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# Welcome to DORiE!
(__D__UNE-__O__perated __Ri__chards equation solving __E__nvironment)

[![build status](http://shangrila.iup.uni-heidelberg.de:30000/ci/projects/1/status.png?ref=master)](http://shangrila.iup.uni-heidelberg.de:30000/ci/projects/1?ref=master)

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DORiE is a software suite for solving Richard's Equation. The core feature is a C++ PDE-solver powered by [DUNE](https://dune-project.org/). It implements a Discontinous Galerkin (DG) discretization scheme on structured rectangular and unstructured simplex grids in two and three spatial dimensions, and makes use of advanced features like adaptive grid refinement.

The suite encapsulates a documentation and various tools for program setup, program testing, and output analysis, which are mostly written in Python.

DORiE is developed and maintained by the [DORiE Developers](mailto:dorieteam@iup.uni-heidelberg.de) of the [TS-CCEES](http://ts.iup.uni-heidelberg.de/) research group at IUP Heidelberg, in collaboration with [Ole Klein](https://conan.iwr.uni-heidelberg.de/people/oklein/) and the [Scientific Computing Group](https://conan.iwr.uni-heidelberg.de/) of IWR Heidelberg, supervised by [Kurt Roth](http://ts.iup.uni-heidelberg.de/people/prof-dr-kurt-roth/). 


# Installation Instructions

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DORiE is a [DUNE](https://dune-project.org/) module and requires several other DUNE modules as well as third party software packages. Installation can be handled manually on your local machine, but it's recommended to use the virtualization software [Docker](https://www.docker.com/) instead.

In any case, DORiE is configured, build, and installed via the [DUNE Buildsystem](https://dune-project.org/doc/installation/), using the `dunecontrol` script to handle DUNE-internal dependencies.

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## Docker Installation
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Install Docker on your machine. Then, download the [DORiE DUNE Environment Repository](https://hub.docker.com/r/dorie/dune-env/) from [Dockerhub](https://hub.docker.com/), by executing

    docker pull dorie/dune-env

Run a new container from the v2.4 image by calling

    docker run -i -t dorie/dune-env:2.4 /bin/bash

Additionally, use the `-v` option of the `run` command to mount a local directory into the container:

    -v <hostdir/dorie>:/opt/dune/dorie

This way, you can access the content of the (still empty) folder of the virtual machine from your local `<hostdir>/dorie` directory.

Next, `git clone` the DORiE repository into the shared folder. Enter the container, and execute

    dunecontrol --only=dorie all

to build DORiE.

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### Update DUNE
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The DUNE modules in the repository might be outdated. You can update to the newest versions by calling

    dunecontrol update

Then compile all modules again by executing

    dunecontrol all

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## Manual Installation
Installing all packages manually can be quite an effort, but useful for developers who want to easily access documentation material and source files of the dependency packages. Whenever possible, dependencies should be installed using a package manager, like [APT](https://wiki.ubuntuusers.de/APT/) on Ubuntu or [Homebrew](http://brew.sh/) on Mac. Manual installation on a Windows environment is strongly discouraged!

### Dependencies
Depending on your system configuration, there will be more packages necessary to install the software on your machine. See the step-by-step manual for further details.

| Software | Version/Branch | Comments |
| ---------| -------------- | -------- |
| CMake | >= 3.0 |
| doxygen |
| GCC | >= 5 |
| git |
| pkg-config |
| HDF5 | | MPI library
| FFTW3 | | MPI library
| METIS |
| ParMETIS |
| Python | 3 |
| Python Pip | 3 |
| OpenMPI | >= 2 |
| SuperLU | >=5 |
| ----- | ----- | ----- |
| Breathe | | Install via `pip` |
| Sphinx | | Install via `pip` |
| VirtualEnv | | Install via `pip` |
| ----- | ----- | ----- |
[UG](https://gitlab.dune-project.org/ug/ug) | 3.12.1 | Follow the [IWR Installation Instructions](http://www.iwr.uni-heidelberg.de/frame/iwrwikiequipment/software/ug)
| [dune-common](https://gitlab.dune-project.org/core/dune-common) | releases/2.4
| [dune-geometry](https://gitlab.dune-project.org/core/dune-geometry) | releases/2.4
| [dune-grid](https://gitlab.dune-project.org/core/dune-grid) | releases/2.4
| [dune-istl](https://gitlab.dune-project.org/core/dune-istl) | releases/2.4
| [dune-localfunctions](https://gitlab.dune-project.org/core/dune-localfunctions) | releases/2.4
| [dune-typetree](https://gitlab.dune-project.org/pdelab/dune-typetree) | releases/2.4
| [dune-pdelab](https://gitlab.dune-project.org/pdelab/dune-pdelab) | releases/2.4
| [dune-python](https://gitlab.dune-project.org/quality/dune-python) | releases/2.4
| [dune-testtools](https://gitlab.dune-project.org/quality/dune-testtools) | releases/2.4

