FEniCS: Difference between revisions
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(these instructions work for Fenics as it was in October 2017, so adding a git checkout to get a commit from that time. Also modifying modules somewhat) |
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module load hdf5-mpi/1.8.18 boost eigen python/3 | 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 | mkdir fenics && cd fenics | ||
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git clone https://bitbucket.org/fenics-project/ffc.git | git clone https://bitbucket.org/fenics-project/ffc.git | ||
git clone https://bitbucket.org/fenics-project/dolfin.git | git clone https://bitbucket.org/fenics-project/dolfin.git | ||
cd dolfin | |||
git checkout -b october2017 41bab805a945ecd | |||
cd .. | |||
chmod u+w ~/fenics/*/.git/objects/pack/* | chmod u+w ~/fenics/*/.git/objects/pack/* | ||
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|lang="sh" | |lang="sh" | ||
|contents= | |contents= | ||
module load hdf5-mpi/1.8.18 boost eigen python/3 | 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 ~/software/dolfin/share/dolfin/dolfin.conf | ||
source ~/fenics/bin/activate | source ~/fenics/bin/activate | ||
Revision as of 02:43, 8 March 2018
FEniCS is a popular open-source computing platform for solving partial differential equations (PDEs).
Installation instructions
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
git clone https://bitbucket.org/fenics-project/dolfin.git
cd dolfin
git checkout -b october2017 41bab805a945ecd
cd ..
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