Future-proof serialization

[tdunning]

Currently, we depend on Java's serialization which is not a good strategy.

It would be much better to do our own and make all the different kinds of Digest use interchangeable formats.

[Nikko78]

You can overload Java serialization process to save what you want, for example in my example, methods getBytes and fromBytes already implements in your Digest classes.

In this example, fields of object are ignored and only declared "digestEncodeWithBytes" field is declared :

public abstract class TDigest implements Serializable {

    // For serialisation, overload ObjectInput/OutputStream reflection
    private static final ObjectStreamField[] serialPersistentFields = {
        new ObjectStreamField("digestEncodeWithBytes", byte[].class)
    };

    // Or use getBytes(ByteBuffer) instead
    public abstract byte[] getBytes();

    // Serialization create the object which implements this abstract class, so call a method to init it
    protected abstract void initWithBytes(byte[] b);

    /**
     * Overload {@link ObjectOutputStream#defaultWriteObject()}
     *
     * @param oos object output stream use for write
     * @throws IOException error during write process
     */
    private void writeObject(ObjectOutputStream oos) throws IOException {
        oos.putFields().put("digestEncodeWithBytes", getBytes());
        oos.writeFields();
    }

    /**
     * Overload {@link ObjectInputStream#defaultReadObject()}
     *
     * @param ois object input stream use for read
     * @throws IOException error during read process
     * @throws ClassNotFoundException class use in serialised stream unknown
     */
    private void readObject(ObjectInputStream ois) throws IOException, ClassNotFoundException {
        Object o = ois.readFields().get("digestEncodeWithBytes", null);
        if (o != null) {
            byte[] b = (byte[]) o;
            initWithBytes(b);
        }
    }
}

You can also overwrite deserialisation with : link

class HackedObjectInputStream extends ObjectInputStream {

    public HackedObjectInputStream(InputStream in) throws IOException {
        super(in);
    }

    @Override
    protected ObjectStreamClass readClassDescriptor() throws IOException, ClassNotFoundException {
        ObjectStreamClass resultClassDescriptor = super.readClassDescriptor();

        if (resultClassDescriptor.getName().equals("oldpackage.Clazz"))
            resultClassDescriptor = ObjectStreamClass.lookup(newpackage.Clazz.class);

        return resultClassDescriptor;
    }
}

[anvinjain]

Isn't it possible to add a Transcoder interface which has byte[] asBytes(SerializationModel) and SerializationModel fromBytes(byte[]) methods? SerializationModel here being a java object that is good enough to represent any digest. TDigest interface can now have a create method that takes SerializationModel as input which all digests implement. Basically taking out byte-level concerns out of the digest impls.

You can provide a default transcoder which does serialization similar to how it's done today (with bugfixes), while keeping the flexibility of accepting PRs from others that implement transcoders for other formats. If this line of thought makes sense to you and more importantly if we can come up with a common model to represent all digests, I will be happy to contribute a PR!

A little background: we have a project that does jvm profiling for clusters and all our components talk Protobuf. We deal with latencies, scheduler delays and other metrics and streaming quantiles make a lot of sense. Hence the interest in adopting tdigest but it does not have protobuf support today nor the design is friendly enough to submit a PR for the same

[tdunning]

Are you suggesting that we have different serialization models for, say, protibuf and any other format?

…

On Jun 28, 2017 11:29 AM, "Ankur Jain" ***@***.***> wrote: Isn't it possible to add a Transcoder interface which has byte[] asBytes(SerializationModel) and SerializationModel fromBytes(byte[]) methods? SerializationModel here being a java object that is good enough to represent any digest. TDigest interface can now have a create method that takes SerializationModel as input which all digests implement. You can provide a default transcoder which does serialization similar to how it's done today (with bugfixes), while keeping the flexibility of accepting PRs from others that implement transcoders for other formats. If this line of thought makes sense to you and more importantly if we can come up with a common model to represent all digests, I will be happy to contribute a PR! A little background: we have a project <https://github.com/Flipkart/fk-prof> that does jvm profiling for clusters and all our components talk Protobuf. We deal with latencies, scheduler delays and other metrics and streaming quantiles make a lot of sense. Hence the interest in adopting tdigest but it does not have protobuf support today nor the design is friendly enough to submit a PR. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#87 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPSetRnVRmB9xUdO1FkVyYNZFR3i6w0ks5sIpt8gaJpZM4NClUZ> .

[anvinjain]

No. Basically, I wanted to enable bring your own serialization logic with some sane ones provided by the lib. By SerializationModel, I am implying one java class something on the lines of:

class SerializationModel {
    int encodingType; double min; double max; float compression; // ... and other members
}

class MergingDigest {
    // ...
    static MergingDigest fromSerializationModel(SerializationModel);
}

interface Transcoder {
    byte[] asBytes(SerializationModel);
    SerializationModel fromBytes(byte[]);
}

class ProtobufTranscoder implements Transcoder {
    // ...
}

This keeps the byte magic out of digest implementations and they are responsible for generating a uniform on-heap representation (which is SerializationModel, I know this name sucks)
Users can instantiate any out of the box transcoder or write their own. A way to maintain backward compatibility would be for MergingDigest, etc to optionally take a transcoder as constructor param and use that (or default one if not provided) to keep existing asBytes, fromBytes method working.

If you have any other ideas on how tdigest can support multiple serialization formats (and hopefully you consider that as a feature to be added in the first place), would love to hear about them.

