Python

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

Getting Arbor

The easiest way to get Arbor is with pip:

pip3 install arbor

Every point release it pushed to the Python Package Index. If you wish to install another version, it is also possible to use Setuptools directly on a local copy of the source code, or instruct pip to install directly from our git repository:

# use setuptools and python directly
git clone https://github.com/arbor-sim/arbor.git --recursive
python3 install ./arbor/setup.py

# tell pip to build and install from master
pip install git+https://github.com/arbor-sim/arbor.git

Note

You will need to have some development packages installed in order to build Arbor this way. For Debian/Ubuntu: sudo apt install build-essential python-dev, Fedora/Red Hat/CentOS: sudo yum install @development-tools python-devel.

Note

Arbor’s Setuptools process simplifies installation for common configurations on laptops and workstations by calling CMake under the hood.

To install Arbor on a HPC cluster, or to configure Arbor with system-specific options, we recommend using the CMake build process.

To test that Arbor is available in Python, try the following in a Python 3 interpreter to see information about the version and enabled features:

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

Advanced Options

By default Arbor is installed with multi-threading enabled. To enable more advanced forms of parallelism, 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. This might require choosing an appropriate architecture using --arch.

  • --arch: CPU micro-architecture to target. By default this is set to native.

If calling setup.py the flags must come after install on the command line, and if being passed to pip they must be passed via --install-option. The examples below demonstrate this for both pip and setup.py.

Vanilla install with no additional features enabled:

pip3 install arbor
python3 ./arbor/setup.py install

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

pip3 install --install-option='--mpi' ./arbor
python3 ./arbor/setup.py install --mpi

Compile with vectorization on a system with SkyLake: architecture:

pip3 install --install-option='--vec' --install-option='--arch=skylake' arbor
python3 ./arbor/setup.py install --vec --arch=skylake

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

pip3 install --install-option='--gpu=cuda' ./arbor
python3 ./arbor/setup.py install  --gpu=cuda

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

pip3 install --install-option='--gpu=cuda-clang' ./arbor
python3 ./arbor/setup.py install --gpu=cuda-clang

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

pip3 install --install-option='--gpu=hip' ./arbor
python3 ./arbor/setup.py install --gpu=hip

Note

Setuptools compiles the Arbor C++ library and wrapper, which can 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.

Note

Detailed instructions on how to install using CMake are in the Python configuration section of the installation guide. CMake is recommended for developers, integration with package managers such as Spack and EasyBuild, and users who require fine grained control over compilation and installation.

Note

To report 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.

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'

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.

Python 2

Python 2 reached end of life in January 2020. Arbor only provides support for Python 3.6 and later.

Note

It might be possible to install and run Arbor using Python 2.7 by setting the PYTHON_EXECUTABLE variable when configuring CMake. However, Arbor is not tested against Python 2.7, and we won’t be able to provide support.