enspara

MSMs at Scale

Reference

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

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

Building the docs

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 html

Running the tests

Enspara 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:

pytest

By 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