FEniCS

Installing FEniCS

The following

Step 0 (Optional): Clean out your environment

Before installing FEniCS, you might want to remove previous installations of petsc4py/FEniCS, in order to prevent conflicts when installing.

• Remove directories that contain previous installations of petsc4py/fenics. Directories can be removed by typing rm -rf directory_name.

• Previous installations of petsc4py/FEniCs might have data in hidden directories. Hidden directories can be seen by typing ls -a. Spend some time looking through hidden directories and remove anything associated with previous petsc4py/FEniCS installations.

• Check the environment variables (they can be listed with the penv command) and remove anything that points to previous installations of petsc4py/FEniCS.

Step 1 (Optional): Install petsc4py

Installing petsc4py is not required if you just want to use standalone FEniCS. However, petsc4py is needed in order to directly interface with PETSc, if that is something you wish to do.

To install petsc4py on Graham, first go to your home directory by typing cd $HOME. Then, run the following script:

module purge
module load hdf5-mpi/1.8.18 boost eigen python/3.5 scipy-stack/2017b petsc/3.8.2 fftw-mpi/3.3.6 mpi4py

git clone https://bitbucket.org/petsc/petsc4py.git
cd petsc4py
git fetch && git checkout maint-3.8

python setup.py build
python setup.py install --user

export PYTHONPATH=$HOME/.local/lib/python3.5/site-packages:$PYTHONPATH

When the script completes, petsc4py should be installed. The contents of the script are based on the official petsc4py installation instructions (https://www.mcs.anl.gov/petsc/petsc4py-current/docs/usrman/install.html), so consider looking there if something goes wrong.