Deal.ii

The official official deal.II tutorials are quite comprehensive and well documented. I will give a short overview about the most interesting tutorials for us.

This tutorial deals with a general introduction to how the deal.II tutorials work in general. It specifically deals with two techniques: *How to generate triangulation objects *How to loop over all cells

This tutorial deals with the definition of degrees of freedom on meshes, and how they can be renumbered to give better sparsity patterns.

This tutorial deals with solving the first system with zero boundary conditions and how the basic structure of a deal.II program looks like:

• make the grid
• setup the system
• assemble the system
• solve the system
• output of the results

This tutorial deals with “dimension independent programming” and how non-homogeneous Dirichlet boundary conditions can be applied by introducing two new classes denoting the right hand side and the Dirichlet boundary conditions.

This tutorial deals with

• computations on successively refined grids (laying out foundations for adaptive grids)
• reading in a coarse grid generated by an automatic mesh generator
• optimization to speed up computation
• debugging and safe programming
• using preconditioned iterative solvers

This tutorial deals with the handling of locally refined grids.

This tutorial deals with the handling of vector valued problems - specifically with an elastic problem as example.

There is a bug in the step-18 tutorial of deal.II 7.2.0! Add following line in the beginning of its “refine_initial_grid()” function:

refine_initial_grid()

triangulation.clear_user_data();

The current versions can be downloaded from the deal.II download page.

After downloading deal.II copy it to the folder where you want to keep the library. Unpack it via

tar xzf "deal.II-X.Y.Z.tar.gz"

Unpacking it will create a subdirectory deal.II. Go into this directory and run

./configure --without-petsc
./make all

Download PETSc and unpack it. Go into the PETSc directory and configure it via

basic configuration PETsc

# ./configure --with-cc=gcc --with-fc=gfortran --download-f-blas-lapack --download-openmpi --with-shared-libraries=1 --with-dynamic-loading=1
./configure --with-shared-libraries=1 --with-cc=mpicc --with-fc=mpif90 --with-dynamic-loading=1 --download-f-blas-lapack

PETSc instructs you how to make it - in my case

2013-02-27 -- Dominik Steinberger>
make PETSC_DIR=/home/steido/bin/PETSc/petsc-3.3-p6 PETSC_ARCH=arch-linux2-c-debug all

Take the values for PETSC_DIR and PETSC_ARCH and put it into your .bashrc together with a new value for LD_LIBRARY_PATH

export PETSC_DIR="${HOME}/bin/PETSc/petsc-3.3-p6"
export PETSC_ARCH="arch-linux2-c-debug"
export LD_LIBRARY_PATH="${PETSC_DIR}/${PETSC_ARCH}/lib:${LD_LIBRARY_PATH}" 

Download METIS, unpack it and go in its directory and make it

make config prefix="${HOME}/bin/METIS/metis-5.0.2" shared=1
make install

add to .bashrc

export METIS_DIR="${HOME}/bin/METIS/metis-5.0.2"

Go to your deal.II directory and configure it for PETSc and METIS

configure deal.II with PETSc and METIS

./configure --enable-mpi --disable-threads  CC=mpicc CXX=mpicxx --with-petsc="${PETSC_DIR}" --with-petsc-arch="${PETSC_ARCH}" --with-metis="${METIS_DIR}"
<code>
 
Make deal.II
</code bash>
make all

other possible options:

MPI optimization::     --with-mpi-dir=/usr/lib/openmpi/ --with-cc=mpicc --with-fc=mpif90 --with-CXX=mpixx --with-blas-lapack-dir=/opt/intel/mkl   --with-cpu=corei7-avx --mtune=corei7-avx --with-trilinos=/usr/net/modules/corei7-avx-6/trilinos-10.12.2 --with-metis=/usr/net/modules/corei7-avx-6/metis510-a

# #########
# petsc 3.3
# #########
 
# configure, follow install instructions
./configure --with-shared-libraries=1 --with-cc=mpicc --with-fc=mpif90 --with-dynamic-loading=1
 
 
# ##############
# profile/bashrc
# ##############
 
# petsc Path
export PETSC_ARCH=$"arch-linux2-c-debug"
export PETSC_DIR="${HOME}/bin/petsc-3.3-p5"
export LD_LIBRARY_PATH="${HOME}/bin/petsc-3.3-p5/arch-linux2-c-debug/lib"
 
# ###########
# metis 5.0.2
# ###########
unzip tar
make config prefix="${HOME}/bin/metis-5.0.2" shared=1
make install
cp "${HOME}/bin/metis-5.0.2/lib/libmetis.so" "${HOME}/bin/metis-5.0.2/libmetis/libmetis.so"
 
# ###########
# deal.ii 7.2
# ###########
./configure --enable-mpi --disable-threads  CC=mpicc CXX=mpicxx --with-petsc=/home/sliebenstein/bin/petsc3.3-p5 --with-petsc-arch=arch-linux2-c-debug --with-metis=/home/sliebenstein/bin/metis-5.0.2
 
#check if the env variables are set correctly
echo "$PETSC_ARCH"
echo "$PETSC_DIR"
echo "$LD_LIBRARY_PATH"

UPDATE: A WAY better possibility is to use an cmake file (only working with version 8.0 or higher.

  cmake -G"Eclipse CDT4 - Unix Makefiles" -DDEAL_II_DIR=/path/to/deal.II .

To use Eclipse's autocompletion features it has to be configured to work with deal.II. The Eclipse deal.II wiki page provides a comprehensive step by step guide to set up Eclipse for deal.II