Serialize Guava's MinMaxPriorityQueue

Question

After a few days researching why my Flink application is not working properly I've came to the conclusion that the problem resides in a MinMaxPriorityQueue I am using.

It seems that this structure is not serializable. I've tried several ways to serialize it:

env.getConfig.registerTypeWithKryoSerializer(classOf[MinMaxPriorityQueue[Double]], classOf[JavaSerializer])
env.getConfig.registerTypeWithKryoSerializer(classOf[MinMaxPriorityQueue[java.lang.Double]], classOf[ProtobufSerializer]);
env.getConfig().addDefaultKryoSerializer(MyCustomType.class, TBaseSerializer.class);

all of them without luck.

However I've found this: Serializing Guava's ImmutableTable

Is there an equivalent to MinMaxPriorityQueue, or a way to serialize it?

Update

I've translated Tomasz into scala:

class MinMaxPriorityQueueSerializer extends Serializer[MinMaxPriorityQueue[Object]] {
  private[this] val log = LoggerFactory.getLogger(this.getClass)
  setImmutable(false)
  setAcceptsNull(false)

  val OPTIMIZE_POSITIVE = true

  override def read(kryo: Kryo, input: Input, aClass: Class[MinMaxPriorityQueue[Object]]): MinMaxPriorityQueue[Object] = {
    log.error("Kryo READ")
    val comparator: Ordering[Object] = kryo.readClassAndObject(input).asInstanceOf[Ordering[Object]]
    val size = input.readInt(OPTIMIZE_POSITIVE)

    val queue: MinMaxPriorityQueue[Object] = MinMaxPriorityQueue.orderedBy(comparator)
      .expectedSize(size)
      .create()

    (0 to size).foreach(_ => queue.offer(kryo.readClassAndObject(input)))

    queue
  }

  override def write(kryo: Kryo, output: Output, queue: MinMaxPriorityQueue[Object]): Unit = {
    log.error("Kryo WRITE")
    kryo.writeClassAndObject(output, queue.comparator)

    val declaredSize = queue.size
    output.writeInt(declaredSize, OPTIMIZE_POSITIVE)

    val actualSize = queue.toArray.foldLeft(0) {
      case (z, q) =>
        kryo.writeClassAndObject(output, q)
        z + 1
    }

    Preconditions.checkState(
      declaredSize == actualSize,
      "Declared size (%s) different than actual size (%s)", declaredSize, actualSize)
  }
}

And set kryo in flink to use that Serializer:

env.getConfig.addDefaultKryoSerializer(classOf[MinMaxPriorityQueue[Double]], classOf[MinMaxPriorityQueueSerializer])       

env.getConfig.registerTypeWithKryoSerializer(classOf[MinMaxPriorityQueue[Double]], classOf[MinMaxPriorityQueueSerializer])

However it seems it gets never called, since I do not see anywhere in the logs the outputs of log.error("Kryo READ") and log.error("Kryo WRITE")

And the transformation still returns an empty MinMaxPriorityQueue, even I am updating it.

Update 2

I've implemented the SerializerTester, but I am getting a bufferUnderflow:

object Main {

  def main(args: Array[String]) {

    val tester = new MinMaxPriorityQueueSerializerTester()

    val inQueue: MinMaxPriorityQueue[java.lang.Double] = MinMaxPriorityQueue.create()
    inQueue.add(1.0)

    val outputStream = new ByteArrayOutputStream()
    tester.serialize(outputStream, inQueue)

    val inputStream = new ByteArrayInputStream(outputStream.toByteArray())
    val outQueue: MinMaxPriorityQueue[java.lang.Double] = tester.deserialize(inputStream);

    System.out.println(inQueue);
    System.out.println(outQueue);

  }

  class MinMaxPriorityQueueSerializerTester {
    val kryo = new Kryo
    kryo.setInstantiatorStrategy(new StdInstantiatorStrategy)
    registerMinMaxSerializer();
    //  allowForClassesWithoutNoArgConstructor(); // needed to serialize Ordering

    def registerMinMaxSerializer() {
      kryo.addDefaultSerializer(classOf[MinMaxPriorityQueue[java.lang.Double]], new MinMaxPriorityQueueSerializer());
    }

    def serialize(out: OutputStream, queue: MinMaxPriorityQueue[java.lang.Double]) {
      // try (Output output = new Output(out)) {
      val output = new Output(out)
      kryo.writeClassAndObject(output, queue)
      //      kryo.writeObject(output, queue)
      //}
      output.flush
    }

    def deserialize(in: InputStream): MinMaxPriorityQueue[java.lang.Double] = {
      //try (Input input = new Input(in)) {
      val input = new Input(in)
      //kryo.readObject(input, classOf[MinMaxPriorityQueue[java.lang.Double]])
      kryo.readClassAndObject(input).asInstanceOf[MinMaxPriorityQueue[java.lang.Double]]
      //p}
    }
  }

