FEniCS

FEniCS is a popular open-source computing platform for solving partial differential equations (PDEs).

Installation instructions

These are instructions for installing FEniCS version 2.0.

File : fenics_install.sh

module load hdf5-mpi/1.8.18 boost eigen python/3.5 scipy-stack/2017b petsc/3.7.5 fftw-mpi/3.3.6

mkdir fenics && cd fenics
git clone https://bitbucket.org/fenics-project/fiat.git
git clone https://bitbucket.org/fenics-project/instant.git
git clone https://bitbucket.org/fenics-project/dijitso.git
git clone https://bitbucket.org/fenics-project/ufl.git
git clone https://bitbucket.org/fenics-project/ffc.git
wget https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-2017.2.0.tar.gz
tar xvfz dolfin-2017.2.0.tar.gz
mv dolfin-2017.2.0 dolfin
chmod u+w ~/fenics/*/.git/objects/pack/*

pyvenv ~/fenics
source ~/fenics/bin/activate
cd fiat    && pip3 install . && cd -
cd instant && pip3 install . && cd -
cd dijitso && pip3 install . && cd -
cd ufl     && pip3 install . && cd -
cd ffc     && pip3 install . && cd -
pip3 install ply
cd dolfin
mkdir build && cd build

cmake .. -DDOLFIN_SKIP_BUILD_TESTS=true -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include  -DCMAKE_INSTALL_PREFIX=$HOME/software/dolfin -DCMAKE_SKIP_RPATH=ON -DRT_LIBRARY=$EBROOTNIXPKGS/lib64/librt.so -DHDF5_C_LIBRARY_dl=$EBROOTNIXPKGS/lib64/libdl.so -DHDF5_C_LIBRARY_m=$EBROOTNIXPKGS/lib64/libm.so -DHDF5_C_LIBRARY_pthread=$EBROOTNIXPKGS/lib64/libpthread.so -DHDF5_C_LIBRARY_z=$EBROOTNIXPKGS/lib/libz.so

nice make -j 8 install && cd -
sed -i s'^export LD_LIBRARY_PATH=/lib^#export LD_LIBRARY_PATH=/lib^' ~/software/dolfin/share/dolfin/dolfin.conf

To run the installed program, perform the following operations to set up your environment:

File : fenics_run.sh

module load hdf5-mpi/1.8.18 boost eigen python/3.5 scipy-stack/2017b petsc/3.7.5 fftw-mpi/3.3.6
source ~/software/dolfin/share/dolfin/dolfin.conf
source ~/fenics/bin/activate

FEniCS add-ons

First install FEniCS following instructions above.

mshr

File : mshr_install.sh

module load hdf5-mpi/1.8.18 boost eigen python/3 python35-scipy-stack/2017a petsc/3.7.5 fftw-mpi/3.3.6

export CMAKE_PREFIX_PATH=/home/$USER/software/dolfin/share/dolfin/cmake/:$CMAKE_PREFIX_PATH

git clone https://bitbucket.org/fenics-project/mshr.git
cd mshr
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/software/mshr   -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=ON
make
make install

Then run

File : fenics_mshr_run.sh

module load hdf5-mpi/1.8.18 boost eigen python/3 python35-scipy-stack/2017a petsc/3.7.5 fftw-mpi/3.3.6
source ~/software/dolfin/share/dolfin/dolfin.conf
source ~/fenics/bin/activate
export PYTHONPATH=$HOME/software/mshr/lib/python3.5/site-packages:$PYTHONPATH
export LD_LIBRARY_PATH=$HOME/software/mshr/lib:$LD_LIBRARY_PATH