Python Installation

Arbor’s Python API will be the most convenient interface for most users.

Note

Arbor requires Python version 3.6 and later. It is advised that you update pip as well.

Getting Arbor

Every point release of Arbor is pushed to the Python Package Index. For x86-64 Linux and MacOS plaftorms, we provide binary wheels. The easiest way to get Arbor is with pip:

pip3 install arbor

Note

For other platforms, pip will build Arbor from source. You will need to have some development packages installed in order to build Arbor this way.

  • Ubuntu/Debian: git cmake gcc python3-dev python3-pip libxml2-dev

  • Fedora/CentOS/OpenSuse: git cmake gcc-c++ python3-devel python3-pip libxml2-devel

  • MacOS: get brew here and run brew install cmake clang python3 libxml2

  • Windows: the simplest way is to use WSL and then follow the instructions for Ubuntu.

To test that Arbor is available, try the following in a Python interpreter to see information about the version and enabled features:

>>> import arbor
>>> print(arbor.__version__)
>>> print(arbor.__config__)

You are now ready to use Arbor! You can continue reading these documentation pages, have a look at the Python API reference, or visit the Tutorials.

Note

To get help in case of problems installing with pip, run pip with the --verbose flag, and attach the output (along with the pip command itself) to a ticket on Arbor’s issues page.

Customising Arbor

If you wish to get the latest Arbor straight from the master branch in our git repository, you can run:

pip3 install git+https://github.com/arbor-sim/arbor.git

If you want to work on Arbor’s code, you can get a copy of our repo and point pip at the local directory:

# get your copy of the Arbor source
git clone https://github.com/arbor-sim/arbor.git --recursive
# make your changes and then instruct pip to build and install the local source
pip3 install ./arbor/

Every time you make changes to the code, you’ll have to repeat the second step.

Advanced options

By default Arbor is installed with multi-threading enabled. To enable more advanced forms of parallelism, Arbor comes with a few compilation options. These can be used on both local (pip3 install ./arbor) and remote (pip3 install arbor) copies of Arbor. Below we assume you are working off a local copy.

The following optional flags can be used to configure the installation:

  • --mpi: Enable MPI support (requires MPI library).

  • --gpu: Enable GPU support for NVIDIA GPUs with nvcc using cuda, or with clang using cuda-clang (both require cudaruntime). Enable GPU support for AMD GPUs with hipcc using hip. By default set to none, which disables gpu support.

  • --vec: Enable vectorization. The --arch argument, documented below, may also have to be set appropriately to generated vectorized code. See Architecture for details.

  • --arch: CPU micro-architecture to target. The advised default is native. See here for a full list of options.

  • --makejobs: Specify the amount of jobs to make the project with for faster build times on multicore systems. By default set to 2.

Vanilla install with no additional features enabled:

pip3 install arbor

With MPI support. This might require loading an MPI module or setting the CC and CXX environment variables:

pip3 install --install-option='--mpi' ./arbor

Compile with vectorization on a system with a SkyLake architecture:

pip3 install --install-option='--vec' --install-option='--arch=skylake' arbor

Enable NVIDIA GPUs (compiled with nvcc). This requires the CUDA toolkit:

pip3 install --install-option='--gpu=cuda' ./arbor

Enable NVIDIA GPUs (compiled with clang). This also requires the CUDA toolkit:

pip3 install --install-option='--gpu=cuda-clang' ./arbor

Enable AMD GPUs (compiled with hipcc). This requires setting the CC and CXX environment variables

pip3 install --install-option='--gpu=hip' ./arbor

Note

Setuptools compiles the Arbor C++ library and wrapper, as well as dependencies you did not have installed yet (e.g. numpy). It may take a few minutes. Pass the --verbose flag to pip to see the individual steps being performed if you are concerned that progress is halting.

If you had Arbor installed already, you may need to remove it first before you can (re)compile it with the flags you need.

Note

Detailed instructions on how to install using CMake are in the Python configuration section of the installation guide. CMake is recommended if you need more control over compilation and installation, plan to use Arbor with C++, or if you are integrating with package managers such as Spack and EasyBuild.

Dependencies

If a downstream dependency requires Arbor be built with a specific feature enabled, use requirements.txt to define the constraints. For example, a package that depends on arbor version 0.3 or later with MPI support would add the following to its requirements:

arbor >= 0.3 --install-option='--gpu=cuda' \
             --install-option='--mpi'

Note on performance

The Python interface can incur significant memory and runtime overheads relative to C++ during the model building phase, however simulation performance is the same for both interfaces.