Chunked arrays


Arrays can be very large and may not fit in memory. In this case, you may not be able to use an in-memory array such as an xarray. A solution to this problem is to cut up the large array into many small arrays, called chunks. Not only do the chunks fit comfortably in memory, but this also allows to process them in parallel, including in a distributed environment (although this is not supported yet).

Formats for the storage of arrays such as Zarr specifically target chunked arrays. Such formats are becoming increasingly popular in the field of big data, since the chunks can be stored in the cloud.

In-memory chunked arrays

This may not look very useful at first sight, since each chunk (and thus the whole array) is hold in memory. It means that it cannot work with very large arrays, but it may be used to parallelize an algorithm, by processing several chunks at the same time.

An in-memory chunked array has the following type:

#include <xtensor/xchunked_array.hpp>

using data_type = double;
// don't use this code:
using inmemory_chunked_array = xt::xchunked_array<xarray<xarray<data_type>>>;

But you should not directly use this type to create a chunked array. Instead, use the chunked_array factory function:

#include <xtensor/xchunked_array.hpp>

std::vector<std::size_t> shape = {10, 10, 10};
std::vector<std::size_t> chunk_shape = {2, 3, 4};
auto a = xt::chunked_array<double>(shape, chunk_shape);
// a is an in-memory chunked array
// each chunk is an xarray<double>, and chunks are hold in an xarray
// thus a is an xarray of xarray<double> elements
a(3, 9, 2) = 1.;  // this will address the chunk of index (1, 3, 0)
                  // and in this chunk, the element of index (1, 0, 2)

Chunked arrays implement the full semantic of xarray, including lazy evaluation.

Stored chunked arrays

These are arrays whose chunks are stored on a file system, allowing for persistence of data. In particular, they are used as a building block for the xtensor-zarr library.

For further dedails, please refer to the documentation of xtensor-io.