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https://issues.apache.org/jira/browse/SPARK-12222?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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Apache Spark reassigned SPARK-12222:
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Assignee: (was: Apache Spark)
> deserialize RoaringBitmap using Kryo serializer throw Buffer underflow
> exception
> --------------------------------------------------------------------------------
>
> Key: SPARK-12222
> URL: https://issues.apache.org/jira/browse/SPARK-12222
> Project: Spark
> Issue Type: Bug
> Components: Spark Core
> Affects Versions: 1.6.0
> Reporter: Fei Wang
>
> 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
> }
> ...
> }
> ```
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