Installation

TileDB is distributed in two main components: the core TileDB library and the high-level APIs. The core library implements all TileDB functionality, and the APIs define the interfaces to the core library for different programming languages.

Depending on your intended use of TileDB, you will need to install the core TileDB library, or one of the high-level APIs such as for Python, or both. When installing a high-level TileDB API, the corresponding installation of the core library has been automated where possible.

Quick Installation

Apart from these quick installation steps, the rest of this page details how to configure and build custom installations of the core TileDB library itself from source or the pre-built packages.

C or C++ APIs

To use TileDB with the C or C++ APIs:

macOS

# Homebrew:
$ brew update
$ brew install tiledb-inc/stable/tiledb

# Or Conda:
$ conda install -c conda-forge tiledb

Linux

# Conda:
$ conda install -c conda-forge tiledb

# Or Docker:
$ docker pull tiledb/tiledb
$ docker run -it tiledb/tiledb

Windows

# Conda
> conda install -c conda-forge tiledb

# Or download the pre-built release binaries from:
# https://github.com/TileDB-Inc/TileDB/releases

Once you install TileDB, visit the Usage page for how to build and link your programs against TileDB.

Python API

To use TileDB with the Python API:

# Pip:
$ pip install tiledb

# Or Conda:
$ conda install -c conda-forge tiledb-py

Both the Pip and Conda packages will automatically build and locally install the core library in addition to the Python interface. Full build and install instructions for the Python API can be found at the TileDB-Inc/TileDB-Py repo.

R API

To use TileDB with the R API:

> # From the R REPL
> install.packages("devtools")
> library(devtools)
> devtools::install_github("TileDB-Inc/[email protected]")
...
> library(tiledb)
> tiledb::libtiledb_version()
major minor patch
1     3     0

TileDB needs to be installed beforehand (from a package or from source) for the TileDB-R package to build and link correctly. Full build and install instructions for the R API can be found at the TileDB-Inc/TileDB-R repo.

Golang API

To use TileDB with the Golang API:

# Go Get
$ go get -v github.com/TileDB-Inc/TileDB-Go

Go get will automatically build and locally install the Golang interface.

TileDB needs to be installed beforehand (from a package or from source) for the TileDB-Go library to build and link correctly. Full build and install instructions for the Golang API can be found at the TileDB-Inc/TileDB-Go repo.

Pre-built Packages

Homebrew

The core TileDB library can be installed easily using the Homebrew package manager for macOS. Install instructions for Homebrew are provided on the package manager’s website.

To install the latest stable version of TileDB

$ brew update
$ brew install tiledb-inc/stable/tiledb

HDFS and S3 backends are enabled by default. To disable one or more backends, use the --without- switch to disable them

$ brew install tiledb-inc/stable/tiledb --without-s3
$ brew install tiledb-inc/stable/tiledb --without-hdfs

A full list of build options can be viewed with the info command

$ brew info tiledb-inc/stable/tiledb

Other helpful brew commands:

  • brew upgrade tiledb-inc/stable/tiledb: Upgrade to the latest stable version of TileDB
  • brew uninstall tiledb-inc/stable/tiledb: Uninstall TileDB

The Homebrew Tap is located at https://github.com/TileDB-Inc/homebrew.

Docker

TileDB is available as a pre-built Docker image

$ docker pull tiledb/tiledb
$ docker run -it tiledb/tiledb

which uses the latest TileDB version, or

$ docker pull tiledb/tiledb:<version>
$ docker run -it tiledb/tiledb:<version>

which uses a specific TileDB version (ex. <version> could be 1.2.0).

More info at the TileDB Docker Hub repo and the TileDB-Docker GitHub repo.

Conda

A package for TileDB is available for the Conda package manager. Conda makes it easy to install software into separate distinct environments on Windows, Linux, and macOS

$ conda create -n tiledb
$ conda activate tiledb
$ conda install -c conda-forge tiledb

If you are compiling / linking against the TileDB conda package, you may need to explicity add the conda path after activating the environment with conda activate tiledb (conda activate sets the CONDA_PREFIX environment variable)

$ export CPATH=$CONDA_PREFIX/include
$ export LIBRARY_PATH=$CONDA_PREFIX/lib
$ export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

Or, instead of exporting those environment variables, you can pass them as command line flags during compilation

$ g++ -std=c++11 example.cpp -o example -I$CONDA_PREFIX/include -L$CONDA_PREFIX/lib -ltiledb

Windows Binaries

You can download pre-built Windows binaries in the .zip file from the latest TileDB release. You can then simply configure your project (if using Visual Studio) according to the Windows usage instructions.

