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From "bright chen (JIRA)" <j...@apache.org>
Subject [jira] [Created] (APEXCORE-635) Proposal: Manage memory to avoid memory copy and garbage collection
Date Thu, 02 Feb 2017 23:13:51 GMT
bright chen created APEXCORE-635:
------------------------------------

             Summary: Proposal: Manage memory to avoid memory copy and garbage collection
                 Key: APEXCORE-635
                 URL: https://issues.apache.org/jira/browse/APEXCORE-635
             Project: Apache Apex Core
          Issue Type: Wish
            Reporter: bright chen


Manage memory to avoid memory copy and garbage collection

The aim of this proposal is to reuse the memory to avoid the garbage collection and avoid
unnecessary memory copy to increase the performance. In this proposal the term serde means
serialization and deserialization. It’s same as codec.

Currently, apex by default use DefaultStatefulStreamCodec for serde, which extends Kryo and
optimize it by replace class by class id. And application developer can optimize serializer
by implement interface StreamCodec. 

First, let’s look into the default codec DefaultStatefulStreamCodec. It basically optimize
serde by replace class name by class id as my understanding. And the state information only
send before sending first tuple, it’s kind like configuration for serde. So I suggest to
separate this feature from serde. The benefit is the customized serde can still use this feature.
And the kryo have some limitation which I’ll state later.


Second, Let’s look at the customized serde. Let’s stand from application developer point
of view and look at how to implement StreamCodec. I take a simple tuple List<String>
as example.

The first solution is use kryo. This is basically same as apex default codec.

The second solution is implement StreamCodec for String and List, and ListSerde delegate String
to StringSerde. The benefit of this solution is the StringSerde ListSerde can be reused. The
problem is there need a lot of temporary memory and memory copy. Following is the sample implement.
Class StringCodec {
  Slice toByteArray(String o) {
    byte[] b = o.getBytes(“UTF8”);              // new bytes
    byte[] b1 = new byte[b1.length + 4];      // new bytes
    set the length of the string at the first 4 bytes
    System.arrayCopy(b, 0, b1, 4, b.length);   //copy bytes
    return new Slice(b1);
  }

class ListSerde<T> {
  StreamCodec itemSerde;  //the serde for serialize/deserialize item

  Slice toByteArray(List<T> list) {
    Slice[] itemSlices = new Slice[list.size()];
    int size = 0;
    int index = 0;
    for(T item : list) {
      Slice slice = itemSerde.toByteArray(item);
      size += slice.length;
      itemSlices[index++] = slice;
    }
    byte[] b = new byte[size+4];                   //allocated the memory
    set the length of the list at the first 4 bytes
    copy the data from itemSlices
    return new Slice(b);
  }
}
  
from above code, we can see that around 2 times of required memory were allocated and data
copied twice( one copy maybe special to string, but another copy is mandatory). And when bytes
written to the socket, all allocated memory can’t be reused but need to be garbage collected.

The above tuple only have two levels, if the tuple have n level, n times of required memory
would be allocated and n-1 time of data copy is required.

The third solution could be allocate memory and then pass the memory and offset to item serde.
There are some problems for this solution:
How to pass the memory from caller? As our previous interface only pass the object but no
way to pass memory. So the pass of memory will depends on implementation.
Another big problem of this solution is it hard to reallocate proper memory(For this special
case, it probably can allocate 2 times of all string length. ). And the memory allocated more
than required would be wasted until data send to the socket(or allocate exact memory and copy
the data to avoid waste memory). And the code also need to handle the case if memory is not
enough. 
The fourth solution could be treat whole object as flat, allocate memory and handle it. For
example as following. This solution solve the problem of pass memory. But it has other problems
of third solution and introduced some other problems:

Can’t reuse the code: we already have the StringSerde, but ListSerde<String> have
to implement almost same logic again. 
The serializeItemToMemory() method should be implemented depend on different item type.
class ListSerde<T> {
  Slice toByteArray(List<T> list) {
    byte[] b = new byte[…];      //hard estimate proper size.
    int size = 0;
    for(T item : list) {
      int length = serializeItemToMemory(item, b, size); 
      size += length;
    }
    Allocate new memory to copy data if don’t have waste memory
  }
}
So, from the analysis of these solutions. It’s not easy to implement good and reusable customize
serde.



Third, let’s look at the Kryo serde. Kryo provides Output, so each field serde write to
the same Output. This approach solve the memory problem. But the Output has some problem too.

The Output, as a stream, can only write continuously. But it would be problem. For example,
when Serialize String to LV format. We don’t know what the length could be before serialization.

The Output don’t have cache, which means the serialized data must copy to the outside and
manage them.
The allocated memory can’t be reused without extra management.
Another copy is required when add partition information.
The memory allocated for different object are not continuous. Which mean need another copy
when merge multiple serialized tuple into one block to send to socket.


My suggest solution is:

Add SerializationBuffer which extends from kryo Output and write data to BlockStream. 
BlockStream manages a list of block; BlockStream can reserve space; BlockStream can reset
the memory when data not used any more. We probably can use unsafe mode to increase the performance
for this part in the future.
Add MemReuseCodec interface which extends StreamCodec, Deprecated Slice toByteArray(T o) and
add method void toByteArray(T o, SerializationBuffer output); Here, toByteArray will not return
slice, as the codec could be the top level codec or a codec of a field. Call SerializationBuffer.toSlice()
to get the slice of serialized data.
In Publisher, keep two lists/arrays of slices, one list/array for serialize the tuples, another
list/array for sending to the socket. When wake up for writing, switch the lists/arrays. Then
merge the slice to large slice and call socket write. Reset the stream after data written.

So the previous ListSerde can be implemented as following:
class ListSerde<T> {
  MemReuseCodec itemSerde;  //the serde for serialize/deserialize item

  void toByteArray(List<T> list, SerializationBuffer buffer) {
    for(T item : list) {
      itemSerde.toByteArray(item, buffer);
    }
  }
}

The benefit of this mechanism
the memory can be reused instead of garbage collected after data send to socket 
avoid unnecessary memory copy. Basically can avoid all extra copy required by kryo.
the data which send to socket can be easily merged in a block without extra memory copy.
can easily integrate with Kryo serde due to SerializationBuffer extends from Output. 


The work need to do to integrate this mechanism to Apex without modifying netlet
Add  MemReuseCodec field in BufferServerPublisher, which initialize in setup() if the codec
implements MemReuseCodec
Change the DefaultStatefulStreamCodec to implement by using SerializationBuffer
For integrate with socket, basically it only need to override write(byte[] message, int offset,
int size) and write(). But unfortunately, write() is final. So need following walk around.
Add interface ListenerExt which only have one method writeExt(); Change BufferServerPublisher
implements ListenerExt. Add DefaultEventLoopExt which extends DefaultEventLoop and override
handleSelectedKey, for selection key OP_WRITE, if it’s attachment implements ListenerExt,
call ListenerExt.writeExt(); else call write().



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