FEniCS

From Alliance Doc
Revision as of 17:36, 22 October 2019 by Cwant (talk | contribs) (Update script and installation instructions)
Jump to navigation Jump to search
Other languages:

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

FEniCS can be built with various extensions, so we do not offer a single, global installation. Please choose between

  • Installation in a virtual environment
  • Using a Singularity container

Installation in a virtual environment

These are instructions for installing FEniCS version 2017.2.0.

You can run the script below by copying it to the cluster you are using and running bash fenics-install.sh.

Note that the installation will warn you that the installation will create (or replace) an installation directory, and will give usage instructions when it has successfully completed the installation. The script can be modified to change the installation directory if needed.


File : fenics-install.sh

#!/bin/bash

set -e

FENICS_INSTALL=${HOME}/fenics
FENICS_VERSION=2017.2.0
PYBIND11_VERSION=2.2.3
MODULES="hdf5-mpi/1.8.18\
 boost\
 eigen\
 python/3.5\
 scipy-stack/2017b\
 petsc/3.7.5\
 fftw-mpi/3.3.6\
 ipp/9.0.4\
 gcc/5.4.0"

module load $MODULES

main () {
    warning_install
    make_fenics_directory
    download_py_packages $FENICS_VERSION
    make_py_packages
    make_pybind11
    make_dolfin
    print_instructions
}

warning_install () {
    echo "---------------------------------------------------------------"
    echo "WARNING: THE FENICS/DOLFIN INSTALL WILL WIPE OUT THIS DIRECTORY"
    echo "     $FENICS_INSTALL "
    echo
    echo "IF YOU DON'T WANT THIS TO HAPPEN, PRESS CTRL-C TO ABORT"
    echo "PRESS ANY KEY TO CONTINUE"
    echo "---------------------------------------------------------------"
    read -n 1
}

print_instructions () {
    echo "---------------------------------------------------------------"
    echo "TO USE FENICS/DOLFIN, YOU NEED TO DO:"
    echo
    echo "module load $MODULES"
    echo "source $FENICS_INSTALL/bin/activate"
    echo "source $FENICS_INSTALL/share/dolfin/dolfin.conf"
    echo "---------------------------------------------------------------"
}

make_fenics_directory () {
    rm -rf $FENICS_INSTALL
    mkdir -p $FENICS_INSTALL && cd $FENICS_INSTALL
}

download_py_packages () {
    version=$1
    cd $FENICS_INSTALL
    git clone --branch=$version https://bitbucket.org/fenics-project/fiat.git
    git clone --branch=$version https://bitbucket.org/fenics-project/instant.git
    git clone --branch=$version https://bitbucket.org/fenics-project/dijitso.git
    git clone --branch=$version https://bitbucket.org/fenics-project/ufl.git
    git clone --branch=$version https://bitbucket.org/fenics-project/ffc.git
    git clone --branch=$version https://bitbucket.org/fenics-project/dolfin.git
    git clone --branch=$version https://bitbucket.org/fenics-project/mshr.git
    git clone --branch=v$PYBIND11_VERSION \
	https://github.com/pybind/pybind11.git
 
    chmod u+w ~/fenics/*/.git/objects/pack/*

    mkdir -p $FENICS_INSTALL/pybind11/build
    mkdir -p $FENICS_INSTALL/dolfin/build
    mkdir -p $FENICS_INSTALL/mshr/build
}

make_pybind11 () {
    cd $FENICS_INSTALL/pybind11/build

    source $FENICS_INSTALL/bin/activate

    cmake -DPYBIND11_TEST=off \
	  -DCMAKE_INSTALL_PREFIX=$HOME/fenics \
	  -DPYBIND11_CPP_STANDARD=-std=c++11 ..
    nice make -j8 install
}

make_py_packages () {
    cd $FENICS_INSTALL
    virtualenv --no-download $FENICS_INSTALL
    source $FENICS_INSTALL/bin/activate
    pip3 install ply
    pip3 install numpy
    cd $FENICS_INSTALL/fiat    && pip3 install .
    cd $FENICS_INSTALL/instant && pip3 install .
    cd $FENICS_INSTALL/dijitso && pip3 install .
    cd $FENICS_INSTALL/ufl     && pip3 install .
    cd $FENICS_INSTALL/ffc     && pip3 install .
}

make_dolfin () {
    cd $FENICS_INSTALL/dolfin/build

    source $FENICS_INSTALL/bin/activate

    cmake .. -DDOLFIN_SKIP_BUILD_TESTS=true \
	  -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include \
	  -DCMAKE_INSTALL_PREFIX=$HOME/fenics \
	  -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=$EBROOTNIXPKGS/lib/libz.so \
	  -DLIB_ifcore_pic=$EBROOTIFORT/lib/intel64/libifcore.so \
	  -DLIB_ipgo=$EBROOTIPP/lib/intel64/libipgo.a \
	  -DLIB_decimal=$EBROOTIPP/lib/intel64/libdecimal.a \
	  -DLIB_irc_s=$EBROOTIPP/lib/intel64/libirc_s.a

    nice make -j 8 install
    cd $FENICS_INSTALL/dolfin/python && pip3 install .
}

main



FEniCS add-ons

First install FEniCS following instructions above.