Building from Source

TileDB has been tested on Ubuntu Linux (v.14.04+), CentOS Linux (v.7+), macOS El Capitan (v.10.11) and Windows (7+), but TileDB should work with any reasonably recent version of Ubuntu, CentOS, macOS or Windows with an installed compiler supporting C++11.

macOS/Linux

Begin by downloading a release tarball or by cloning the TileDB GitHub repo and checking out a release tag (where <version> is the version you wish to use (e.g., 1.2.0)

$ git clone https://github.com/TileDB-Inc/TileDB
$ git checkout <version>
$ cd TileDB

To configure TileDB, use the bootstrap script

$ mkdir build
$ cd build
$ ../bootstap <flags>
$ # Or use CMake directly instead of bootstrap:
$ # cmake <flags> ..

The flags for the bootstrap script and the CMake equivalents are as follows:

Flag Description CMake Equivalent
--help Prints command line flag options n/a
--prefix=PREFIX Install files in tree rooted at PREFIX (defaults to TileDB/dist) CMAKE_INSTALL_PREFIX=<PREFIX>
--dependency=DIRs Colon separated list to binary dependencies CMAKE_PREFIX_PATH=<DIRs>
--enable-debug Enable debug build CMAKE_BUILD_TYPE=Debug
--enable-coverage Enable build with code coverage support CMAKE_BUILD_TYPE=Coverage
--enable-verbose Enable verbose status messages TILEDB_VERBOSE=ON
--enable-hdfs Enables building with HDFS storage backend support TILEDB_HDFS=ON
--enable-s3 Enables building with S3 storage backend support TILEDB_S3=ON
--enable-static-tiledb Enables building TileDB as a static library TILEDB_STATIC=ON
--disable-werror Disables building with the -Werror flag TILEDB_WERROR=OFF
--disable-cpp-api Disables building the TileDB C++ API TILEDB_CPP_API=OFF
--disable-tbb Disables use of TBB for parallelization TILEDB_TBB=OFF
--disable-tests Disables building the TileDB test suite TILEDB_TESTS=OFF

To build after configuration, run the generated make script

$ make -j <nprocs>

To install to the configured prefix

$ make install-tiledb

Other helpful makefile targets:

  • make check: Runs the tests
  • make examples: Builds the examples

Windows

Building TileDB on Windows has been tested to work with Microsoft Visual Studio 2015 and later. You can install the free Community Edition if you’d like the full IDE, or the Build Tools if you don’t need or want the IDE installed.

During the Visual Studio setup process, make sure the Git for Windows component is selected if you do not already have a working Git installation. Also be sure to select the CMake component if you do not have a working CMake installation.

In addition, you will need to install PowerShell (free).

To build and install TileDB, first open PowerShell and clone the TileDB repository

> git clone https://github.com/TileDB-Inc/TileDB
> cd TileDB

Next, ensure the CMake binaries are in your path. If you installed Visual Studio, execute

> $env:Path += ";C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin"
> # If you installed the build tools, instead execute:
> # $env:Path += ";C:\Program Files (x86)\Microsoft Visual Studio\2017\BuildTools\Common7\IDE\CommonExtensions\Microsoft\CMake\CMake\bin"

Create a build directory and configure TileDB

> mkdir build
> cd build
> ..\bootstrap.ps1 <flags>
> # Or use CMake directly:
> # cmake <flags> ..

The flags for the bootstrap script and the CMake equivalents are as follows:

Flag Description CMake Equivalent
-? Display a usage message. n/a
-Prefix Install files in tree rooted at PREFIX (defaults to TileDB\dist) CMAKE_INSTALL_PREFIX=<PREFIX>
-Dependency Semicolon separated list to binary dependencies. CMAKE_PREFIX_PATH=<DIRs>
-CMakeGenerator Optionally specify the CMake generator string, e.g. “Visual Studio 15 2017”. Check ‘cmake –help’ for a list of supported generators. -G <generator>
-EnableDebug Enable debug build CMAKE_BUILD_TYPE=Debug
-EnableVerbose Enable verbose status messages. TILEDB_VERBOSE=ON
-EnableS3 Enables building with the S3 storage backend. TILEDB_S3=ON
-EnableStaticTileDB Enables building TileDB as a static library TILEDB_STATIC=ON
-DisableWerror Disables building with the /WX flag TILEDB_WERROR=OFF
-DisableCppApi Disables building the TileDB C++ API TILEDB_CPP_API=OFF
-DisableTBB Disables use of TBB for parallelization TILEDB_TBB=OFF
-DisableTests Disables building the TileDB test suite TILEDB_TESTS=OFF

