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ZEP 3 — Variable chunking

Authors:

Status: Draft

Type: Specification

Created: 2022-10-17

Abstract

To allow the chunks of a zarr array to be rectangular grid rather than a regular grid, with the chunk lengths along any dimension a list of integers rather than a single chunk size.

Motivation and Scope

Two specific use cases have motivated this, given below. However, this generalisation of Zarr’s storage model can be seen as an optional enhancement, and the same data model as currently used by dask.array.

  • when producing a kerchunked dataset, the native chunking of the targets cannot be changed. It is common to have non-regular chunking on at least one dimension, such as a time dimension with one sample per day and chunks of one month or one year. The change would allow these datasets to be read via kerchunk, and/or converted to zarr with equivalent chunking to the original. Such data cannot currently be represented in zarr.
  • awkward arrays, ragged arrays and sparse data can be represented as a set of one-dimensional arrays, with an appropriate metadata description convention. The size of a chunks of each component array corresponding to a logical chunk of the overall array will not, in general be equal with each other in a single chunk, nor consistent between chunks, as each row in the matrix can have a variable number of non-zero values
  • sensor data, may not come in fixed increments; variably chunked storage would be great for parallel writing. With variable chunk sizes, just need to make sure offsets are correct once done. Otherwise, write locations for chunks are dependent on previous chunks.
  • in some cases, parts of the overall data array may have very different data distributions, and it can be very convenient to partition the data by such characteristics to allow, for example, for more efficient encoding schemes.
  • when filtering regular table data on one column and applying to other columns, you necessarily end up with an unequal number of values in each chunk, which zarr does not currently handle.

Usage and Impact

Creation

zarr.create(1000, chunks=((100, 300, 500, 100),))

Backward Compatibility

This change is fully backward compatible - all old data will remain usable. However, data written with variable chunks will not be readable by older versions of Zarr. It would be reasonable to wish to backport the feature to v2.

Detailed description

Currently, the array metadata specifies the chunking scheme like (see https://zarr-specs.readthedocs.io/en/latest/core/v3.0.html#chunk-grid)

{
  "type": "regular", 
  "chunk_shape": [10, 10],
  "separator":"/"
}

The proposal is to allow metadata of the form

{
  "type": "rectangular", 
  "chunk_shape": [[5, 5, 5, 15, 15, 20, 35], 10],
  "separator":"/"
}

Each element of chunk_shape, corresponding to each dimension of the array, may be a single integer, as before, or a list of integers which add up to the size of the array in that dimension. In this example, the single value of 10 for the chunks on the second dimension would be identical to [10, 10, 10, 10, 10, 10, 10, 10, 10, 10]. The number of values in the list is equal to the number of chunks along that dimension. Thus, a “rectangular” grid may be fully compatible as a “regular” grid.

The data index bounds on a dimension of each hyperrectangle is formed by a cumulative sum of the chunks values, starting at 0.

bounds_axis0 = [0, 5, 10, 15, 30, 45, 65, 100]
bounds_axis1 = [0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]

such that key “c0/0” contains values for indices along the first dimension (0, 5] and (0, 10] on the second dimension. An array index of (17, 17) would be found in key “c3/1”, index (2, 2).

Dask

dask.array uses rectangular chunking internally, and is one of the major consumers of zarr data. Much of the code translating logical slices into slices on the individual chunks should be reusable.

Parquet/ Arrow

Arrow describes tables as a collection of record batches. There is no restriction on the size of these batches. This is not only very flexible, but can be used as an indexing strategy for low cardinality columns within parquet.

dataset_name/
  year=2007/
    month=01/
       0.parq
       1.parq
       ...
    month=02/
       0.parq
       1.parq
       ...
    month=03/
    ...
  year=2008/
    month=01/
    ...
  ...

This feature was cited as one of the reasons parquet was chose over zarr for dask dataframes: https://github.com/dask/dask/issues/1599

awkward array

https://github.com/zarr-developers/zarr-specs/issues/62

Implementation

It is to be hoped that much code can be adapted from dask.array, which already allows variable chunk sizes on each dimension.

Alternatives

Just tune chunk sizes

https://github.com/zarr-developers/zarr-specs/issues/62#issuecomment-1100806513

Discussion

References and Footnotes

This document has been placed in the public domain.