homebrew-dealIIsuite

IMPORTANT NOTICE

This repository is no longer being maintained. 
The authors have switched to Spack https://github.com/LLNL/spack .

A collection of formulae needed to install deal.II on OS-X, as well as Linux desktop machines and clusters. For Linux users, provided below are instructions on how to install on:

• A. Ubuntu 14.04 (desktop version)
• B. Mac OS-X
• C. CentOS cluster

Caveats

You cannot have homebrew-science tapped at the same as this repository. Until this PR is merged, we have a conflict with homebrew-science. If you encounter any conflicts due to duplicate formulae, then please untap the problematic (other) repositories.

brew untap homebrew/science

There are several packages that cannot be installed on Linux at the moment. When these issues are solved then this README will be updated to include the most comprehensive set of build options for deal.II on Linux.

Known problem libraries include:

• freeimage does not build on Ubuntu, and therefore opencascade cannot be built.
• netcdf requires manual intervention to be built. To install it, you must use a along the lines of

LD_LIBRARY_PATH=~/.linuxbrew/Cellar/netcdf/4.3.3.1/lib brew install netcdf --with-fortran --with-cxx-compat

See here for a discussion.

A. Ubuntu 14.04 desktop version

Note that you can choose to use either the BLAS/LAPACK libraries that are provided by the system or install them through Linuxbrew with the openblas package.

For the full list of instructions as to how to install Linuxbrew, please see this link. The instructions given here are what we personally consider to be the least invasive.

For your convenience, the instructions that follow in the next few sections have been compiled into a script that can be extracted from the installation_scripts directory inside this repository or downloaded, made executable through the command

chmod +x <path_to_script>/install_Ubuntu.sh

and run to install deal.II with minimal intervention. However, you use this script at your own risk. It will ask for the administrator password once up front in order to install some essential build packages. Of course, you can modify the script to set any personal preferences that you may have with respect to the installed packages.

1. Install system packages

Firstly there are some mandatory packages that are required for the build process

# Essential build packages
sudo apt-get install build-essential curl git m4 ruby texinfo libbz2-dev libcurl4-openssl-dev libexpat-dev libncurses-dev zlib1g-dev csh subversion
# Compilers
sudo apt-get install gcc g++ gfortran

1.1. Install optional system packages

Optional MPI packages:

# Use system MPI
sudo apt-get install mpi-default-bin libopenmpi-dev

Optional cmake package:

# System CMake
sudo apt-get install cmake

Optional BLAS/LAPACK packages:

# Extra packages for system blas/lapack
sudo apt-get install libblas-dev liblapack-dev

2. Get and configure Linuxbrew

2.1. Put to your .bash_profile or .bashrc

These (or comparable) lines must be put into .bash_profile or .bashrc to set the installation path for Linuxbrew as well as certain environment variables.

# Linuxbrew
export HOMEBREW_PREFIX=~/.linuxbrew
export HOMEBREW_LOGS=~/Logs/linuxbrew
export HOMEBREW_CACHE=~/Cache/linuxbrew
export PATH="$HOMEBREW_PREFIX/bin:$PATH"
export MANPATH="$HOMEBREW_PREFIX/share/man:$MANPATH"
export INFOPATH="$HOMEBREW_PREFIX/share/info:$INFOPATH"

You can also enable bash auto-completion if you install the bash-completion package.

## If possible, enable bash completion
if [ -f $HOMEBREW_PREFIX/etc/bash_completion ]; then
    . $HOMEBREW_PREFIX/etc/bash_completion
fi

The following lines are optional (dependent on whether you'll be using some system-provided BLAS/LAPACK that is NOT in the system path). To give some idea as to how one would set this up, here is the equivalent for using the Ubuntu-provided libraries (which would be redundant to add since Linuxbrew will pick these ones up automatically.)

## Optional [for when using system BLAS/LAPACK]
export HOMEBREW_BLASLAPACK_NAMES="blas;lapack"
export HOMEBREW_BLASLAPACK_LIB="/usr/lib"
export HOMEBREW_BLASLAPACK_INC="/usr/include"

That is to say that if you want to use BLAS/LAPACK from Ubuntu, it should be enough just to ignore setting HOMEBREW_BLASLAPACK_XXX. In order to use openblas, install it first (brew install openblas) and then it will be used automatically. In order to use another library (such as Intel MKL), you need to fill out the above settings accordingly.