To build after configuration

> cmake --build . --config Release

To install

> cmake --build . --target install-tiledb --config Release

Other helpful build targets:

  • cmake --build . --target check --config Release: Runs the tests
  • cmake --build . --target examples --config Release: Builds the examples

Warning

If you build libtiledb in Release mode (resp. Debug), make sure to build check and examples in Release mode as well (resp. Debug), otherwise the test and example executables will not run properly.

Warning

Should you experience any problem with the build, it is always a good idea to delete the build and dist directories in your TileDB repo path and restart the process, as cmake’s cached state could present some unexpected problems.

Cygwin

Cygwin is a Unix like environment and command line interface for Microsoft Windows that provides a large collection of GNU / OpenSource tools (including the gcc toolchain) and supporting libraries that provide substantial POSIX API functionality. TileDB is able to compile from source in the Cygwin environment if Intel TBB is disabled and some TileDB dependencies are installed as Cygwin packages.

The following Cygwin packages need to be installed:

  • gcc / g++
  • git
  • cmake
  • make
  • lz4-devel
  • zlib-devel
  • libzstd-devel (+src)
  • bzip2 (+src)
  • openssl-devel

You can then clone and build TileDB using git / cmake / make:

$ git clone https://github.com/TileDB-Inc/TileDB
$ cd TileDB && mkdir build && cd build
$ cmake -DTILEDB_TBB=OFF ..
$ make
$ make check

Build Requirements

TileDB requires a recent version (3.3 or later) of the CMake build system, and a compiler supporting C++11. For compression, TileDB relies on the following libraries:

When building from source, TileDB will locate these dependencies if already installed on your system, and locally install (not system-wide) any of them that are missing.

Optional Dependencies

TBB

Some TileDB internals are parallelized using the Intel Threaded Building Blocks library. The TileDB build system will install this library if it is not already present on your system. You can disable the TBB dependency when configuring the TileDB build, in which case TileDB will fall back on serial implementations of several algorithms. As a part of the TileDB installation process, the TBB dynamic library will also be installed in the same destination as the TileDB dynamic library. The TBB headers are not installed with TileDB.

S3

Backend support for S3 stores requires the AWS C++ SDK. Similarly to the required dependencies, the TileDB build system will install the SDK locally if it is not already present on your system (when the S3 build option is enabled).

TileDB also integrates well with the S3-compliant minio object store.

HDFS

Backend support for the Hadoop File System HDFS is optional. TileDB relies on the C interface to HDFS provided by libhdfs to interact with the distributed filesystem.

During the build process the following environmental variables must be set:

  • JAVA_HOME: Path to the location of the Java installation.
  • HADOOP_HOME: Path to the location of the HDFS installation.
  • CLASSPATH: The Hadoop jars must be added to the CLASSPATH before interacting with libhdfs.

Consult the HDFS user guide for installing, setting up, and using the distributed Hadoop file system.

Note

HDFS is not currently supported on Windows.

Dependency Installation

If any dependencies are not found pre-installed on your system, the TileDB build process will download and build them automatically. Preferentially, any dependencies built by this process will be built as static libraries, which are statically linked against the TileDB shared library during the build. This simplifies usage of TileDB, as it results in a single binary object, e.g. libtiledb.so that contains all of the dependencies. When installing TileDB, only the TileDB include files and the dynamic object libtiledb.so will be copied into the installation prefix.

If TileDB is itself built as a static library (using the TILEDB_STATIC=ON CMake variable or corresponding bootstrap flag), the dependency static libraries must be installed alongside the resulting static libtiledb.a object. This is because static libraries cannot be statically linked together into a single object (at least not in a portable way). Therefore, when installing TileDB all static dependency libraries will be copied into the installation prefix alongside libtiledb.a.

Note

The TBB dependency is also built as a static library by default (except on Windows). If you require a dynamically-linked TBB, use the TILEDB_TBB_SHARED=ON CMake variable. Note that the libtbb.so shared library will then be installed alongside libtiledb.so during installation.