Introduction

Welcome to TileDB!

TileDB is a library that efficiently manages large-scale, n-dimensional, dense and sparse array data.

Here you will find tutorials that should serve as a gradual introduction to help you understand basic TileDB concepts, such as dense versus sparse arrays, all the way through more advanced topics such as data consistency and performance tuning.

TileDB can be found at GitHub, open-sourced under the permissive MIT License.

What is Array Data?

Array data are collections of elements or cells, where each cell is uniquely indexed by a coordinate tuple in an arbitrary number of orthogonal dimensions. The figure below shows examples of 1D, 2D and 3D arrays. It is easy to identify a single cell or any subset of cells using array notation, such as A[2] for cell with index 2 in vector A, or C[2:3, 1:3] for cells in rows 2, 3 and columns 1, 2, 3 in 2D array C. Such a cell subselection is called slicing and is the most fundamental operation for array data. Moreover, each cell may contain arbitrary information, beyond just an integer or a real number (e.g., a string, or a custom object).

_images/intro_arrays.png

Example 1D, 2D and 3D arrays

If every cell in the array has an associated value, we call the array dense. If the majority of cells do not have a value, i.e. many cells have “undefined” or “empty” values, we call the array sparse.

A real-world example of a 2D dense array is a pixel-based image file. Each pixel is identified by a unique (x,y) coordinate pair, and each pixel can store information such as its RGB values. Video is a 3D dense array example, where each frame is a 2D dense image across an extra (discretized) dense time dimension. Sparse data is also very common in the real world, such as time-based data where irregular gaps occur between events (as opposed to regular samples). Geo-locations on maps can be modeled as 2D sparse arrays, whereas point cloud data (e.g., LiDAR) is a good 3D sparse array example. There are numerous other examples seeming irrelevant to arrays that are actually best represented as arrays, including genomics data, even relational database tables!

What is TileDB?

With TileDB you gain the ability to quickly query array-structured data using rectangular slices, quickly update existing arrays with new or changed data, and easily optimize your physical data organization for maximizing compression and read performance.

What does it mean when we say TileDB “manages” your data? It means that when you ingest data into a TileDB array, the library takes care of all of the metadata handling required for fast slicing, writes and updates. The TileDB library also handles lower-level details like data compression, parallel execution and file I/O, and interfacing with a variety of storage backends, such as parallel file systems like Lustre and HDFS, or cloud data stores such as AWS S3.

TileDB does all of this through a familiar library-based approach. To ingest data into TileDB’s persistent format, you write a program that links with the TileDB library and makes API calls to create, write to and read from TileDB arrays. It is simple to choose whether your arrays should be stored as files and directories on your local disk, or objects in a remote cloud storage system such as S3. TileDB is a thin software layer that sits between your applications and the supported storage backend, exposing API bindings for a wide set of programming languages (e.g., C, C++, Python, Java and R).

_images/intro_architecture.png

TileDB is a thin layer between the user applications and the storage backends

Features

Novel Format

TileDB introduces a novel multi-dimensional array format that effectively handles both dense and sparse data, exposing a unified array API. TileDB’s concept of immutable, append-only fragments allows also for efficient updates. TileDB adopts a columnar format for the various types of values (attributes) stored in the arrays, enabling compressibility and efficient attribute subselection.

Compression

TileDB offers high compression ratios while allowing efficient slicing via its tile-based approach. TileDB can compress array data with a growing number of compressors, such as GZIP, BZIP2, LZ4, ZStandard, double-delta and run-length encoding.

Parallelism

All the TileDB internals (e.g., compression/decompression, file I/O, slicing, etc.) are fully parallelized. TileDB’s thread-/process-safe and asynchronous writes and reads enables users to build powerful parallel analytics on top of the TileDB array storage manager (e.g., using OpenMP or MPI).

Portability

TileDB works on Linux, macOS and Windows, offering easy installation packages, binaries and Docker containerization. The users can integrate TileDB with the tools of their favorite platform to manage massive multi-dimensional array data.

Language Bindings

Although TileDB is built in C++, it comes with a growing set of bindings, including C, C++, Python, Java and R. TileDB enables users to continue using their favorite data science applications, while being empowered to work on immense amounts of data, beyond what can be stored in main memory.

Multiple Backends

TileDB transparently stores the user arrays across multiple backends such as HDFS or S3-compliant object stores (like AWS S3, minio, or Ceph). TileDB’s API is the same regardless of where the array is stored.

Key-value Store

Users can store any persistent metadata with TileDB’s key-value storage functionality. A TileDB key-value store is implemented as a TileDB sparse array and inherits all its benefits (such as compression, parallelism, and multiple backend support).

Virtual Filesystem

TileDB adds general file management and IO into the mix for any supported storage backend, via its unified “virtual filesystem” (VFS) API.

