README.md

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

![build status](http://shangrila.iup.uni-heidelberg.de:30000/dorie/dorie-new/badges/master/build.svg)

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 / cubic 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, supervised by [Kurt Roth](http://ts.iup.uni-heidelberg.de/people/prof-dr-kurt-roth/), in collaboration with [Ole Klein](https://conan2.iwr.uni-heidelberg.de/people/oklein/) and the [Scientific Computing Group](https://conan2.iwr.uni-heidelberg.de/) of IWR Heidelberg. 


# Installation Instructions

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 for inexperienced users it is recommended to use the deployment software [Docker](https://www.docker.com/) instead.

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

## Docker Installation - Simple Setup
This setup is intended for users who simply want to start computations with DORiE.

Install Docker on your machine. Then, use `git clone` to download the DORiE repository into a suitable directory on your machine. Enter the directory, and call

    docker build -t dorie .

Docker will use a prepared image from Dockerhub and install DORiE into it. You can now call DORiE via the Docker deamon from any directory `dir` on your machine:

    docker run -i -t -v <dir>:/sim dorie <command>

The `-v` option tells docker to mount the directory into the container work directory (`sim`).

In the section 'Usage' you will find a list of possible commands. Note that input and output files can only be placed in the `<dir>` directory or subdirectories thereof. You must use relative paths in the DORiE configuration files.

## Docker Installation - Interactive Setup
This setup is intended for advanced users. You will gain access to the DORiE module outside the container, and be able to make changes to the source code.

We have prepared a [DORiE DUNE Environment Image on Dockerhub](https://hub.docker.com/r/dorie/dune-env/), which is a modified image of the Ubuntu OS that has all dependencies readily installed. The current version is 2.4 (referencing the DUNE module version 2.4).
Run a new container from this image by calling

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

Docker will automatically download the image if necessary. 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. *Mounting directories is not possible after your container has been started!*

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

    dunecontrol --only=dorie all

to build DORiE. Lastly, install the DORiE binaries by calling

    dunecontrol --only=dorie make install

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

    dunecontrol update

Then compile and install all modules again by executing

    dunecontrol all && dunecontrol make install


## Manual Installation
Installing all packages manually can be quite an effort, but useful for developers who want to have easy access to the source files or users who prefer to run DORiE without the Docker overhead. 

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 DORiE on your machine. See the step-by-step manual for further details.

| Software | Version/Branch | Comments |
| ---------| -------------- | -------- |
| CMake | >= 2.8.12 |
| GCC | >= 5 |
| git |
| pkg-config |
| HDF5 | | with MPI support
| FFTW3 | | with MPI support
| Python | 2.7 or 3.x |
| pip | 2.7 or 3.x |
| MPI | | Tested with OpenMPI and Mpich
| SuperLU | 4.3 or 5.x |
| 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

If you also want to build the documentation, you will additionally need to install Doxygen, Sphinx and Breathe.

### Step-by-step Instructions
These instructions are suitable for a clean **Ubuntu** or **Mac OS X** setup. The main difference between the two systems is the package manager. Debian-based systems have the APT manager already built in. On Mac, we recommend installing [Homebrew](http://brew.sh/). If you prefer to use [MacPorts](https://www.macports.org/), you need to check if some of the packages require different installation options than displayed here. 

1. Install third party packages:
    
    **Ubuntu:**
    
        apt update 
        apt install autoconf bison cmake flex gcc-5 g++-5 gfortran-5 \
                    git libatlas-base-dev libfftw3-dev libfftw3-mpi-dev \
                    libfreetype6-dev libhdf5-mpi-dev libopenmpi-dev libpng-dev \
                    libsuperlu-dev libxft-dev python-dev python-pip python-sphinx \
                    python-breathe doxygen

    **Mac OS X:**

        brew update
        brew install automake cmake doxygen gcc libtool libpng open-mpi \
                    pkg-config superlu
        brew install hdf5 --with-mpi
        brew install fftw --with-mpi

