_posts/2017-10-15-fast-python-serialization-with-ray-and-arrow.md

---
layout: post
title: "Fast Python Serialization with Ray and Apache Arrow"
excerpt: "This post describes how serialization works in Ray."
date: 2017-10-15 14:00:00
author: Philipp Moritz, Robert Nishihara
categories: [application]
---

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*This was originally posted on the [Ray blog][11]. [Philipp Moritz][12] and [Robert Nishihara][13] are graduate students at UC Berkeley.*

This post elaborates on the integration between [Ray][1] and [Apache Arrow][2].
The main problem this addresses is [data serialization][3].

From [Wikipedia][3], **serialization** is

> ... the process of translating data structures or object state into a format
> that can be stored ... or transmitted ... and reconstructed later (possibly
> in a different computer environment).

Why is any translation necessary? Well, when you create a Python object, it may
have pointers to other Python objects, and these objects are all allocated in
different regions of memory, and all of this has to make sense when unpacked by
another process on another machine.

Serialization and deserialization are **bottlenecks in parallel and distributed
computing**, especially in machine learning applications with large objects and
large quantities of data.

## Design Goals

As Ray is optimized for machine learning and AI applications, we have focused a
lot on serialization and data handling, with the following design goals:

1. It should be very efficient with **large numerical data** (this includes
NumPy arrays and Pandas DataFrames, as well as objects that recursively contain
Numpy arrays and Pandas DataFrames).
2. It should be about as fast as Pickle for **general Python types**.
3. It should be compatible with **shared memory**, allowing multiple processes
to use the same data without copying it.
4. **Deserialization** should be extremely fast (when possible, it should not
require reading the entire serialized object).
5. It should be **language independent** (eventually we'd like to enable Python
workers to use objects created by workers in Java or other languages and vice
versa).

## Our Approach and Alternatives

The go-to serialization approach in Python is the **pickle** module. Pickle is
very general, especially if you use variants like [cloudpickle][4]. However, it
does not satisfy requirements 1, 3, 4, or 5. Alternatives like **json** satisfy
5, but not 1-4.

**Our Approach:** To satisfy requirements 1-5, we chose to use the
[Apache Arrow][2] format as our underlying data representation. In collaboration
with the Apache Arrow team, we built [libraries][7] for mapping general Python
objects to and from the Arrow format. Some properties of this approach:

- The data layout is language independent (requirement 5).
- Offsets into a serialized data blob can be computed in constant time without
reading the full object (requirements 1 and 4).
- Arrow supports **zero-copy reads**, so objects can naturally be stored in
shared memory and used by multiple processes (requirements 1 and 3).
- We can naturally fall back to pickle for anything we can’t handle well
(requirement 2).

**Alternatives to Arrow:** We could have built on top of
[**Protocol Buffers**][5], but protocol buffers really isn't designed for
numerical data, and that approach wouldn’t satisfy 1, 3, or 4. Building on top
of [**Flatbuffers**][6] actually could be made to work, but it would have
required implementing a lot of the facilities that Arrow already has and we
preferred a columnar data layout more optimized for big data.

## Speedups

Here we show some performance improvements over Python’s pickle module. The
experiments were done using `pickle.HIGHEST_PROTOCOL`. Code for generating these
plots is included at the end of the post.

**With NumPy arrays:** In machine learning and AI applications, data (e.g.,
images, neural network weights, text documents) are typically represented as
data structures containing NumPy arrays. When using NumPy arrays, the speedups
are impressive.

The fact that the Ray bars for deserialization are barely visible is not a
mistake. This is a consequence of the support for zero-copy reads (the savings
largely come from the lack of memory movement).

<div align="center">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/speedups0.png" width="365" height="255">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/speedups1.png" width="365" height="255">
</div>

Note that the biggest wins are with deserialization. The speedups here are
multiple orders of magnitude and get better as the NumPy arrays get larger
(thanks to design goals 1, 3, and 4). Making **deserialization** fast is
important for two reasons. First, an object may be serialized once and then
deserialized many times (e.g., an object that is broadcast to all workers).
Second, a common pattern is for many objects to be serialized in parallel and
then aggregated and deserialized one at a time on a single worker making
deserialization the bottleneck.

**Without NumPy arrays:** When using regular Python objects, for which we
cannot take advantage of shared memory, the results are comparable to pickle.

<div align="center">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/speedups2.png" width="365" height="255">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/speedups3.png" width="365" height="255">
</div>

These are just a few examples of interesting Python objects. The most important
case is the case where NumPy arrays are nested within other objects. Note that
our serialization library works with very general Python types including custom
Python classes and deeply nested objects.

## The API

The serialization library can be used directly through pyarrow as follows. More
documentation is available [here][7].

```python
x = [(1, 2), 'hello', 3, 4, np.array([5.0, 6.0])]
serialized_x = pyarrow.serialize(x).to_buffer()
deserialized_x = pyarrow.deserialize(serialized_x)
```

It can be used directly through the Ray API as follows.

```python
x = [(1, 2), 'hello', 3, 4, np.array([5.0, 6.0])]
x_id = ray.put(x)
deserialized_x = ray.get(x_id)
```

## Data Representation

We use Apache Arrow as the underlying language-independent data layout. Objects
are stored in two parts: a **schema** and a **data blob**. At a high level, the
data blob is roughly a flattened concatenation of all of the data values
recursively contained in the object, and the schema defines the types and
nesting structure of the data blob.

