Installation

Installation

Requirements

Use Linux for the widest feature support. SUMMIT requires Python 3.10 or newer, a C++17 compiler, OpenMP, and BLAS/LAPACK. Conda installs the numerical libraries and Python packages listed in environment.yml; install a compiler separately if one is unavailable on your system.

On macOS, a compiler with OpenMP support is needed. The Linux direct G×E backend is unavailable there.

Standard installation

git clone https://github.com/sriramlab/SUMMIT.git
cd SUMMIT
conda env create -f environment.yml
conda activate summit
python -m pip install .

Verify the commands:

summit --help
summit pgs --help
summit reference --help

The distribution is currently named gwldcore; its Python package and main command are named summit. A normal install compiles the native modules.

Generalized G×E reference estimation

The generalized reference executor currently requires a Linux build linked to pthread BLIS. The standard OpenBLAS installation supports the other analysis paths, but does not satisfy this executor's build check.

For a site-specific BLIS build, configure GXELDCORE_USE_PRIVATE_BLIS and the archive/include locations in CMakeLists.txt. The accompanying source metadata is supplied by the person building that library. This setup is needed only for the direct generalized reference executor; it is not an extra input to an analysis.

Development installation

From an activated environment:

python -m pip install --no-build-isolation -e .

Reinstall after changing native code or console entry points, using the same native build configuration. python -m summit also runs the command-line interface.

See Troubleshooting for compiler and library errors.