README.md

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

[![build status](https://zwackelmann.iup.uni-heidelberg.de:10443/dorie/dorie/badges/master/build.svg)](https://zwackelmann.iup.uni-heidelberg.de:10443/dorie/dorie/commits/master)

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/) and the [DUNE-PDELab](https://dune-project.org/modules/dune-pdelab/) module. 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](http://www.iup.uni-heidelberg.de/), supervised by [Kurt Roth](http://ts.iup.uni-heidelberg.de/people/prof-dr-kurt-roth/), 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](https://typo.iwr.uni-heidelberg.de/home/). 


# 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 2.5.1 (referencing the DUNE module version 2.5). We will run a new container from this image and mount some local directory `<hostdir>/dorie` into it by calling

    docker run -v <hostdir>/dorie:/opt/dune/dorie -i -t dorie/dune-env:2.5.1 /bin/bash

Docker will automatically download the image if necessary. Now 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 (mounted) folder. Enter the container, and execute

    dunecontrol --only=dorie all
    
to build DORiE, or

    MAKE_FLAGS="-j <N>" dunecontrol --only=dorie all

to build in parallel on `N` processes. Lastly, install the DORiE binaries by calling

    dunecontrol --only=dorie make install

### Update DUNE
The DUNE modules (as well as DORiE itself) 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 | 3.x |
| pip | 3.x |
| MPI | | Tested with OpenMPI
| SuperLU | 4.3 or 5.x |
| [dune-common](https://gitlab.dune-project.org/core/dune-common) | releases/2.5
| [dune-geometry](https://gitlab.dune-project.org/core/dune-geometry) | releases/2.5
| [dune-grid](https://gitlab.dune-project.org/core/dune-grid) | releases/2.5
| [dune-uggrid](https://gitlab.dune-project.org/staging/dune-uggrid) | releases/2.5
| [dune-istl](https://gitlab.dune-project.org/core/dune-istl) | releases/2.5
| [dune-localfunctions](https://gitlab.dune-project.org/core/dune-localfunctions) | releases/2.5
| [dune-functions](https://gitlab.dune-project.org/staging/dune-functions) | releases/2.5
| [dune-typetree](https://gitlab.dune-project.org/staging/dune-typetree) | releases/2.5
| [dune-pdelab](https://gitlab.dune-project.org/pdelab/dune-pdelab) | releases/2.5


### Optional Packages
| Software | Version/Branch | Comments |
| ---------| -------------- | -------- |
| [dune-testtools](https://gitlab.dune-project.org/quality/dune-testtools) | master | Handles system tests
| [doxygen](http://www.stack.nl/~dimitri/doxygen/) | | Builds documentation
| [METIS](http://glaros.dtc.umn.edu/gkhome/views/metis) | 5 | For parallel runs
| [ParMETIS](http://glaros.dtc.umn.edu/gkhome/views/metis) | 4 | For parallel runs


### 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.

If you installed [Anaconda](https://conda.io/docs/user-guide/install/download.html) on your machine, you don't need to install Python or Pip. Simply skip these packages when using the package managers for installing the software. However, notice the warnings when compiling DORiE below!

1. **Mac OS X** users need to start by installing the Apple Command Line Tools by executing

        xcode-select --install

1. Install third party packages:
    
    **Ubuntu:**
    
        apt update 
        apt install cmake doxygen 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 python3-dev python3-pip

    **Mac OS X:**

        brew update
        brew install cmake doxygen gcc libpng open-mpi \
                    pkg-config python3 superlu
        brew install hdf5 --with-mpi
        brew install fftw --with-mpi

1. The parallel linear solver of DORiE can make use of the ParMETIS package. If you want to run DORiE in parallel on multiple processes, additionally install METIS and ParMETIS:

    **Ubuntu:**

        apt install libmetis-dev libparmetis-dev

    **Mac OS X:** _Support is dropped because ParMETIS is currently unavailable from Homebrew._

    **Parallel runs without these two packages are possible but not supported!**

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

        export CC=gcc-7
        export CXX=g++-7

    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.

4. Clone the DUNE modules and DORiE into a suitable folder on your machine. Use `git checkout` to switch to the correct branches (see above). Enter the parent folder, and call

        CMAKE_FLAGS="-DDUNE_PYTHON_VIRTUALENV_SETUP=True -DDUNE_PYTHON_ALLOW_GET_PIP=True" ./dune-common/bin/dunecontrol all

    to build all DUNE modules. Additionally, you can add `MAKE_FLAGS="-j X"` before the call to `dunecontrol` to compile on `X` processes in parallel.

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

    **Warning:** Anacoda supplies its own version of HDF5 which is typically found first by CMake. If you have Anaconda installed on your machine, add

        `HDF5_ROOT=/usr/local`

    to the `CMAKE_FLAGS` in the call to `dunecontrol` above.
 
5. After a successful build you can call the `dorie` wrapper located in `dorie/build-cmake/bin` from anywhere on your machine, but it is more handy to add this location to your search path. You can add the directory to your `PATH` variable by calling

        PATH=<path/to/>dorie/build-cmake/bin:$PATH

    However, this will only last for your current terminal session. Another option is to add this path permanently in your shell configuration file.

    **Installing DUNE and DORiE via `make install` into your usual work environment is strongly discouraged!**


## 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

## Start an interactive Docker session

In case you built DORiE using `docker build` and want to start an interactive session, e.g. to build the documentation or do some debugging, you can do so by specifying a custom entrypoint for the container:

    docker run -i -t --entrypoint=/bin/bash -v <dir>:/sim dorie

This way, an interactive bash session inside the container will be started (instead of directly running DORiE). Note that DUNE and DORiE are located in `/opt/dune`.

## 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

or navigate to the `dorie/build-cmake` directory and call

    make doc

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

## Run, DORiE, Run!
If you made the DORiE wrapper directory available through your `PATH` variable, you can call it by simply executing

    dorie <command>

You can always find the wrapper in the `dorie/build-cmake/bin` folder of your installation and call it directly with

    <path/to/>dorie/build-cmake/bin/dorie <command>

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](https://zwackelmann.iup.uni-heidelberg.de:10443/dorie/dorie/issues), 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](https://zwackelmann.iup.uni-heidelberg.de:10443/dorie/dorie/issues/new), or write to the [DORiE developer mailing list](mailto:dorieteam@iup.uni-heidelberg.de).