[tdunning]

I think your design is fine. It bottlenecks the essential qualities of the t-digest. How about we find a better name for the SerializationModel (it might have other uses, even). Here are some suggestions that are probably all problematic, but might get your thoughts going: DigestEssence DigestInfo DigestBasics NopDigest I am happy to see a pull request on this.

…

On Wed, Jun 28, 2017 at 2:12 PM, Ankur Jain ***@***.***> wrote: No. Basically, I wanted to enable *bring your own serialization logic* with some sane ones provided by the lib. By SerializationModel, I am implying *one* java class something on the lines of: class SerializationModel { int encodingType; double min; double max; float compression; // ... and other members } class MergingDigest { // ... static MergingDigest fromSerializationModel(SerializationModel); } interface Transcoder { byte[] asBytes(SerializationModel); SerializationModel fromBytes(byte[]); } class ProtobufTranscoder implements Transcoder { // ... } This keeps the byte magic out of digest implementations and they are responsible for generating a uniform on-heap representation (which is SerializationModel, I know this name sucks) Users can instantiate any out of the box transcoder or write their own. A way to maintain backward compatibility would be for MergingDigest, etc to optionally take a transcoder as constructor param and use that (or default one if not provided) to keep existing asBytes, fromBytes method working. If you have any other ideas on how tdigest can support multiple serialization formats (and hopefully you consider that as a feature to be added in the first place), would love to hear about them. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#87 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPSesAY04FzicNDHZsPsrRBi9sfOaSHks5sIsHAgaJpZM4NClUZ> .

[anvinjain]

Or DigestModel? I see this as a dto representing digests.
Sure, I have some free time next week so expect a PR then.

[anvinjain]

You mention interchangeability of digest implementations. Presently, MergingDigest and AvlTreeDigest serialize different values so their serialized representation is not equivalent. Will need your inputs on structure of DigestModel and what fields of MergingDigest/AvlTreeDigest map to DigestModel fields.
The straightforward ones are min, max, compression, mean[]. But rest differ across impls.

[tdunning]

DigestModel sounds fine!

…

On Thu, Jun 29, 2017 at 1:59 AM, Ankur Jain ***@***.***> wrote: Or DigestModel? I see this as a dto representing digests. Sure, I have some free time next week so expect a PR then. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#87 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPSep3HR4T2pY3XN19AhSJZeFZkiNnUks5sI2drgaJpZM4NClUZ> .

[anvinjain]

@tdunning Need your inputs on what DigestModel looks like. As mentioned in previous comment, presently different fields are serialized across digest implementations

[tdunning]

Yes, currently different fields are serialized, but we should synchronize that. The minimum set includes: - compression factor - min and max values observed - centroid positions - centroid weights Implementations that use point by point insertion may also have special fields to maintain sort ordering of centroids with the same location (due to repeated data points, generally). This isn't done yet, but I think it may get added soon. I am pretty sure that this additional information does not need to be included in the serialized form if we make the assumption that centroids are serialized in the internal ordering. The MergingDigest also stores an extra sizing parameter which determines the size of the input buffer. This can be dealt with by adding a parameter to the DigestModel constructor or by just using a default value. Recent speedups have made this parameter much less important. Do you see other variations?

…

On Wed, Jul 5, 2017 at 2:43 AM, Ankur Jain ***@***.***> wrote: @tdunning <https://github.com/tdunning> Need your inputs on what DigestModel looks like. As mentioned in previous comment, presently different fields are serialized across digest implementations — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#87 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPSetbdm61jI_Yp5jkcmyR-rXf2YYy3ks5sK1q_gaJpZM4NClUZ> .

[anvinjain]

Apart from bufferSize, MergingDigest serializes lastUsedCell. For verbose encoding, this is deserialized and set as a property in digest. For small encoding, lastUsedCell additionally represents the values to read and assign in mean/weight array. Rest of the array seems to be zero-filled since n(array size) is part of serde as well.

Also, oddly MergingDigest#asBytes serializes tempMean.length but MergingDigest#fromBytes (verbose) does not expect it to be present in buffer. Is it a known issue or am I missing something there?

[tdunning]

In that context, `lastUsedCell` is just the number of active centroids. The rest of the array is definitely zero filled (and this is even tested, I believe).

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On Sat, Jul 8, 2017 at 8:05 AM, Ankur Jain ***@***.***> wrote: Apart from bufferSize, MergingDigest serializes lastUsedCell. For verbose encoding, this is deserialized and set as a property in digest. For small encoding, lastUsedCell additionally represents the values to read and assign in mean/weight array. Rest of the array seems to be zero-filled since n(array size) is part of serde as well — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#87 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAPSeibIamsN_PyYXr4Dlj3l_7ik5J8Eks5sL5rFgaJpZM4NClUZ> .

[tdunning]

@anvinjain Do you have a PR coming?

We need to cut the new major release. If you can't get this in soon, it will have to wait.

[anvinjain]

No, PR will take some time. Have paused work on this for few weeks.

…

________________________________ From: Ted Dunning <notifications@github.com> Sent: Wednesday, August 2, 2017 5:16:10 AM To: tdunning/t-digest Cc: Ankur Jain; Mention Subject: Re: [tdunning/t-digest] Future-proof serialization (#87) @anvinjain<https://github.com/anvinjain> Do you have a PR coming? We need to cut the new major release. If you can't get this in soon, it will have to wait. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#87 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AITW_tmwQrLZSQmX7pOKU20z0IJc3aEaks5sT7jCgaJpZM4NClUZ>.