Comparison to HDF5

HDF5 is arguably the most popular multi-dimensional array storage software, with a strong presence in High Perfomance Computing for over 30 years. While heavily inspired by HDF5, TileDB brings many novel ideas to array data management, several of which are adapted from Databases. The most important differences between TileDB and HDF5 are outlined below.

Sparse Array Support

TileDB was designed from the ground up to efficiently store and access both dense and sparse arrays. In contrast, HDF5 is a dense array storage manager.

Parallelism

TileDB is fully parallelized internally. Specifically, it performs slicing, compression/decompression, even file I/O with multiple threads transparently from the user, scaling gracefully with the number of available threads/cores. This is particularly important for compression/decompression, since now you can compress your massive data without compromising read performance. In addition, TileDB is thread- and process-safe, providing more flexibility for users accustomed to parallel programming with OpenMP or MPI. On the contrary, HDF5 is not multi-threaded; it was originally designed to work well with MPI on HPC systems.

Emphasis on Storing Multiple Values in Cells and Columnar Format

TileDB adapts several ideas from Databases. Each array cell in TileDB is regarded as a tuple, and each cell tuple adheres to some common array schema. An element of a cell tuple is called an attribute value. Attributes in TileDB have the same meaning as in Databases, i.e., they are different fields in the cell. TileDB stores all cell values on each attribute in a separate file, i.e., it adopts a columnar format. This means that each TileDB data file corresponds to a different projection of the array on a single attribute. This leads to better data compressibility and more efficient access in case the user is interested in a subset of the array attributes upon reads.

HDF5 does not have this concept of cell fields/attributes. Note that HDF5 uses “attribute” to refer to some piece of array metadata. HDF5 does support storing structs, which can be regarded as collections of attributes. However, it stores all the values of a cell struct object contiguously, preventing the user from efficiently retrieving a subset of the struct fields, and considerably hindering compression.

Multi-File Format and Immutability

HDF5 stores an array in a single file. Each update modifies this single file in-place. TileDB instead stores each array as a collection of files stored in a “directory” (physical directory in the local filesystem, or a collection of objects with a common name prefix on an object store). Any update (or, more accurately, any batch of updates) creates a new subdirectory under the array directory. Every file in TileDB is immutable. TileDB’s approach prevents corruption during a failed update. This means that you do not need to nuke your entire (potentially huge) array just because a single cell update failed and corrupted your file. Therefore, TileDB offers better fault-tolerance and recovery, as well as the opportunity to build extra useful features, such as versioning, time-traveling and an “undo” functionality for updates.

Handling of Variable-Sized Cell Values

TileDB has native support for cell values with variable sizes. In contrast to HDF5’s VL datatypes, TileDB stores all cell values contiguously in a single file, following the same grouping into tiles as the fixed-sized values. In addition, it stores the starting offsets of the cell values in a separate file. Since the offsets are sorted in ascending order, they are highly compressible. This technique leads to both large compression ratio and rapid slicing, exhibiting comparable performance to the fixed-sized counterparts.

Storage Backend Support

TileDB is optimized for various storage backends (including HDFS and AWS S3), all supported in the core, open-source library. This means that (i) this feature is free, and (ii) you get to use it with the embeddable TileDB library, without having to set up or communicate with an extra service. On the contrary, the HDF5 software does not ship S3 and HDFS support by default. The HDF Group offers a cloud service with HDFS/S3 integration as part of their Enterprise Support for HDF5, but this is not open-source/free.

Modern Build System

TileDB offers a modern build system that works on Linux, macOS and Windows, with automatic installation of all dependencies. TileDB ships with all its compressors by default. This makes it easier to share compressed data, since they are all compressed using the same suit of compressors. In contrast, HDF5 does not ship with all compressors, but rather offers compressor plug-ins that must be build separately. This can make it difficult to share compressed data if end users have different compressors installed (or none).

Comparison to SciDB

SciDB is a popular array database management system. Its functionality, architecture and targeted user base are vastly different from those of TileDB (and HDF5) SciDB is a distributed database service, not an embeddable library like TileDB. Applications interface with SciDB via sockets (ODBC connectors), sending queries written in SciDB’s query language (called AQL). On the contrary, TileDB is a leightweight layer that brings the data from storage directly to the application via library API calls with minimal overhead (avoiding any serialization/deserialization costs). SciDB supports a wide set of database-like operators and features, including analytics, ACID consistency properties, access control, etc. In contrast, TileDB is an array storage manager that provides effective compression and efficient slicing, while being easily integrated with higher level programming languages. TileDB (currently) focuses on IO, leaving the computational tasks to the applications built on top of it.

Contributing

If you would like to contribute to TileDB, visit our GitHub repository to view the list of tracked issues. You can also see developer documentation at the wiki (also on GitHub).

History

TileDB was originally created at the Intel Science and Technology Center for Big Data, a collaboration between Intel Labs and MIT. The research project was published in a VLDB 2016 paper. TileDB, Inc. was founded in February 2017 to continue the further development and maintenance of the TileDB software.