Input.java#L124), i.e. write the bug-fixed version of `Input.skip(long count)` in KryoInputDataInputBridge's `skipBytes` method:
```
class KryoInputDataInputBridge(input: KryoInput) extends DataInput {
...
override def skipBytes(n: Int): Int = {
var remaining: Long = n
while (remaining > 0)

{ val skip = Math.min(Integer.MAX_VALUE, remaining).asInstanceOf[Int] input.skip(skip) remaining -= skip }

n
}
...
}
```

Issue Links

• links to: [Github] Pull Request #10213 (scwf)
• links to: [Github] Pull Request #10253 (adrian-wang)