Use Numba to work with Apache Arrow in pure Python

03 August 2018, 11 minutes to read

Apache Arrow is an in-memory memory format for columnar data. In more “plain” English, it is a standard on how to store DataFrames/tables in memory, independent of the programming language. One of its most prominent uses is for the @pandas_udf decorator in Apache Spark to move data quickly between Scala and Python/pandas.

Furthermore, it also brought the reading of Apache Parquet files to the Python world. While yet known for benefiting I/O, there is not yet much analytic implemented on top of it. As the focus of Arrow is on performance, the core of the Python package is based on the C++ implementation. At the moment there are already some analytic kernels implemented. As the implementation of these functions yet only happened on the C++ level and many Python developers only want to write Python code, they were unable to extend Arrow with more functionality.

Fast for-loops on numerical data

One of the main things you learn when you start with scientific computing in Python is that you should not write for-loops over your data. Instead you are advised to use the vectorized functions provided by packages like numpy. The major share of computations can be represented as a combination of fast NumPy operations. But in the end, there are still some that cannot be expressed efficiently with NumPy. In these cases ones has to resort to slow Python for-loops.

As an alternative to these for-loops, people often use Cython to write compiled code that provides similar performance to NumPy operations. This provides a good combination of a Python-like language with the performance benefits of code written in C/C++. One of the disadvantages of C/C++ and Cython is that you need to compile your code ahead-of-time which is in stark contrast to the typical just-in-time interpreted Python code.

Numba for just-in-time compiled, efficient Python code

The between fast, compiled scientific code and the simple, interpreted nature of Python is closed by Numba. Numba is a just-in-time compiler based on the LLVM compiler infrastructure that inspects math-heavy Python code at runtime. It will then produce fast, vectorized native machine instructions that often even beat the performance of NumPy operations slightly.

In contrast to PyPy, Numba is not a generic Python just-in-time compiler but is focused on accelerating code that works on non-Python memory regions like the contents of NumPy arrays. You can apply it to a function by using the @numba.jit decorator. A typical example where Numba can greatly improve the performance of your code is when you write one of those for-loops over numerical data. Although you were always told, that they will be horribly slow in comparison to using NumPy operations, sometimes, they are unavoidable.

To highlight the benefits of Numba, we take a small example of an for-loop over a NumPy array. We look at two variants: a simple for-loop and the same code just-in-time compiled with Numba. You possibly will also find an implementation in NumPy without Numba for this code but we just use it here for demonstration purposes.

import numpy as np

arr = np.arange(1000000)
result = np.zeros_like(arr)

def py_adapt(arr, result):
    for i in range(len(arr) - 1):
        result[i] = np.sqrt(arr[i] * arr[i + 1])

Profiling the pure-Python approach:

%timeit py_adapt(arr, result)
# 3.35 s ± 20.3 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

Implementing the same but using a Numba decorator this time.

from numba import jit

@jit
def nb_adapt(arr, result):
    for i in range(len(arr) - 1):
        result[i] = np.sqrt(arr[i] * arr[i + 1])
%timeit nb_adapt(arr, result)
# 5.83 ms ± 91.6 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)

This small example shows the power of Numba: A simple Python loop can be turned into efficient numerical code only by the addition of a decorator.

Applying the magic of Numba to Apache Arrow

Numba has built-in support for NumPy arrays and Python’s memoryview objects. As Arrow arrays are made up of more than a single memory buffer, they don’t work out of the box with Numba. To integrate them with Numba, we need to understand how Arrow arrays are structured internally. As they are all nullable, each array has a valid bitmap where a bit per row indicates whether we have a null or a valid entry. Depending of the type of the array, we have one or more memory buffers to store the data.

For the set of primitive types (int, float, bool), there is simply another buffer that contains the data, just like in a NumPy array. In the case of strings, we have two additional buffers. There is one buffer that contains the actual characters of all strings in the array, one string after the next ones. To find the start and end points of the strings, we also have an offsets buffer that contains the start index of each string in the characters array. To reconstruct the string at position i, we take its starting point s_i and the one of the next string s_i+1. The string then is represented by the characters in values[s_i:s_i+1].