    Install the PyPi package manager pip by downloading the [get_pip.py](https://bootstrap.pypa.io/get-pip.py) script and calling

        sudo -H python get_pip.py

2. Install the necessary Python packages using `pip`:

    **Ubuntu:**
        
        python -m pip install virtualenv

    **Mac OS X:**

        sudo -H python -m pip install virtualenv sphinx==1.3.6 breathe --ignore-installed

3. **Mac OS X** only: 
    1. The Apple Clang compiler shipped with CMake is not suitable for compiling DUNE and UG. Before proceeding, call

            export CC=gcc-6
            export CXX=g++-6

        to enfore the Homebrew'd GCC compiler. Note that this variable export only lasts for your current terminal session. Always make sure that the configuration tool actually finds GCC instead of the Apple Clang.

3. Clone the specified version of UG into a suitable folder on your machine. Install it by calling

        autoreconf -is
        ./configure --enable-parallel --without-x --enable-dune --enable-system-heap
        make && make install

4. Clone the DUNE modules and DORiE into a suitable folder on your machine. Make sure that you check out the correct branches (2.4 release branch). Enter the parent folder, and call

        ./dune-common/bin/dunecontrol all

    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.
 
5. To install all DUNE packages into system locations (so you can call `dunecontrol` and `dorie` from anywhere), you can run

        ./dune-common/bin/dunecontrol make install

    This may require `sudo` rights on your machine. If you choose not to do this, make sure to append the location of `dunecontrol` (`dune-common/bin`) and `dorie` (`dorie/build-cmake/bin`) to your search path.


## 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:

* [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.

# Usage

## Documentation

The documentation of the current `master` branch can be found [online](http://dorie-docs.gitballoon.com) (password: `richards`).

The documentation can be built after DORiE has been properly configured (i.e., by calling `dunecontrol`). Note that you might have to re-configure DORiE once after installing it, because some dependencies are installed at configure time (e.g. by `dunecontrol --only=dorie configure`). To build the documentation, just run

    dunecontrol --only=dorie make doc

The documentation files can now be found in the subfolder `dorie/build-cmake/doc`.

## Run, DORiE, Run!
During `make install`, DORiE installs a wrapper to access the functions and executables of DORiE from any location on your device. After a successful installation, you can call the wrapper by simply executing

    dorie <command>

If you did not run `dunecontrol make install`, you can find the wrapper in the `dorie/build-cmake/bin` folder of your installation.

To start your first simulation run, create a new directory and enter it. Place some exemplary configuration and boundary condition data files in there by calling

    dorie create

DORiE encapsulates two routines, the Parameter Field Generator (PFG) and the main program routine. Each takes a single `.ini` configuration file as arguments.

Tweak the paramters to your liking and then call

    dorie pfg <inifile>

to create a parameter field file. Make sure that you instruct the main routine to call the file you just created. Then call

    dorie run <inifile>

to execute the main program.

List all available commands and find further help by executing

    dorie --help

or

    dorie <command> --help

## Troubleshooting
CMake heavily caches the results of its configuration process. In case you encounter errors or strange behavior, especially after an update, you should delete the DORiE build folder (called `build-cmake` by default) and re-install DORiE using `dunecontrol`.

If the problem persists, 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), or create an issue yourself. For problems related to the installation, refer to the sections below.

### Debugging
DORiE can be built with debugging flags via CMake. To do so, run

    CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Debug" dunecontrol --only=dorie all

After building, a debugger can hook into the executables.

**Note:** If no `CMAKE_BUILD_TYPE` is specified during re-configuration, the last configuration build type is used. If no CMake files exist, it defaults to `Release`. You will find the actual value displayed in the final output of CMake.

To re-create a release build, configure DORiE with the release build type by executing

    CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Release" dunecontrol --only=dorie all

#### Debugging inside Docker
A debugger needs special security privileges usually not provided by the Docker engine. To enable debugging inside Docker, these privileges have to be granted when calling `docker run` by adding the options

    --security-opt seccomp=unconfined

The debugger `gdb` is pre-installed in the Docker container.

### DORiE is running, but I suspect that something is wrong
You can execute system tests in order to ensure that DORiE is running correctly and producing the expected results:

    ARGS="--output-on-failure" dunecontrol --only=dorie make test

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).