Software Engineering for Data Scientists

Small Big Data: large data on a single computer

As described in Alex Voss, Ilia Lvov, and Jon Lewis’s Small Big Data manifesto, you don’t need a Big Data cluster to process large amounts of data; a single computer is often sufficient. And quite often, the key bottleneck is memory.

Lacking CPU, your program runs slower; lacking memory, your program crashes. So how do exactly do you process larger-than-RAM datasets in Python?

To help you learn the relevant techniques, I’ve written the following series of articles, which will help you reduce and manage memory use in your data-processing Python code.

Code structure

1. Copying data is wasteful, mutating data is dangerous
   Copying data wastes memory, and modifying or mutating data in-place can lead to bugs. A compromise between the two is “hidden mutability”.

2. Clinging to memory: how Python function calls can increase your memory usage
   Python will automatically release memory for objects that aren’t being used. But sometimes function calls can unexpectedly keep objects in memory. Learn about Python memory management, how it interacts with function calls, and what you can do about it.

3. Massive memory overhead: Numbers in Python and how NumPy helps
   Storing integers or floats in Python has a huge overhead in memory. Learn why, and how NumPy makes things better.

4. Too many objects: Reducing memory overhead from Python instances
   Objects in Python have large memory overhead; create too many objects, and you’ll use far more memory than you expect. Learn why, and what do about it.

Data management techniques

1. Estimating and modeling memory requirements for data processing
   How much memory does your process actually need? How much will it need for different inputs? Learn to how measure and model memory usage for data processing batch jobs.

2. When your data doesn’t fit in memory: the basic techniques
   You can still process data that doesn’t fit in memory by using four basic techniques: spending money, compression, chunking, and indexing.

Pandas

1. Reducing Pandas memory usage #1: lossless compression
   How do you load a large CSV into Pandas without using as much memory? Learn the basic techniques: dropping columns, lower-range numeric dtypes, categoricals, and sparse columns.

2. Reducing Pandas memory usage #2: lossy compression
   In this article you’ll learn techniques that lose some details in return for reducing memory usage.

3. Reducing Pandas memory usage #3: Reading in chunks
   By loading and then processing a file into Pandas in chunks, you can load only part of the file into memory at any given time.

4. Fast subsets of large datasets with Pandas and SQLite
   You have a large amount of data, and you want to load only part into memory as a Pandas dataframe. CSVs won’t cut it: you need a database, and the easiest way to do that is with SQLite.

5. From chunking to parallelism: faster Pandas with Dask
   Processing your data in chunks lets you reduce memory usage, but it can also speed up your code. Because each chunk can be processed independently, you can process them in parallel, utilizing multiple CPUs. For Pandas (and NumPy), Dask is a great way to do this.

NumPy

1. Reducing NumPy memory usage with lossless compression
   By changing how you represent your NumPy arrays, you can significantly reduce memory usage: by choosing smaller dtypes, and using sparse arrays. You’ll also learn about cases where this won’t help.

2. Loading NumPy arrays from disk: mmap() vs. Zarr/HDF5
   If your NumPy array doesn’t fit in memory, you can load it transparently from disk using either mmap() or the very similar Zarr and HDF5 file formats. Here’s what they do, and why you’d choose one over the other.

3. The mmap() copy-on-write trick: reducing memory usage of array copies
   Usually, copying an array and modifying it doubles the memory usage. But by utilizing the operating system’s mmap() call, you only pay the cost for the parts of the copy that you changed.

Tools

1. Fil: a new Python memory profiler for data scientists and scientists
   Fil is a new memory profiler which shows you peak memory usage, and where that memory was allocated. It’s designed specifically for the needs of data scientists and scientists running data processing pipelines.

2. Debugging out-of-memory crashes in Python
   Debugging out-of-memory crashes can be tricky. Learn how the Fil memory profiler can help you find where your memory use is happening.

3. Debugging Python server memory leaks with the Fil profiler
   When your server is leaking memory, the Fil memory profiler can help you spot the buggy code.

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Performance optimization