2.2 Install Linuxbrew and basic packages

Now that the environmental variables have been set we can install Linuxbrew itself.

git clone https://github.com/Homebrew/linuxbrew.git $HOMEBREW_PREFIX

You may wish to install bash-completion to assist you with filling out Linuxbrew commands if you do any customisation of the commands listed hereafter.

brew install bash-completion

Before we can install the deal.II packages, Linuxbrew needs some basic packages

brew install pkg-config
brew install openssl && brew postinstall openssl

A more recent version of ruby (circa 2.2) is needed for the formulae in this repository. For Ubuntu 14.04, we need to update it.

brew install ruby

Should you not have installed the system cmake then you should install it now.

brew install cmake --without-docs

Should you wish to make use of openmpi instead of the system libraries, then we need to first install a Java runtime environment as well

# Install the Java runtime environment
sudo apt-get install default-jre
# Install OpenMPI
brew install openmpi --c++11

3. Get this collection of formulae and install the deal.II suite

Firstly we need to tap the various repositories from which to fetch the packages and build information.

# Tap this repository
brew tap davydden/dealiisuite

Now you might optionally install openblas (should you not wish to use the system-provided BLAS/LAPACK)

brew install openblas

The optional boost libraries can be configured with C++11 support if you have installed, or are willing to install, openmpi.

# Boost configuration if OpenMPI has been installed
brew install boost --with-mpi --c++11 --without-single

Otherwise this should not be selected (as openmpi is currently a dependency)

# Boost configuration if OpenMPI installation is not desired
brew install boost --with-mpi --without-single

Now we can install all of the other (optional) dependencies of deal.II

brew install hdf5 --with-mpi --c++11
brew install hypre --with-mpi --without-check
brew install metis
brew install parmetis
brew install superlu_dist
brew install scalapack --without-check
brew install mumps
brew install petsc --without-check
brew install arpack --with-mpi
brew install slepc --without-check
brew install p4est --without-check

Installing trilinos is very resource intensive (it consumes a lot of memory when linking, especially with GCC). It may be useful to limit the number of make jobs to lighten the memory load, at the expense of build time.

HOMEBREW_MAKE_JOBS=2 brew install trilinos

Finally you can build the latest stable release of build deal.II

# Latest stable release
brew install dealii

or the developer version (which may be necessary at this moment due to a bug in the configure script for deal.II 8.3.0)

# Developer version
brew install dealii --HEAD

B. Mac OS-X

Note that you can choose to use either the BLAS/LAPACK libraries that are provided by the system (veclibfort) or install them through Homebrew with the openblas package.

For the full list of instructions as to how to install Homebrew, please see this link. The instructions given here are what we personally consider to be the least invasive.

1. Install external software

Mandatory software which installs clang, the C++ compiler

xcode-select --install

You then "need" to accept the xcode licence

xcodebuild -license

2. Get and configure Homebrew

2.1. Put to your .bash_profile or .bashrc

These (or comparable) lines must be put into .bash_profile or .bashrc to set the installation path for Homebrew as well as certain environment variables.

# Homebrew
export HOMEBREW_PREFIX=~/.homebrew
export PATH="$HOMEBREW_PREFIX/bin:$PATH"
export MANPATH="$HOMEBREW_PREFIX/share/man:$MANPATH"
export INFOPATH="$HOMEBREW_PREFIX/share/info:$INFOPATH"

## Enable bash completion
if [ -f $HOMEBREW_PREFIX/etc/bash_completion ]; then
    . $HOMEBREW_PREFIX/etc/bash_completion
fi

2.2 Install Homebrew and basic packages

Now that the environmental variables have been set we can install Homebrew itself.

git clone https://github.com/Homebrew/homebrew.git $HOMEBREW_PREFIX

You may wish to install bash-completion to assist you with filling out Homebrew commands if you do any customisation of the commands listed hereafter.

brew install bash-completion

Before we can install the deal.II packages, Homebrew needs some basic packages

brew install openssl && brew postinstall openssl
brew install cmake
brew install openmpi --c++11

4. Get a collection of formulae and install the deal.II suite

Note that for OS-X the homebrew-science repository has a fully functional set of formulae that work both with the system BLAS/LAPACK libraries as well as OpenBLAS. There are an additional set of dependencies that deal.II can be safely be built against. So we can happily use it as a repository instead of this one and therefore recommend it

# Untap this repository to prevent conflicting packages
brew untap davydden/dealiisuite
# Tap the more complete Homebrew-Science repository
brew tap homebrew/science

