blosc2 3.0.0b1

Python wrapper for the C-Blosc2 library

A Python wrapper for the extremely fast Blosc2 compression library

Author:

The Blosc development team

Contact:

[e-mail]

Github:

https://github.com/Blosc/python-blosc2

Actions:

PyPi:

NumFOCUS:

Code of Conduct:

What it is

C-Blosc2 is the new major version of C-Blosc, and is backward compatible with both the C-Blosc1 API and its in-memory format. Python-Blosc2 is a Python package that wraps C-Blosc2, the newest version of the Blosc compressor.

Starting with version 3.0.0, Python-Blosc2 is including a powerful computing engine that can operate on compressed data that can be either in-memory, on-disk or on the network. This engine also supports advanced features like reductions, filters, user-defined functions and broadcasting (still in beta). You can read our tutorial on how to use this new feature at: https://github.com/Blosc/python-blosc2/blob/main/doc/getting_started/tutorials/03.lazyarray-expressions.ipynb and https://github.com/Blosc/python-blosc2/blob/main/doc/getting_started/tutorials/03.lazyarray-udf.ipynb

In addition, Python-Blosc2 aims to leverage the full C-Blosc2 functionality to support super-chunks (SChunk), multi-dimensional arrays (NDArray), metadata, serialization and other bells and whistles introduced in C-Blosc2.

Note: Blosc2 is meant to be backward compatible with Blosc(1) data. That means that it can read data generated with Blosc, but the opposite is not true (i.e. there is no forward compatibility).

NDArray: an N-Dimensional store

One of the more useful abstractions in Python-Blosc2 is the NDArray object. It can write and read n-dimensional datasets in an extremely efficient way thanks to a n-dimensional 2-level partitioning, allowing to slice and dice arbitrary large and compressed data in a more fine-grained way:

To wet you appetite, here it is how the NDArray object performs on getting slices orthogonal to the different axis of a 4-dim dataset:

We have blogged about this: https://www.blosc.org/posts/blosc2-ndim-intro

We also have a ~2 min explanatory video on why slicing in a pineapple-style (aka double partition) is useful:

Operating with NDArrays

The NDArray objects can be operated with very easily inside Python-Blosc2. Here it is a simple example:

import numpy as np
import blosc2

N = 10_000
na = np.linspace(0, 1, N * N, dtype=np.float32).reshape(N, N)
nb = np.linspace(1, 2, N * N).reshape(N, N)
nc = np.linspace(-10, 10, N * N).reshape(N, N)

# Convert to blosc2
a = blosc2.asarray(na)
b = blosc2.asarray(nb)
c = blosc2.asarray(nc)

# Expression
expr = ((a ** 3 + blosc2.sin(c * 2)) < b) & (c > 0)

# Evaluate and get a NDArray as result
out = expr.eval()
print(out.info)

As you can see, the NDArray instances are very similar to NumPy arrays, but behind the scenes it holds compressed data that can be operated in a very efficient way with the new computing engine that is included in Python-Blosc2.

So as to whet your appetite, here it is the performance (with a MacBook Air M2 with 24 GB of RAM) that you can reach when the operands fit comfortably in-memory:

In this case, performance is a bit far from top-level libraries like Numexpr or Numba, but it is still pretty nice (and probably using CPUs with more cores than M2 would allow closing the performance gap even further). One important thing to know is that the memory consumption when using the LazyArray.eval() method is very low, because the output is an NDArray object that is compressed and in-memory by default. On its hand LazyArray.__getitem__() method returns an actual NumPy array, so it is not recommended to use it for large datasets, as it will consume quite a bit of memory (but it can still be convenient for small outputs).

It is important to note that the NDArray object can use memory-mapped files as well, and the benchmark above is actually using a memory-mapped file as the storage for the operands. Memory-mapped files are very useful when the operands do not fit in-memory, while keeping good performance.

And here it is the performance when the operands do not fit well in-memory:

In the latter case, the memory consumption lines look a bit crazy, but this is because what is displayed is the real memory consumption, not the virtual one (so, during the evaluation the OS has to swap out some memory to disk). In this case, the performance when compared with top-level libraries like Numexpr or Numba is very competitive.

You can find the benchmark for the above examples at: https://github.com/Blosc/python-blosc2/blob/main/bench/ndarray/lazyarray-expr.ipynb

Installing

Blosc is now offering Python wheels for the main OS (Win, Mac and Linux) and platforms. You can install binary packages from PyPi using pip:

pip install blosc2

Documentation

The documentation is here:

https://blosc.org/python-blosc2/python-blosc2.html

Also, some examples are available on:

https://github.com/Blosc/python-blosc2/tree/main/examples

Building from sources

python-blosc2 comes with the C-Blosc2 sources with it and can be built in-place:

git clone https://github.com/Blosc/python-blosc2/
cd python-blosc2
git submodule update --init --recursive
python -m pip install -r requirements-build.txt
python setup.py build_ext --inplace

That’s all. You can proceed with testing section now.

Testing

After compiling, you can quickly check that the package is sane by running the tests:

python -m pip install -r requirements-tests.txt
python -m pytest  (add -v for verbose mode)

Benchmarking

If curious, you may want to run a small benchmark that compares a plain NumPy array copy against compression through different compressors in your Blosc build:

PYTHONPATH=. python bench/pack_compress.py

License

The software is licenses under a 3-Clause BSD license. A copy of the python-blosc2 license can be found in LICENSE.txt.

Mailing list

Discussion about this module is welcome in the Blosc list:

[e-mail]

https://groups.google.es/group/blosc

Mastodon

Please follow @Blosc2 to get informed about the latest developments. We lately moved from Twitter to Mastodon.

Citing Blosc

You can cite our work on the different libraries under the Blosc umbrella as:

@ONLINE{blosc,
  author = {{Blosc Development Team}},
  title = "{A fast, compressed and persistent data store library}",
  year = {2009-2024},
  note = {https://blosc.org}
}

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Make compression better!