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Basic Concepts

Global cell order and tiling

Whenever multi-dimensional data is stored on disk or memory it must be laid out in some linear order, since these storage media are single-dimensional. This choice of ordering can significantly impact application performance, since it affects which cells are near each other in storage. In TileDB, we call the mapping from multiple dimensions to a linear order the global cell order.

A desirable property is that cells that are accessed together should be co-located on the disk and in memory, to minimize disk seeks, page reads, and cache misses. The best choice of global cell order is dictated by application-specific characteristics; for example, if an application reads data a row-at-a-time, data should be laid out in rows. A columnar layout in this case will result in a massive number of additional page reads.

As we explain later, array compression is a desirable property that reduces both storage space and IO overhead. Arrays are typically accessed by slicing a portion (or subarray) of the array, instead of bringing the entire array into main memory from the filesystem backend. This suggests that compression must be performed on a block-based manner, i.e., the cells must be organized into groups such that the cells of each group are compressed/accessed always together. In TileDB, we call such a group of cells a tile. The array tiling can affect (or help shape) the global cell order.

Below we explain how the user can flexibly specify the tiling and global cell order for the case of dense and sparse arrays separately.

Dense case

TileDB offers various ways to define the global cell order for an array, enabling the user to tailor the array storage to his or her application for maximum performance. For dense arrays, the global cell order is specified in three steps. First, the user decomposes the array domain into space tiles by specifying a tile extent per dimension (e.g., 2x2 tiles). This effectively creates equi-sized hyper-rectangles (i.e., each containing the same number of cells) that cover the entire array domain. Second, the user determines the cell order within each space tile, which can be either row-major or column-major. Third, the user determines a tile order, which is also either row-major or column-major. Figure 2 shows the global cell orders resulting from different choices in these three steps (the space tiles are depicted in blue).

Figure 2: Global cell order in dense arrays

Figure 2: Global cell order in dense arrays

Sparse case

The notion of a global cell order also applies to sparse arrays. However, creating sparse tiles is somewhat more complex because simply using tiles of fixed logical size could lead to many empty tiles for very sparse arrays. Even if we suppressed storage of empty tiles, skew in many sparse datasets would create tiles of highly varied capacity, leading to ineffective compression, metadata overheads, and some very small tiles where seek times represent a large fraction of access cost. Therefore, to address the case of sparse tiles, we introduce the notion of data tiles.

A data tile is a group of non-empty cells. It is the atomic unit of IO and compression (as discussed below), and has a crucial role during reads. Similarly to a space tile, a data tile is enclosed in the logical space by a hyper-rectangle. For the dense array case, each data tile has a one-to-one mapping to a space tile, i.e., it encompasses the cells included in the space tile. The same may not hold for in sparse arrays.

For the sparse case, TileDB instead allows the user to specify a data tile capacity, and creates the data tiles such that they all have the same number of non-empty cells, equal to the capacity. To implement this, assuming that the fixed capacity is denoted by c, TileDB simply traverses the cells in the global cell order imposed by the space tiles and creates one data tile for every c non-empty cells. A data tile of a sparse array is represented in the logical space by the tightest hyper-rectangle that encompasses the non-empty cells it groups, called the minimum bounding rectangle (MBR). Figure 3 illustrates various data tiles resulting from different global cell orders, assuming that the tile capacity is 2. The space tiles are depicted in blue color and the (MBR of the) data tiles in black. Note that data tiles in the sparse case may overlap, but each non-empty cell corresponds to exactly one data tile.

Figure 3: Global cell order in sparse arrays

Figure 3: Global cell order in sparse arrays

Compression

TileDB employs tile-based compression. Additionally, it allows the user to select different compression schemes on a per-attribute basis, as attributes are stored separately (as discussed below). Compression is an important feature of TileDB and, therefore, we include more details in a separate section Compression.

The data tile (in both dense and sparse arrays) is the atomic unit of IO and compression.

Fragments

A fragment is a timestamped snapshot of a batch of array updates, i.e., a collection of array modifications carried out via write operations and made visible at a particular time instant. For instance, the initial loading of the data into the array constitutes the first array fragment. If at a later time a set of cells is modified, then these cells constitute the second array fragment, and so on. In that sense, an array is comprised of a collection of array fragments, each of which can be regarded as a separate array, whose collective logical overlap composes the current logical view of the array. A fragment can be either dense or sparse. Dense fragments are used only with dense arrays, but sparse fragments may be applied to both dense and sparse arrays.

Figure 4 shows an example of an array with three fragments; the first two are dense and the third is sparse. Observe that the second fragment is dense within a hyper-rectangular subarray, whereas any cell outside this subarray is empty. The figure also illustrates the collective logical view of the array; the cells of the most recent fragments overwrite those of the older ones.

Figure 4: Fragment examples

Figure 4: Fragment examples

The fragments are the key concept that enables TileDB to perform rapid writes. If the number of fragments is reasonable, then their presence does not significantly affect the read performance. In the event that numerous fragments are created and the read performance becomes unsatisfactory, TileDB employs an efficient consolidation mechanism that coalesces fragments into a single one. Consolidation can happen in parallel in the background, while reads and writes continue to access the array. The concept of fragments and their benefits are explained later in this tutorial.

Array Schema and Fragment Metadata

TileDB stores metadata about every array, as well as for each fragment. The array schema contains information about the definition of the array, such as the number, names and types of dimensions and attributes, the dimension domains, the space tile extents, data tile capacity, and the compression types. The fragment metadata contain summary information about the physical organization of the stored array data in a fragment, such as the start offsets of the compressed tiles in the file, the MBRs for sparse arrays, etc.

The array schema and fragment metadata constitute internal information managed solely by TileDB. This is different from the arbitrary metadata that the user may wish to attach to an array, which can be done via TileDB's key-value store store functionality.

Basic Concepts