4.1. With system BLAS/LAPACK

brew install boost --with-mpi --c++11
brew install gsl
brew install scalapack
brew install mumps
brew install metis
brew install parmetis
brew install hypre --with-mpi
brew install superlu43
brew install superlu_dist
brew install arpack --with-mpi --without-check
brew install hdf5 --with-mpi --c++11
brew install netcdf --with-fortran --with-cxx-compat
brew install suite-sparse
brew install hwloc
brew install sundials --with-mpi
brew install fftw --with-mpi --with-fortran
brew install petsc
brew install slepc
brew install p4est
brew install adol-c
brew install cppunit
brew install doxygen --with-graphviz
brew install glpk
brew install glm
brew install trilinos
brew install dealii

4.2. With OpenBLAS

brew install boost --with-mpi --c++11
brew install gsl
brew install openblas
brew install scalapack --with-openblas
brew install mumps --with-openblas
brew install metis
brew install parmetis
brew install hypre --with-mpi --with-openblas
brew install superlu43 --with-openblas
brew install superlu_dist --with-openblas
brew install arpack --with-mpi --with-openblas --without-check
brew install hdf5 --with-mpi --c++11
brew install netcdf --with-fortran --with-cxx-compat
brew install suite-sparse --with-openblas
brew install hwloc
brew install sundials --with-mpi
brew install fftw --with-mpi --with-fortran
brew install petsc --with-openblas
brew install slepc --with-openblas
brew install p4est --with-openblas
brew install adol-c
brew install cppunit
brew install doxygen --with-graphviz
brew install glpk
brew install glm
brew install trilinos --with-openblas
brew install dealii --with-openblas

C. CentOS cluster

For your convenience, the instructions that follow in the next few sections have been compiled into a script that can be extracted from the installation_scripts directory inside this repository or downloaded, made executable through the command

chmod +x <path_to_script>/install_CentOS.sh

and run to install deal.II with minimal intervention. However, you use this script at your own risk. Of course, you can modify the script to set any personal preferences that you may have with respect to the installed packages.

Below is the detailed instruction to make it work with CentOS cluster and native openmpi, gcc, cmake, git, MKL.

1. Put to your .bash_profile

# CentOS related:
module load gcc
module load openmpi/1.8.3-gcc
module load mkl
module load cmake
module load git/2.2.1

# Linuxbrew
export HOMEBREW_BUILD_FROM_SOURCE=1
export HOMEBREW_PREFIX=$WOODYHOME/.linuxbrew
export HOMEBREW_LOGS=$WOODYHOME/Logs/HOMEBREW
export HOMEBREW_CACHE=$WOODYHOME/Cache/HOMEBREW
export PATH="$HOMEBREW_PREFIX/bin:$PATH"
export MANPATH="$HOMEBREW_PREFIX/share/man:$MANPATH"
export INFOPATH="$HOMEBREW_PREFIX/share/info:$INFOPATH"

# BLAS-LAPACK
export HOMEBREW_BLASLAPACK_NAMES="mkl_intel_lp64;mkl_sequential;mkl_core"
export HOMEBREW_BLASLAPACK_LIB="${MKLROOT}/lib/intel64"
export HOMEBREW_BLASLAPACK_INC="${MKLROOT}/include"

# compilers
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export FF=mpif77

2. Get and configure Linuxbrew

git clone https://github.com/Homebrew/linuxbrew.git $HOMEBREW_PREFIX

Linuxbrew needs ruby. If you do not have one on the front-end or it's too old, compile it yourself:

wget https://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.3.tar.gz
tar xvzf ruby-2.2.3.tar.gz ruby-2.2.3
cd ruby-2.2.3
./configure --prefix=$HOMEBREW_PREFIX
make
make install

Make simlinks for GCC to make sure Linuxbrew picks it up

ln -s `which gcc` $HOMEBREW_PREFIX/bin/gcc-`gcc -dumpversion |cut -d. -f1,2`
ln -s `which g++` $HOMEBREW_PREFIX/bin/g++-`g++ -dumpversion |cut -d. -f1,2`
ln -s `which gfortran` $HOMEBREW_PREFIX/bin/gfortran-`gfortran -dumpversion |cut -d. -f1,2`

Finally, Linuxbrew needs openssl

brew install openssl && brew postinstall openssl

3. Get this collection of formulae and install the deal.II suite

brew tap davydden/dealiisuite

brew install boost --with-mpi --without-single
brew install hdf5 --with-mpi --c++11 --without-cxx
brew install hypre --with-mpi --without-check
brew install metis
brew install parmetis
brew install superlu_dist
brew install scalapack --without-check
brew install mumps
brew install petsc --without-check
brew install slepc --without-check --without-arpack
brew install p4est --without-check
brew install trilinos
brew install numdiff
brew install oce
brew install dealii --without-arpack --HEAD