MSMs at Scale
If you use enspara for published research, please cite us:
Porter, J.R., Zimmerman, M.I. and Bowman, G.R., 2019. Enspara: Modeling molecular ensembles with scalable data structures and parallel computing. The Journal of chemical physics, 150(4), p.044108.
Installation is documented here.
Current installation instructions are (using mamba):
git clone https://github.com/bowman-lab/enspara
cd enspara
mamba env create -f environment.yaml
mamba activate enspara
pip install -e .
Alternatively, you can install packages directly:
git clone https://github.com/bowman-lab/enspara
mamba create -n enspara -c conda-forge cython numpy mdtraj scipy python=3.12 mpi4py
mamba activate enspara
cd enspara
pip install -e .
Optionally, install pytests to run the tests:
mamba install -c conda-forge pytest
Enspara uses sphinx for documentation. They're a bit of a work in progress, but most of the most important stuff is documented already.
cd docs
make htmlEnspara uses pytest as a test discovery and running tool. To run the
tests, you should first make sure you have the development dependencies
installed then, from the enspara directory, run:
pytestBy default this runs without MPI.
If you wish to explicitly skip the MPI tests, you can run:
pytest -m 'not mpi'If you want to run the MPI tests, you can run:
mpirun -n 2 python -m pytest -m 'mpi' --with-mpi