You can create an issue in Guava's Github repo and request that feature. There was [issue #615](https://github.com/google/guava/issues/615), which mentioned `MinMaxPriorityQueue`, but it wasn't included in the scope of the ticket in the end. — Grzegorz Rożniecki, Jun 28 '18 at 16:20
@Xaerxess, thanks, I've opened it : https://github.com/google/guava/issues/3192 — Alejandro Alcalde, Jun 28 '18 at 16:57
@elbaulp Could you post the stack trace of the bufferUnderflow? — Tomasz Linkowski, Jun 29 '18 at 10:26
nevermind, I changed to use this implementation of intervalHeap: https://github.com/allenbh/gkutil_java/blob/master/src/gkimfl/util/IntervalHeap.java as it works out of the box. Thank you for your help, I am accepting your answer. — Alejandro Alcalde, Jun 29 '18 at 11:28
@elbaulp Thanks, even though my answer didn't really solve your problem. You might consider posting a separate answer mentioning how you solved it in case anyone else has a similar problem. — Tomasz Linkowski, Jun 29 '18 at 11:56

score 3 · Accepted Answer · answered Jun 28 '18 at 18:07

You can use a custom Kryo Serializer.

Here is a sample one (in Java):

class MinMaxPriorityQueueSerializer extends Serializer<MinMaxPriorityQueue<Object>> {

    private static final boolean OPTIMIZE_POSITIVE = true;

    protected MinMaxPriorityQueueSerializer() {
        setAcceptsNull(false);
        setImmutable(false);
    }

    @Override
    public void write(Kryo kryo, Output output, MinMaxPriorityQueue<Object> queue) {
        kryo.writeClassAndObject(output, queue.comparator());

        int declaredSize = queue.size();
        output.writeInt(declaredSize, OPTIMIZE_POSITIVE);

        int actualSize = 0;
        for (Object element : queue) {
            kryo.writeClassAndObject(output, element);
            actualSize++;
        }

        Preconditions.checkState(
                declaredSize == actualSize,
                "Declared size (%s) different than actual size (%s)", declaredSize, actualSize
        );
    }

    @Override
    public MinMaxPriorityQueue<Object> read(Kryo kryo, Input input, Class<MinMaxPriorityQueue<Object>> type) {
        @SuppressWarnings("unchecked")
        Comparator<Object> comparator = (Comparator<Object>) kryo.readClassAndObject(input);
        int size = input.readInt(OPTIMIZE_POSITIVE);

        MinMaxPriorityQueue<Object> queue = MinMaxPriorityQueue.orderedBy(comparator)
                .expectedSize(size)
                .create();

        for (int i = 0; i < size; ++i) {
            queue.offer(kryo.readClassAndObject(input));
        }
        return queue;
    }
}

Here is how you could use it:

class MinMaxPriorityQueueSerializerTester {

    public static void main(String[] args) {
        MinMaxPriorityQueueSerializerTester tester = new MinMaxPriorityQueueSerializerTester();

        MinMaxPriorityQueue<Integer> inQueue = MinMaxPriorityQueue.<Integer>orderedBy(Comparator.reverseOrder())
                .create(Arrays.asList(5, 2, 7, 2, 4));

        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
        tester.serialize(outputStream, inQueue);

        ByteArrayInputStream inputStream = new ByteArrayInputStream(outputStream.toByteArray());
        @SuppressWarnings("unchecked")
        MinMaxPriorityQueue<Integer> outQueue = (MinMaxPriorityQueue<Integer>) tester.deserialize(inputStream);

        System.out.println(inQueue);
        System.out.println(outQueue);
    }

    private final Kryo kryo;

    public MinMaxPriorityQueueSerializerTester() {
        this.kryo = new Kryo();
        registerMinMaxSerializer();
        allowForClassesWithoutNoArgConstructor(); // needed to serialize Ordering
    }

    private void registerMinMaxSerializer() {
        kryo.addDefaultSerializer(MinMaxPriorityQueue.class, new MinMaxPriorityQueueSerializer());
    }

    private void allowForClassesWithoutNoArgConstructor() {
        ((Kryo.DefaultInstantiatorStrategy) kryo.getInstantiatorStrategy())
                .setFallbackInstantiatorStrategy(new StdInstantiatorStrategy());
    }


    public void serialize(OutputStream out, MinMaxPriorityQueue<?> queue) {
        try (Output output = new Output(out)) {
            kryo.writeObject(output, queue);
        }
    }

    public MinMaxPriorityQueue<?> deserialize(InputStream in) {
        try (Input input = new Input(in)) {
            return kryo.readObject(input, MinMaxPriorityQueue.class);
        }
    }
}

@elbaulp I tested this code code in Java, and it worked. Have you tested the serialization in Scala (outside of Flink)? If not, please do (as I did in `MinMaxPriorityQueueSerializerTester`), and then we will know more. — Tomasz Linkowski, Jun 29 '18 at 08:57

score 1 · Answer 2 · answered Jun 29 '18 at 17:01

1

I finally give up and tried to use a different Data Structure and make it Serializable with java.io.Serializable.

This Data Structure is an IntervalHeap implemented here, I just made it Serializable in my project.

All works correctly now.

answered Jun 29 '18 at 17:01

Alejandro Alcalde

5,990
6
39
79

Serialize Guava's MinMaxPriorityQueue

Update

Update 2

2 Answers2