A detailed guide to installing DOLFIN

From The FEniCS project

This aims to be a more complete, fully from source, guide to installing DOLFIN and its dependencies.

It is designed for slightly older GNU/Linux systems, where even the presence of a recent Python, for instance, is not guaranteed. It has been tested on RedHat Enterprise Linux 4 and Ubuntu 8.04. You can also fetch this information in a more ready-to-use manner in the form of a bash script, from [1].

Note that the following list exceeds the minimum number of packages needed to compile DOLFIN. SyFi (and its dependencies GiNaC and CLN) are not part of DOLFIN at all, while PETSc, SLEPc, gts, and SuiteSparse are optional dependencies for DOLFIN. Swig is only needed when the Python interface for DOLFIN is enabled. FErari is also optional.

Requirements

libtool, libxml2, pkg-config, LAPACK, BLAS and a C++ compiler. These should already be included in any standard Linux distribution.

Basic notes

The build instructions on this page incorporate the use of the following environment variables:

# modify the following to fit your needs...

# Where do you want the downloaded source files to go?
export DOWNLOAD_PATH=$HOME/download/src
# Where do you want the downloaded FENICS files to go?
export FENICS_PATH=$HOME/fenics
# Where do you want the compiled software installed?
export INSTALL_PATH=$HOME/build
# Where are your LAPACK and BLAS libraries?
export LAPACKANDBLAS=/usr/lib/atlas
# Where is BOOST installed?
export BOOST_DIR=$INSTALL_PATH/include/BOOST_install
# Where is UMFPACK?
export UMFPACK_DIR=/usr/include/suitesparse

# What sort of PETSc build do you need?
export PETSC_ARCH=linux-gnu-cxx-opt
# Where is PETSc?
export PETSC_DIR=$DOWNLOAD_PATH/petsc-3.0.0-p8

# What sort of SLEPc build do you need?
export SLEPC_ARCH=linux-gnu-cxx-opt
# Where is SLEPc?
export SLEPC_DIR=$DOWNLOAD_PATH/slepc-3.0.0-p6

# Other interesting environment variables (some of this may change for you)
export PYTHON=$INSTALL_PATH/bin
export PATH=$VTK_DIR/bin:$INSTALL_PATH/share/swig:$HOME/bin:$INSTALL_PATH/bin:$PATH
export LD_LIBRARY_PATH=$BOOST_DIR/lib:$INSTALL_PATH/lib:$INSTALL_PATH/lib/vtk-5.5:$LD_LIBRARY_PATH
export PYTHONPATH=$HOME/lib/python:$INSTALL_PATH/lib/python2.6/site-packages
export DOLF=$FENICS_PATH/dolfin
export PKG_CONFIG_PATH=$DOLF/scons/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/share/pkgconfig:$INSTALL_PATH/lib/pkgconfig:$PKG_CONFIG_PATH

# some others...
export VTK_DATA_ROOT=$DOWNLOAD_PATH/VTKData
export MANPATH=$HOME/share/man:$INSTALL_PATH/man:$INSTALL_PATH/share/man:$MANPATH

You also need to create the following directories

mkdir -p $FENICS_PATH
mkdir -p $INSTALL_PATH

Building the dependencies

Note that older versions of Boost might not work. In the case of RedHat 4, you need to uninstall it using

rpm -e boost

Building Python 2.6

cd $DOWNLOAD_PATH
# you need at least version 2.6.2
# Note: make sure to get everything: the libraries, executables, etc...
#       the binaries are NOT enough!
wget http://python.org/ftp/python/2.6.2/Python-2.6.2.tar.bz2
tar -xjf Python-2.6.2.tar.bz2
cd Python-2.6.2
./configure --prefix=$INSTALL_PATH
make
make install

Building Nose Testing 0.11 for Python

cd $DOWNLOAD_PATH
# you need at least version 0.11
wget http://somethingaboutorange.com/mrl/projects/nose/nose-0.11.1.tar.gz
tar -xzf nose-0.11.1.tar.gz
cd nose-0.11.1
python setup.py install --prefix=$INSTALL_PATH

Building Mercurial 1.3

cd $DOWNLOAD_PATH
wget http://www.selenic.com/mercurial/release/mercurial-1.3.tar.gz
tar -xzf mercurial-1.3.tar.gz
cd mercurial-1.3

# now build it
make install-home

# you can test it by running
hg debuginstall

Building SCons 1.2.0

cd $DOWNLOAD_PATH
wget http://internap.dl.sourceforge.net/sourceforge/scons/scons-1.2.0.tar.gz
tar -xzf scons-1.2.0.tar.gz
cd scons-1.2.0
python setup.py install --prefix=$INSTALL_PATH