As NumPy has no native variable length string type, we’re going to use this as an example. We want to build a fast function that returns us the lengths of all strings in an Arrow StringArray. To represent composite memory structures and provide operations on them, Numba provides the @jitclass decorator. The decorator is applied to a standard Python class. For each member of the class, we need to specify its native type like numba.int32 for a scalar int or numba.float32[:] for a float array. When the class is used in a @jit-decorated function, objects of it can be used just like an ordinary Python class but the generated machine code is highly optimised.

Given the above explanation, we can build a NumbaStringArray class that provides us a convenience interface to the underlying Arrow buffers. In addition, we add a convenience function NumbaStringArray.make that dissects an existing pyarrow.Array instance into the buffer and instantiates the new class.

import numba
import types


@numba.jitclass(
    [
        ("missing", numba.uint8[:]),
        ("offsets", numba.uint32[:]),
        ("data", numba.optional(numba.uint8[:])),
        ("offset", numba.int64),
    ]
)
class NumbaStringArray(object):
    """Wrapper around arrow's StringArray for use in numba functions.

    Usage::

        NumbaStringArray.make(array)
    """

    def __init__(self, missing, offsets, data, offset):
        self.missing = missing
        self.offsets = offsets
        self.data = data
        self.offset = offset

    @property
    def size(self):
        return len(self.offsets) - 1 - self.offset

    def isnull(self, str_idx):
        str_idx += self.offset
        byte_idx = str_idx // 8
        bit_mask = 1 << (str_idx % 8)
        return (self.missing[byte_idx] & bit_mask) == 0

    def byte_length(self, str_idx):
        str_idx += self.offset
        return self.offsets[str_idx + 1] - self.offsets[str_idx]


def _make(cls, sa):
    if not isinstance(sa, pa.StringArray):
        sa = pa.array(sa, pa.string())

    buffers = sa.buffers()
    return cls(
        np.asarray(buffers[0]).view(np.uint8),
        np.asarray(buffers[1]).view(np.uint32),
        np.asarray(buffers[2]).view(np.uint8),
        offset=sa.offset
    )


# @classmethod does not seem to be supported
NumbaStringArray.make = types.MethodType(_make, NumbaStringArray)

To compare the performance with NumPy, we create arrays with a million strings:

import pyarrow as pa
import numpy as np

arrow_array = pa.array([str(i) for i in range(1000000)])
numpy_array = arrow_array.to_pandas()

We build then two nearly equal functions that compute the individual string lengths, one with a NumPy array, the other one on an Arrow array using Numba. One noticeable difference here is that we can turn on the nopython and nogil modes for the Arrow version as it does not have to deal with Python objects. In contrast, as NumPy has no native variable-length string type, we have resort to Python object and thus these modes are not possible.

@numba.jit
def numpy_lengths(array):
    result = np.empty_like(array)
    
    for i in range(len(array)):
        result[i] = len(array[i])
        
    return result
        

@numba.jit(nopython=True, nogil=True)
def arrow_lengths(array):
    result = np.empty(array.size)

    for t in range(array.size):
        if array.isnull(t):
            result[t] = 0
        else:
            result[t] = array.byte_length(t)
    
    return result
%timeit numpy_lengths(numpy_array)
# 363 ms ± 7.88 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
# Takes 11us, so no real performance impact
numba_array = NumbaStringArray.make(arrow_array)
%timeit arrow_lengths(numba_array)
# 42 ms ± 1.09 ms per loop (mean ± std. dev. of 7 runs, 10 loops each)

This leads us to a near 10x performance increase while still staying in pure Python. One could probably get better performance by switching to C++ and being more careful about alignment, vectorisation, … but for a simple first pass, this is an extremely grateful result.

Use Case

While this is a nice example on how to combine Numba and Apache Arrow, this is actual code that was taken from Fletcher. There we are in the process of building a pure-Python library that combines Apache Arrow and Numba to extend pandas with the data types are available in Arrow. While you need some C++ knowledge in the main Arrow project, you can get started building fast columnar code in pure Python there.


Previous

AHL Python Hackathon April 2018

Three weeks ago MAN AHL organised an opensource hackathon at their London office. As part of the Hackathon people should contribute to one of the PyData artifacts they regularly use. To support them in making their first contribution, AHL also coordinated that several core committers of opensource projects were present at the event. I joined in as the representative of the Apache Arrow project.