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Installing via pip

For Windows 10, OSX, and Linux and Python versions 3.6-3.9 direct installation with OpenMP support should work via [pip]:

pip install pyapr

We recommend using a virtual environment (see below).

CUDA functionality is currently not enabled when installing via pip. For this, it is necessary to build the package from source.

Installing from source

Dependencies

LibAPR is included as a submodule, and built alongside the wrappers. This requires the following packages:

  • HDF5 1.8.20 or higher
  • OpenMP > 3.0 (optional, but recommended)
  • CMake 3.6 or higher
  • LibTIFF 4.0 or higher

pyapr additionally requires Python 3, and the packages listed in requirements.txt.

Installing dependencies on Linux

On Ubuntu, install the cmake, build-essential, libhdf5-dev and libtiff5-dev packages (on other distributions, refer to the documentation there, the package names will be similar). OpenMP support is provided by the GCC compiler installed as part of the build-essential package.

Installing dependencies on OSX

On OSX, install the cmake, hdf5 and libtiff homebrew packages and have the Xcode command line tools installed. If you want to compile with OpenMP support, also install the llvm package (this can also be done using homebrew), as the clang version shipped by Apple currently does not support OpenMP.

Note for windows users

Please see LibAPR for the latest windows install instructions.

Building

The repository requires submodules, and needs to be cloned recursively:

git clone --recursive https://github.com/AdaptiveParticles/pyapr.git

It is recommended to use a virtual environment, such as virtualenv. To set this up, use e.g.

pip3 install virtualenv
python3 -m virtualenv myenv
source myenv/bin/activate

The required Python packages can be installed via the command

pip install -r requirements.txt

Once the dependencies are installed, pyapr can be built via the setup.py script, e.g. by running

python setup.py install

or

pip install .

in the root directory of the repository.

CMake build options

There are two CMake options that can be given to enable or disable OpenMP and CUDA:

Option Description Default value
PYAPR_USE_OPENMP Enable multithreading via OpenMP ON
PYAPR_USE_CUDA Build available CUDA functionality OFF
PYAPR_PREFER_EXTERNAL_LIBAPR Use an installed version of LibAPR (if found) rather than building it from submodules OFF

When building via the setup.py script, these options can be set via the environment variable EXTRA_CMAKE_ARGS. For example,

EXTRA_CMAKE_ARGS="-DPYAPR_USE_OPENMP=OFF -DPYAPR_USE_CUDA=OFF" python setup.py install

will install the package with both OpenMP and CUDA disabled. If building from an installed version of LibAPR in a non-standard location, help CMake find it, e.g., by passing -DCMAKE_PREFIX_PATH=/path/to/APR. Additional compiler options can be set similarly, e.g. via the variables CMAKE_CXX_FLAGS and CMAKE_CUDA_FLAGS

OpenMP support on OSX

To use the homebrew-installed clang for OpenMP support on OSX, modify the call above to

CPPFLAGS="-I/usr/local/opt/llvm/include" LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib" CXX="/usr/local/opt/llvm/bin/clang++" CC="/usr/local/opt/llvm/bin/clang" python setup.py install