**Technical Details:** Python sequences (e.g., dictionaries, lists, tuples,
sets) are encoded as Arrow [UnionArrays][8] of other types (e.g., bools, ints,
strings, bytes, floats, doubles, date64s, tensors (i.e., NumPy arrays), lists,
tuples, dicts and sets). Nested sequences are encoded using Arrow
[ListArrays][9]. All tensors are collected and appended to the end of the
serialized object, and the UnionArray contains references to these tensors.

To give a concrete example, consider the following object.

```python
[(1, 2), 'hello', 3, 4, np.array([5.0, 6.0])]
```

It would be represented in Arrow with the following structure.

```
UnionArray(type_ids=[tuple, string, int, int, ndarray],
           tuples=ListArray(offsets=[0, 2],
                            UnionArray(type_ids=[int, int],
                                       ints=[1, 2])),
           strings=['hello'],
           ints=[3, 4],
           ndarrays=[<offset of numpy array>])
```

Arrow uses Flatbuffers to encode serialized schemas. **Using only the schema, we
can compute the offsets of each value in the data blob without scanning through
the data blob** (unlike Pickle, this is what enables fast deserialization). This
means that we can avoid copying or otherwise converting large arrays and other
values during deserialization. Tensors are appended at the end of the UnionArray
and can be efficiently shared and accessed using shared memory.

Note that the actual object would be laid out in memory as shown below.

<div align="center">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/python_object.png" width="600">
</div>
<div><i>The layout of a Python object in the heap. Each box is allocated in a
different memory region, and arrows between boxes represent pointers.</i></div>
<br />

The Arrow serialized representation would be as follows.

<div align="center">
<img src="{{ site.baseurl }}/assets/fast_python_serialization_with_ray_and_arrow/arrow_object.png" width="400">
</div>
<div><i>The memory layout of the Arrow-serialized object.</i></div>
<br />

## Getting Involved

We welcome contributions, especially in the following areas.

- Use the C++ and Java implementations of Arrow to implement versions of this
for C++ and Java.
- Implement support for more Python types and better test coverage.

## Reproducing the Figures Above

For reference, the figures can be reproduced with the following code.
Benchmarking `ray.put` and `ray.get` instead of `pyarrow.serialize` and
`pyarrow.deserialize` gives similar figures. The plots were generated at this
[commit][10].

```python
import pickle
import pyarrow
import matplotlib.pyplot as plt
import numpy as np
import timeit


def benchmark_object(obj, number=10):
    # Time serialization and deserialization for pickle.
    pickle_serialize = timeit.timeit(
        lambda: pickle.dumps(obj, protocol=pickle.HIGHEST_PROTOCOL),
        number=number)
    serialized_obj = pickle.dumps(obj, pickle.HIGHEST_PROTOCOL)
    pickle_deserialize = timeit.timeit(lambda: pickle.loads(serialized_obj),
                                       number=number)

    # Time serialization and deserialization for Ray.
    ray_serialize = timeit.timeit(
        lambda: pyarrow.serialize(obj).to_buffer(), number=number)
    serialized_obj = pyarrow.serialize(obj).to_buffer()
    ray_deserialize = timeit.timeit(
        lambda: pyarrow.deserialize(serialized_obj), number=number)

    return [[pickle_serialize, pickle_deserialize],
            [ray_serialize, ray_deserialize]]


def plot(pickle_times, ray_times, title, i):
    fig, ax = plt.subplots()
    fig.set_size_inches(3.8, 2.7)

    bar_width = 0.35
    index = np.arange(2)
    opacity = 0.6

    plt.bar(index, pickle_times, bar_width,
            alpha=opacity, color='r', label='Pickle')

    plt.bar(index + bar_width, ray_times, bar_width,
            alpha=opacity, color='c', label='Ray')

    plt.title(title, fontweight='bold')
    plt.ylabel('Time (seconds)', fontsize=10)
    labels = ['serialization', 'deserialization']
    plt.xticks(index + bar_width / 2, labels, fontsize=10)
    plt.legend(fontsize=10, bbox_to_anchor=(1, 1))
    plt.tight_layout()
    plt.yticks(fontsize=10)
    plt.savefig('plot-' + str(i) + '.png', format='png')


test_objects = [
    [np.random.randn(50000) for i in range(100)],
    {'weight-' + str(i): np.random.randn(50000) for i in range(100)},
    {i: set(['string1' + str(i), 'string2' + str(i)]) for i in range(100000)},
    [str(i) for i in range(200000)]
]

titles = [
    'List of large numpy arrays',
    'Dictionary of large numpy arrays',
    'Large dictionary of small sets',
    'Large list of strings'
]

for i in range(len(test_objects)):
    plot(*benchmark_object(test_objects[i]), titles[i], i)
```

[1]: http://ray.readthedocs.io/en/latest/index.html
[2]: https://arrow.apache.org/
[3]: https://en.wikipedia.org/wiki/Serialization
[4]: https://github.com/cloudpipe/cloudpickle/
[5]: https://developers.google.com/protocol-buffers/
[6]: https://google.github.io/flatbuffers/
[7]: https://arrow.apache.org/docs/python/ipc.html#arbitrary-object-serialization
[8]: http://arrow.apache.org/docs/memory_layout.html#dense-union-type
[9]: http://arrow.apache.org/docs/memory_layout.html#list-type
[10]: https://github.com/apache/arrow/tree/894f7400977693b4e0e8f4b9845fd89481f6bf29
[11]: https://ray-project.github.io/
[12]: https://people.eecs.berkeley.edu/~pcmoritz/
[13]: http://www.robertnishihara.com