Proteus: Computational Methods and Simulation Toolkit

Proteus (http://proteustoolkit.org) is a Python package for rapidly developing computer models and numerical methods.

Installation

mamba install proteus -c conda-forge

For a development installation, you want to install Proteus's dependencies and compile Proteus from source:

mamba env create -f environment-dev.yml #environment-dev-up.yml to try unpinned dependencies
mamba activate proteus-dev
pip install -v -e .

HPC Installation

For installation on high performance environments you may want to install Proteus's dependencies from source as well. We recommend using the PETSc build system to install most of the dependencies. The following is general outline:

Create a basic python environment you can install into:

mamba env create -f petsc-dev.yml
mamba activate petsc-dev

or

python -m venv petsc-dev
pip install setuptools make cmake cython swig pybind11 numpy

Next, build petsc from source

bash scripts/petsc_config_linux_conda_seq.sh #see https://petsc.org/release/install/

Next, build additional C++ dependencies and install into environment prefix (e.g $CONDA_PREFIX or $VIRTUAL_ENV)

https://github.com/projectchrono/chrono #>=9.0.1, with python bindings https://github.com/scorec/core #>=2.2.8, shared, python bindinds not needed https://github.com/xtensor-stack/xtl https://github.com/xtensor-stack/xtensor https://github.com/xtensor-stack/xtensor-python

Finally, locally build and install remaining python dependencies into environment

CC=mpicc CXX=mpicxx MPI_DIR=$MPI_ROOT pip install -v mpi4py==3.1.6 --no-build-isolation --no-binary=:all:
PETSC_DIR=$CONDA_PREFIX PETSC_ARCH="" pip install -v ../petsc/src/binding/petsc4py --no-build-isolation --no-binary=:all:
HDF5_MPI=ON HDF5_DIR=${CONDA_PREFIX} CC=mpicc CXX=mpicxx pip install -v h5py --no-build-isolation --no-binary=:all: #note h5py depends on mpi4py for this config
CC=mpicc CXX=mpicxx pip install -v . --no-build-isolation --no-binary=:all:

Some optional packages can be installed with pip/mamba: py2gmsh, memory_profiler, scipy, pytest.

See https://github.com/erdc/proteus/wiki/How-to-Build-Proteus for old information on building the entire stack.

Developer Information

The source code, wiki, and issue tracker are on GitHub at

https://github.com/erdc/proteus.