Skip to main content

Installation Instructions

SpaRTaNS is a Python 3 package with a custom c++ binding (compiled using pybind11), which relies heavily on MPI and HDF5, through numpy, mpi4py, and h5py.

Building from source​

Currently, SpaRTaNS is distributed from source and built using the scikit-build package.

To build and install the most recent version of SpaRTaNS, you can clone the main branch from the source repository and install:

git clone https://github.com/narang-lab/spartans
cd spartans
pip install .

Troubleshooting​

The scikit-build should handle all dependencies automatically. If you find this is not the case, you can try installing all the dependencies manually before installing SparTaNS:

  • "setuptools"
  • "wheel"
  • "pybind11"
  • "scikit-build"
  • "cmake"
  • "ninja"
  • "mpi4py==3.0.3"
  • "numpy"
  • "h5py"
  • "PyYAML"
  • "parse"
note

Notice the version-pinning on mpi4py, which is likely the installation issues culprit.