Building NumPy 1.3.0

# make sure `LAPACKANDBLAS' is set properly

cd $DOWNLOAD_PATH
# Make sure to get the most recent version
wget http://internap.dl.sourceforge.net/sourceforge/numpy/numpy-1.3.0.tar.gz
tar -xzf numpy-1.3.0.tar.gz
cd numpy-1.3.0
echo "[atlas]" > site.cfg
echo "library_dirs = $LAPACKANDBLAS" >> site.cfg
echo "atlas_libs = lapack, blas" >> site.cfg
python setup.py install --prefix=$INSTALL_PATH

# can test it with
python -c 'import numpy; numpy.test()'

Building Boost 1.39.0

cd $DOWNLOAD_PATH
# you MUST have at least version 1.33.0
wget http://internap.dl.sourceforge.net/sourceforge/boost/boost_1_39_0.tar.bz2
tar -xjf boost_1_39_0.tar.bz2
cd boost_1_39_0

# there is some minor compiling
# you can run `./bootstrap.sh --help' to see the options

# anyway, configure with the `program_options' and `filesystem' libraries
./bootstrap.sh --with-libraries=program_options,filesystem --prefix=$BOOST_DIR --libdir=$BOOST_DIR/lib
# then compile and install (may take a few minutes)
./bjam --layout=system install

Building Swig 1.3.39

cd $DOWNLOAD_PATH
# you MUST have the most recent version (at least 1.3.36)!  Required for `instant' to work properly.
wget http://voxel.dl.sourceforge.net/sourceforge/swig/swig-1.3.39.tar.gz
tar -xzf swig-1.3.39.tar.gz
cd swig-1.3.39
./configure --prefix=$INSTALL_PATH
make
make install

make check-python-examples
make check-python-test-suite

Building Open MPI 1.3.3

cd $DOWNLOAD_PATH
# Make sure to get the most recent version
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.3.tar.bz2
tar -xjf openmpi-1.3.3.tar.bz2
cd openmpi-1.3.3

# NOTE: if you are installing a new version, make sure to clean and
#       fully uninstall the previous version!

# configuring takes about 5~8 minutes
./configure --prefix=$INSTALL_PATH
# making takes about 10~12 minutes
make all
# installing takes about 3 minutes
make install

# can run the following to check the installation
ompi_info

Building PETSc 3.0.0-p8

cd $DOWNLOAD_PATH
# Make sure to get the most recent version
wget ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.0.0-p8.tar.gz
tar -xzf petsc-3.0.0-p8.tar.gz
cd petsc-3.0.0-p8
export PETSC_DIR=$PWD
# configuring will take about 15 mins
# ./config/configure.py --with-mpi-dir=$INSTALL_PATH --with-clanguage=c++ --download-hypre=1 --with-hypre=1 --with-shared=1
./config/configure.py --with-mpi-dir=$INSTALL_PATH --with-umfpack=1 --download-umfpack=1 --with-clanguage=c++ --with-shared=1

# making will take about 30~40 mins
make all

make test

Building SLEPc 3.0.0-p6

cd $DOWNLOAD_PATH
# Make sure to get the most recent version
wget http://www.grycap.upv.es/slepc/download/distrib/slepc-3.0.0-p6.tgz
tar -xzf slepc-3.0.0-p6.tgz
cd slepc-3.0.0-p6
export SLEPC_DIR=$PWD
./config/configure.py
# making will take about 5~10 mins
make all

make test

Building gts 0.7.6

cd $DOWNLOAD_PATH
# Make sure to get the most recent version
wget http://internap.dl.sourceforge.net/sourceforge/gts/gts-0.7.6.tar.gz
tar -xzf gts-0.7.6.tar.gz
cd gts-0.7.6
./configure --prefix=$INSTALL_PATH
make
make install

Building CLN 1.2.2

cd $DOWNLOAD_PATH
wget http://www.ginac.de/CLN/cln-1.2.2.tar.bz2
tar -xjf cln-1.2.2.tar.bz2
cd cln-1.2.2
./configure --prefix=$INSTALL_PATH
make
make install

Building GiNaC 1.5.2

cd $DOWNLOAD_PATH
wget http://www.ginac.de/ginac-1.5.2.tar.bz2
tar -xjf ginac-1.5.2.tar.bz2
cd ginac-1.5.2
./configure --prefix=$INSTALL_PATH
make
make install

Building SuiteSparse 3.4 (with metis 4.0)

cd $DOWNLOAD_PATH
wget http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-3.4.0.tar.gz
tar -xzf SuiteSparse-3.4.0.tar.gz
cd SuiteSparse
export UMFPACK_DIR=$PWD
wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-4.0.tar.gz
tar -xzf metis-4.0.tar.gz
cd metis-4.0
make
cd ..
make

Building VTK+ 5.x

First, get the latest version of `Cmake' and make sure it is in the path. Personally, I just got the binary files and copied them directly into my "$INSTALL_PATH" directory.

