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INSTALL.md

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Installation

Dependencies

SOUPy depends on FEniCS version 2019.1. and hIPPYlib version 3.0.0 or above.

FEniCS needs to be built with the following dependencies enabled:

  • numpy, scipy, matplotlib, mpi4py
  • PETSc and petsc4py (version 3.10.0 or above)
  • SLEPc and slepc4py (version 3.10.0 or above)
  • PETSc dependencies: parmetis, scotch, suitesparse, superlu_dist, ml, hypre
  • (optional): gmsh, mshr, jupyter

Recommended installation using Anaconda

Installation with pip

  1. Create an environment with FEniCS and appropriate dependencies and activate environment

For x86 users:

conda create -n soupy -c conda-forge python=3.11 fenics==2019.1.0 petsc4py==3.19 matplotlib scipy jupyter
conda activate soupy

For ARM users: FEniCS is only available on x86 systems. When running on an ARM based mac with the ARM version of conda installed, add CONDA_SUBDIR=osx-64 before the conda call,

CONDA_SUBDIR=osx-64 conda create -n soupy -c conda-forge python=3.11 fenics==2019.1.0 petsc4py==3.19 matplotlib scipy jupyter

Then configure the environment to be an osx-64 environment

conda activate soupy
conda config --env --set subdir osx-64
  1. Install hIPPYlib via pip
pip install hippylib
  1. Install SOUPy via pip
pip install soupy@git+https://github.com/hippylib/soupy
  1. Clone the SOUPy directory to access examples
git clone https://github.com/hippylib/soupy.git

Examples in the applications directory can now be run.

cd soupy/examples/poisson

Then run in serial

python driver_poisson_mean.py

or with MPI (e.g. using 4 processes)

mpirun -n 4 python driver_poisson_mean.py

We refer to the full FEniCS installation instructions from hIPPYlib for more detail.

Installation for developers

  1. Create an environment with FEniCS with appropriate dependencies (add CONDA_SUBDIR=osx-64 if using ARM conda, see above)
conda create -n soupy -c conda-forge python=3.11 fenics==2019.1.0 petsc4py==3.19 matplotlib scipy jupyter
  1. Clone the hIPPYlib repository.
git clone https://github.com/hippylib/hippylib.git
  1. Clone the SOUPy repository
git clone https://github.com/hippylib/soupy.git
  1. Set the path to the hIPPYlib and SOUPy as environment variables, e.g.
conda activate soupy
conda env config vars set HIPPYLIB_PATH=path/to/hippylib
conda env config vars set SOUPY_PATH=path/to/soupy

Examples in the examples directory can now be run after deactivating and activating the environment again.

Installation with Docker

SOUPy (and hIPPYlib) can be used with a Docker image built with FEniCS/dolfin. The FEniCS documentation provides installation instructions for FEniCS's official images (note these are built on older versions of python). Alternatively, a customized docker image built on the FEniCS 2019.1.0 image with hIPPYlib pre-installed is available here

More recent builds of the docker images with FEniCS that are compatible with the [Frontera(https://frontera-portal.tacc.utexas.edu/) HPC system] at the Texas Advanced Computing Center can be found under the hippylib/tacc-containers repository. The repository also provides instructions for usage on Frontera using Apptainer. Here, we will summarize the procedure for using the image on local machines with Docker.

  1. Pull one the docker images
docker pull uvilla/fenics-2019.1-tacc-mvapich2.3-ib:latest
  1. Under the desired working directory, clone hIPPYlib and SOUPy
git clone https://github.com/hippylib/hippylib.git
git clone https://github.com/hippylib/soupy.git
  1. The images are built for the MPI implementations on TACC systems. When running locally, the environment variables MV2_SMP_USE_CMA=0 and MV2_ENABLE_AFFINITY=0 need to be set.
docker run -e MV2_SMP_USE_CMA=0 -e MV2_ENABLE_AFFINITY=0 -ti -v $(pwd):/home1/ uvilla/fenics-2019.1-tacc-mvapich2.3-ib:latest /bin/bash

This will run the container and bind the current working directory to /home1. The running container should now have /home1/hippylib and /home1/soupy.

  1. With the container running, first set the path to hippylib export HIPPYLIB_PATH=/home1/hippylib. The examples in the SOUPy repository can then be executed as
cd /home1/soupy/examples/poisson
python3 driver_poisson_mean.py

Note: benign MPI warning messages may show up when running on ARM machines.

Building the SOUPy documentation using Sphinx

Documentation for SOUPy can be built using sphinx, along with extensions myst_nb and sphinx_rtd_theme. These can be installed via pip.

To build simply run make html from doc folder.