Installation

The package is partly written in C++ and relies on dolfinx. Users are encouraged to install scifem with pip in an environment where dolfinx is already installed or with conda.

pip

To install the package with pip run

python3 -m pip install scifem --no-build-isolation

To install the development version you can run

python3 -m pip install --no-build-isolation git+https://github.com/scientificcomputing/scifem.git

Note that you should pass the flag --no-build-isolation to pip to avoid issues with the build environment, such as incompatible versions of nanobind.

spack

The spack package manager is the recommended way to install scifem, and especially on HPC systems. For information about the package see: spack-package: py-scifem First, clone the spack repository and enable spack

git clone --depth=2 https://github.com/spack/spack.git
# For bash/zsh/sh
. spack/share/spack/setup-env.sh

# For tcsh/csh
source spack/share/spack/setup-env.csh

# For fish
. spack/share/spack/setup-env.fish

Next create an environment:

spack env create scifem_env
spack env activate scifem_env

Find the compilers on the system

spack compiler find

and install the relevant packages

spack add py-scifem+petsc+hdf5+biomed+adios2 ^mpich ^petsc+mumps+hypre ^py-fenics-dolfinx+petsc4py
spack concretize
spack install

Finally, note that spack needs some packages already installed on your system. On a clean ubuntu container for example one needs to install the following packages before running spack

apt update && apt install gcc unzip git python3-dev g++ gfortran xz-utils -y

conda

To install the package with conda run

conda install -c conda-forge scifem