Next, get the VTK source files. If you have CVS on your LINUX system, then you can do the following. Make sure to run these commands inside your "$DOWNLOAD_PATH" directory:

# Anonymous User Read-Only Access

# You can obtain read-only access to the CVS repository as follows.
cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTK login
#(respond with password vtk)

# Follow the above command by checking out the source code:
cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTK checkout VTK
# this will take about 5+ minutes

This CVS tree is VTK 5.x. Execute the CVS checkout in a clean directory. It will create a VTK directory, overwriting any existing VTK tree. CMake is required for building.

For testing purposes you might wish to checkout the CVS VTKData:

cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTKData login
#(respond with password vtk)

# Follow the above command by checking out the data:
cvs -d :pserver:anonymous@public.kitware.com:/cvsroot/VTKData checkout VTKData
# this will take about 1 minute

Next, we need to generate a temporary build directory. Also see the README.html page that is in the VTK+ sub-directory. Create a sub-directory of "$DOWNLOAD_PATH" that looks like:

$DOWNLOAD_PATH/VTK-build

Change into that directory. And run:

ccmake $DOWNLOAD_PATH/VTK
# make sure ccmake is in your directory path (i.e. the PATH environment variable)

You will then have a console where you can configure stuff. For example, you could set:

BUILD_EXAMPLES                   ON
BUILD_SHARED_LIBS                ON
BUILD_TESTING                    ON
CMAKE_BACKWARDS_COMPATIBILITY    2.4
CMAKE_BUILD_TYPE                 
CMAKE_INSTALL_PREFIX             `$INSTALL_PATH'      <--- replace $INSTALL_PATH by the actual path!!!
DESIRED_QT_VERSION               0
VTK_DATA_ROOT                    `$HOME'/src/VTKData  <--- replace $HOME by the actual path!!!
VTK_LARGE_DATA_ROOT              VTK_LARGE_DATA_ROOT-NOTFOUND
VTK_USE_GEOVIS                   ON
VTK_USE_INFOVIS                  ON
VTK_USE_N_WAY_ARRAYS             ON
VTK_USE_PARALLEL                 ON
VTK_USE_QT                       OFF
VTK_USE_RENDERING                ON
VTK_USE_TEXT_ANALYSIS            OFF
VTK_USE_VIEWS                    ON
VTK_WRAP_JAVA                    OFF
VTK_WRAP_PYTHON                  ON
VTK_WRAP_TCL                     ON

Once that is set, press `c' to configure. Then press `g' to generate. This will put you back at the prompt in the `VTK-build' sub-directory. Next, compile by running:

make
# wait 1+ hour
# Then run
make install

Building portions of the FEniCS project

Building FIAT

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/fiat
cd fiat
python setup.py install --prefix=$INSTALL_PATH

Building FErari

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/ferari
cd ferari
python setup.py install --prefix=$INSTALL_PATH

Building UFC

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/ufc
cd ufc
# must be built with SCons
scons
# now install it
scons install prefix=$INSTALL_PATH

Building UFL

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/ufl
cd ufl
python setup.py install --prefix=$INSTALL_PATH

Building FFC

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/ffc
cd ffc
python setup.py install --prefix=$INSTALL_PATH

Building SyFi

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/syfi
cd syfi/
./configure --prefix=$INSTALL_PATH
make all
make install

Building Viper

# requires VTK
cd $FENICS_PATH
hg clone http://www.fenics.org/hg/viper
cd viper
python setup.py install --prefix=$INSTALL_PATH

Building Instant

cd $FENICS_PATH
# Make sure you have the most recent version of SWIG installed
hg clone http://www.fenics.org/hg/instant
cd instant
python setup.py install --prefix=$INSTALL_PATH

Building DOLFIN

cd $FENICS_PATH
hg clone http://www.fenics.org/hg/dolfin
cd dolfin
# configure
scons configure prefix=$INSTALL_PATH withBoostDir=$BOOST_DIR withUmfpackDir=$UMFPACK_DIR withPetscDir=$PETSC_DIR withSlepcDir=$SLEPC_DIR enableDemos=yes enableScotch=no enableTrilinos=no enableMpi=no enablePetsc=yes enableSlepc=yes enableUmfpack=yes enableParmetis=no enableMtl4=no enableDebug=yes enablePython=yes
# compile
scons
# then install
scons install