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From Davies Liu <dav...@databricks.com>
Subject Re: Python UDF performance at large scale
Date Wed, 24 Jun 2015 06:26:51 GMT
Fare points, I also like simpler solutions.

The overhead of Python task could be a few of milliseconds, which
means we also should eval them as batches (one Python task per batch).

Decreasing the batch size for UDF sounds reasonable to me, together
with other tricks to reduce the data in socket/pipe buffer.

BTW, what do your UDF looks like? How about to use Jython to run
simple Python UDF (without some external libraries).

On Tue, Jun 23, 2015 at 8:21 PM, Justin Uang <justin.uang@gmail.com> wrote:
> // + punya
>
> Thanks for your quick response!
>
> I'm not sure that using an unbounded buffer is a good solution to the
> locking problem. For example, in the situation where I had 500 columns, I am
> in fact storing 499 extra columns on the java side, which might make me OOM
> if I have to store many rows. In addition, if I am using an
> AutoBatchedSerializer, the java side might have to write 1 << 16 == 65536
> rows before python starts outputting elements, in which case, the Java side
> has to buffer 65536 complete rows. In general it seems fragile to rely on
> blocking behavior in the Python coprocess. By contrast, it's very easy to
> verify the correctness and performance characteristics of the synchronous
> blocking solution.
>
>
> On Tue, Jun 23, 2015 at 7:21 PM Davies Liu <davies@databricks.com> wrote:
>>
>> Thanks for looking into it, I'd like the idea of having
>> ForkingIterator. If we have unlimited buffer in it, then will not have
>> the problem of deadlock, I think. The writing thread will be blocked
>> by Python process, so there will be not much rows be buffered(still be
>> a reason to OOM). At least, this approach is better than current one.
>>
>> Could you create a JIRA and sending out the PR?
>>
>> On Tue, Jun 23, 2015 at 3:27 PM, Justin Uang <justin.uang@gmail.com>
>> wrote:
>> > BLUF: BatchPythonEvaluation's implementation is unusable at large scale,
>> > but
>> > I have a proof-of-concept implementation that avoids caching the entire
>> > dataset.
>> >
>> > Hi,
>> >
>> > We have been running into performance problems using Python UDFs with
>> > DataFrames at large scale.
>> >
>> > From the implementation of BatchPythonEvaluation, it looks like the goal
>> > was
>> > to reuse the PythonRDD code. It caches the entire child RDD so that it
>> > can
>> > do two passes over the data. One to give to the PythonRDD, then one to
>> > join
>> > the python lambda results with the original row (which may have java
>> > objects
>> > that should be passed through).
>> >
>> > In addition, it caches all the columns, even the ones that don't need to
>> > be
>> > processed by the Python UDF. In the cases I was working with, I had a
>> > 500
>> > column table, and i wanted to use a python UDF for one column, and it
>> > ended
>> > up caching all 500 columns.
>> >
>> > I have a working solution over here that does it in one pass over the
>> > data,
>> > avoiding caching
>> >
>> > (https://github.com/justinuang/spark/commit/c1a415a18d31226ac580f1a9df7985571d03199b).
>> > With this patch, I go from a job that takes 20 minutes then OOMs, to a
>> > job
>> > that finishes completely in 3 minutes. It is indeed quite hacky and
>> > prone to
>> > deadlocks since there is buffering in many locations:
>> >
>> >     - NEW: the ForkingIterator LinkedBlockingDeque
>> >     - batching the rows before pickling them
>> >     - os buffers on both sides
>> >     - pyspark.serializers.BatchedSerializer
>> >
>> > We can avoid deadlock by being very disciplined. For example, we can
>> > have
>> > the ForkingIterator instead always do a check of whether the
>> > LinkedBlockingDeque is full and if so:
>> >
>> > Java
>> >     - flush the java pickling buffer
>> >     - send a flush command to the python process
>> >     - os.flush the java side
>> >
>> > Python
>> >     - flush BatchedSerializer
>> >     - os.flush()
>> >
>> > I haven't added this yet. This is getting very complex however. Another
>> > model would just be to change the protocol between the java side and the
>> > worker to be a synchronous request/response. This has the disadvantage
>> > that
>> > the CPU isn't doing anything when the batch is being sent across, but it
>> > has
>> > the huge advantage of simplicity. In addition, I imagine that the actual
>> > IO
>> > between the processes isn't that slow, but rather the serialization of
>> > java
>> > objects into pickled bytes, and the deserialization/serialization +
>> > python
>> > loops on the python side. Another advantage is that we won't be taking
>> > more
>> > than 100% CPU since only one thread is doing CPU work at a time between
>> > the
>> > executor and the python interpreter.
>> >
>> > Any thoughts would be much appreciated =)
>> >
>> > Other improvements:
>> >     - extract some code of the worker out of PythonRDD so that we can do
>> > a
>> > mapPartitions directly in BatchedPythonEvaluation without resorting to
>> > the
>> > hackery in ForkedRDD.compute(), which uses a cache to ensure that the
>> > other
>> > RDD can get a handle to the same iterator.
>> >     - read elements and use a size estimator to create the BlockingQueue
>> > to
>> > make sure that we don't store too many things in memory when batching
>> >     - patch Unpickler to not use StopException for control flow, which
>> > is
>> > slowing down the java side
>> >
>> >

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