mshr

File : mshr_install.sh

module load hdf5-mpi/1.8.18 boost eigen python/3.5 scipy-stack/2017b 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=$HOME/software/mshr   -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=ON -DCMAKE_PREFIX_PATH=$NIXUSER_PROFILE:$CMAKE_PREFIX_PATH -DEIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include 

make
make install


Then run


File : fenics_mshr_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
export PYTHONPATH=$HOME/software/mshr/lib/python3.5/site-packages:$PYTHONPATH
export LD_LIBRARY_PATH=$HOME/software/mshr/lib:$LD_LIBRARY_PATH


Using a Singularity container

The following Singularity Recipe will download the FEniCS Docker image, install it, and download additional packages, e.g., various Python packages. This recipe must be run on your own machine, that is, a Linux machine with Singularity installed where you have root access.

To build your FEniCS image using this recipe, run the following command: 

 sudo singularity build FEniCS.simg FEniCS-ComputeCanada-Singularity-Recipe

and then upload FEniCS.simg to your account. The FEniCS Docker image places a number of files in /home/fenics.


File : FEniCS-ComputeCanada-Singularity-Recipe

Bootstrap: docker
From: quay.io/fenicsproject/stable:latest

%post
  sudo apt-get -qq update
  sudo apt-get -y upgrade
  sudo apt-get -y install python-bitstring python3-bitstring
  sudo apt-get -y install python-certifi python3-certifi
  sudo apt-get -y install python-cryptography python3-cryptography
  sudo apt-get -y install python-cycler python3-cycler
  sudo apt-get -y install cython cython3
  sudo apt-get -y install python-dateutil python3-dateutil
  sudo apt-get -y install python-deap python3-deap
  sudo apt-get -y install python-decorator python3-decorator
  sudo apt-get -y install python-ecdsa python3-ecdsa
  sudo apt-get -y install python-ecdsa python3-ecdsa
  sudo apt-get -y install python-enum34
  sudo apt-get -y install python-funcsigs python3-funcsigs
  sudo apt-get -y install ipython ipython3 python-ipython-genutils python3-ipython-genutils
  sudo apt-get -y install python-jinja2 python3-jinja2
  sudo apt-get -y install python-jsonschema python3-jsonschema
  sudo apt-get -y install python-lockfile python3-lockfile
  sudo apt-get -y install python-markupsafe python3-markupsafe
  sudo apt-get -y install python-matplotlib python3-matplotlib
  sudo apt-get -y install python-mistune python3-mistune
  sudo apt-get -y install python-mock python3-mock
  sudo apt-get -y install python-mpmath python3-mpmath
  sudo apt-get -y install python-netaddr python3-netaddr
  sudo apt-get -y install python-netifaces python3-netifaces
  sudo apt-get -y install python-nose python3-nose
  sudo apt-get -y install ipython-notebook ipython3-notebook
  sudo apt-get -y install python-numpy python3-numpy
  sudo apt-get -y install python-pandas python3-pandas
  sudo apt-get -y install python-paramiko python3-paramiko
  sudo apt-get -y install python-path python3-path
  sudo apt-get -y install python-pathlib
  sudo apt-get -y install python-pbr python3-pbr
  sudo apt-get -y install python-pexpect python3-pexpect
  sudo apt-get -y install python-pickleshare python3-pickleshare
  sudo apt-get -y install python-prompt-toolkit python3-prompt-toolkit
  sudo apt-get -y install python-ptyprocess python3-ptyprocess
  sudo apt-get -y install python-pycryptopp
  sudo apt-get -y install python-pygments python3-pygments
  sudo apt-get -y install python-pyparsing python3-pyparsing
  sudo apt-get -y install python-zmq python3-zmq
  sudo apt-get -y install python-requests python3-requests
  sudo apt-get -y install python-scipy python3-scipy
  sudo apt-get -y install python-setuptools python3-setuptools
  sudo apt-get -y install python-simplegeneric python3-simplegeneric
  sudo apt-get -y install python-singledispatch python3-singledispatch
  sudo apt-get -y install python-six python3-six
  sudo apt-get -y install python-sympy python3-sympy
  sudo apt-get -y install python-terminado python3-terminado
  sudo apt-get -y install python-tornado python3-tornado
  sudo apt-get -y install python-traitlets python3-traitlets
  sudo apt-get -y install automake git-core libopenmpi-dev libtool mercurial openmpi-bin 
  sudo apt-get -y install python3-pip python3-venv

  # Clean up downloaded and temporary files...
  sudo apt-get clean
  sudo rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*


Retrieved from "https://docs.alliancecan.ca/mediawiki/index.php?title=FEniCS&oldid=77462"