### Ubuntu Manual Installation
The following instructions follow the installation instructions on a 'clean' Ubuntu system and are similarly executed to create the DORiE Docker image from an Ubuntu Docker image.

1. Install the third party software using `apt-get`:
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        apt-get update && apt-get install -y \
        autoconf \
        bison \
        cmake \
        doxygen \
        flex \
        gcc-5 \
        g++-5 \
        gfortran-5 \
        git \
        libatlas-base-dev \
        libfftw3-dev \
        libfftw3-mpi-dev \
        libfreetype6-dev \
        libhdf5-mpi-dev \
        libmetis-dev \
        libopenmpi-dev \
        libpng-dev \
        libscotchparmetis-dev \
        libsuperlu-dev \
        libxft-dev \
        python3-dev \
        python3-pip

2. Install the necessary Python packages using `pip`:
        
        python3 -m pip install virtualenv
        python3 -m pip install sphinx
        python3 -m pip install breathe

3. Clone UG into a suitable folder on your machine and `git checkout` the specified version. Install it by calling

        autoreconf -is
        ./configure --prefix=<dir> --enable-parallel --without-x --enable-dune --enable-system-heap
        make && make install

    Replace `<dir>` with a installation directory of choice.

4. Clone the DUNE modules and DORiE into a suitable folder on your machine. Make sure that you `git checkout` the specified branches. Enter the folder, and call

        ./dune-common/bin/dunecontrol all -DCMAKE_CXX_FLAGS="-O3"

    If you installed software into paths not appended to your `PATH` variable, you will have to add a custom options file to make sure that CMake finds all packages. See the [DUNE Installation Instructions](https://dune-project.org/doc/installation/) for details. CMake will throw an error if required packages are not found.

## Recommended Third-Party Software

The following software packages are cross-platform, so you should be able to find a release that fits your operating system:
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* [Gmsh](http://gmsh.info/): An open-source CAD that can be used to create the `.msh` files used by DORiE to define triangular meshes.
* [ParaView](http://www.paraview.org/): A powerful post-processing tool for VTK files. Offers both visualization and data analysis tools.
* [Python VTK tools](http://www.vtk.org/Wiki/VTK/Examples/Python): If you want to write your own post-processing in python, you may use these tools which supply readers for binary VTK files.


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# Usage
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## Documentation
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The documentation of the current `master` branch can be found [online](http://dorie-docs.gitballoon.com) (password: `richards`).
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The documentation can be built after DORiE has been properly configured (i.e., by calling `dunecontrol`). Enter the build directory of DORiE (`dorie/build-cmake`) and execute
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    make doc
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The documentation files can now be found in the subfolder `dorie/build-cmake/doc`.
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## Usage
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The DORiE executables each expect a single `.ini` configuration file as input.
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    ./dorie config.ini
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## Troubleshooting
In case you encounter errors or strange behavior, you should first take a look at the [List of Known Bugs](http://shangrila.iup.uni-heidelberg.de:30000/dorie/dorie/issues?assignee_id=&author_id=&label_name=bug&milestone_id=&scope=all&sort=created_desc&state=opened). For problems related to the installation, refer to the sections below.
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### DORiE is running, but I suspect that something is wrong
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You can execute system tests in order to ensure that DORiE is running correctly and producing the expected results. Navigate to the build directory (`dorie/build-cmake`) end execute
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    make test
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You will be informed whether each test has been passed or failed, and you may find additional output in the DORiE build directory.

### Further help
Open an issue, or write to the [DORiE developer mailing list](mailto:dorieteam@iup.uni-heidelberg.de).