NA-MIC Project Weeks

Slicer FEniCS Installation

The following instructions assume that the FEniCS C++ components have been installed in ${MY_FENICS_DIR}. For FEniCS installation instructions see:

Variables

Set paths to Slicer and FEniCS

MY_SLICER_DIR=/opt/slicer/Slicer-4.11.0-2019-06-24-linux-amd64/
MY_FENICS_SRC=~/projects/fenics/fenics-2019.1.0/
MY_FENICS_DIR=/opt/fenics/fenics-2019.1.0/

Set Python dependency versions

MPI4PY_VERSION="==3.0.1"
PETSC4PY_VERSION="==3.11.0"
SLEPC4PY_VERSION="==3.11.0"

Install Python header files

Use this to check your Slicer Python version

${MY_SLICER_DIR}/bin/PythonSlicer --version

Download and install Python header files

wget -P ${MY_SLICER_DIR}/lib/Python/include/python3.6m/ https://github.com/python/cpython/archive/v3.6.7.tar.gz
cd ${MY_SLICER_DIR}/lib/Python/include/python3.6m/
tar --strip-components=2 -zxf v3.6.7.tar.gz cpython-3.6.7/Include

Install FEniCS in Slicer

Set DOLFIN environment variables

source ${MY_FENICS_DIR}/share/dolfin/dolfin.conf

Install Python dependencies

${MY_SLICER_DIR}/bin/PythonSlicer -m pip install mpi4py${MPI4PY_VERSION}
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install petsc4py${PETSC4PY_VERSION}
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install slepc4py${SLEPC4PY_VERSION}

Install FEniCS Python components from source

${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/fiat
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/dijitso
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/ufl
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/ffc
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/dolfin/python
${MY_SLICER_DIR}/bin/PythonSlicer -m pip install ${MY_FENICS_SRC}/mshr/python

Run Slicer

source ${MY_FENICS_DIR}/share/dolfin/dolfin.conf
${MY_SLICER_DIR}/Slicer