README.md 13.7 KB
Newer Older
Dion Haefner's avatar
Dion Haefner committed
1 2 3
# Welcome to DORiE!
(__D__UNE-__O__perated __Ri__chards equation solving __E__nvironment)

4
[![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)
Dion Haefner's avatar
Dion Haefner committed
5

6
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.
7 8 9

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

10
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/). 
11 12 13 14


# Installation Instructions

Dion Haefner's avatar
Dion Haefner committed
15
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.
16

Dion Haefner's avatar
Dion Haefner committed
17
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.
18

19 20 21 22 23 24 25 26 27
## 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:

Dion Häfner's avatar
Dion Häfner committed
28
    docker run -i -t -v <dir>:/sim dorie <command>
29 30 31

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

Dion Häfner's avatar
Dion Häfner committed
32
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.
33 34

## Docker Installation - Interactive Setup
Dion Häfner's avatar
Dion Häfner committed
35
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.
36

37
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 (referencing the DUNE module version 2.5).
38
Run a new container from this image by calling
39

40
    docker run -i -t dorie/dune-env:2.5 /bin/bash
41

Dion Haefner's avatar
Dion Haefner committed
42
Docker will automatically download the image if necessary. Use the `-v` option of the `run` command to mount a local directory into the container:
43 44 45

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

46
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!*
47

Dion Haefner's avatar
Dion Haefner committed
48
Next, use `git clone` to download the DORiE repository into the shared folder. Enter the container, and execute
49 50

    dunecontrol --only=dorie all
51 52 53 54
    
to build DORiE, or

    MAKE_FLAGS="-j <N>" dunecontrol --only=dorie all
55

56
to build in parallel on `N` processes. Lastly, install the DORiE binaries by calling
57 58

    dunecontrol --only=dorie make install
59

60
### Update DUNE
61 62 63 64
The DUNE modules in the repository might be outdated. You can update to the newest versions by calling

    dunecontrol update

65
Then compile and install all modules again by executing
66

67
    dunecontrol all && dunecontrol make install
68

Dion Haefner's avatar
Dion Haefner committed
69

70
## Manual Installation
Dion Häfner's avatar
Dion Häfner committed
71 72 73
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!
74 75

### Dependencies
Dion Haefner's avatar
Dion Haefner committed
76
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.
77 78 79

| Software | Version/Branch | Comments |
| ---------| -------------- | -------- |
Dion Haefner's avatar
Dion Haefner committed
80
| CMake | >= 2.8.12 |
81 82 83
| GCC | >= 5 |
| git |
| pkg-config |
Dion Haefner's avatar
Dion Haefner committed
84 85 86 87
| HDF5 | | with MPI support
| FFTW3 | | with MPI support
| Python | 2.7 or 3.x |
| pip | 2.7 or 3.x |
88
| MPI | | Tested with OpenMPI
Dion Haefner's avatar
Dion Haefner committed
89 90
| SuperLU | 4.3 or 5.x |
| VirtualEnv | | Install via `pip` |
91 92 93
| [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
94
| [dune-uggrid](https://gitlab.dune-project.org/staging/dune-uggrid) | releases/2.5
95 96
| [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
97
| [dune-functions](https://gitlab.dune-project.org/staging/dune-functions) | releases/2.5
98
| [dune-typetree](https://gitlab.dune-project.org/staging/dune-typetree) | releases/2.5
99 100 101
| [dune-pdelab](https://gitlab.dune-project.org/pdelab/dune-pdelab) | releases/2.5
| [dune-python](https://gitlab.dune-project.org/quality/dune-python) | releases/2.5
| [dune-testtools](https://gitlab.dune-project.org/quality/dune-testtools) | releases/2.5
102

Dion Haefner's avatar
Dion Haefner committed
103
If you also want to build the documentation, you will additionally need to install Doxygen, Sphinx and Breathe.
104

105
### Step-by-step Instructions
Dion Häfner's avatar
Dion Häfner committed
106
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. 
Dion Haefner's avatar
Dion Haefner committed
107 108

1. Install third party packages:
Lukas Riedel's avatar
Lukas Riedel committed
109
    
110
    **Ubuntu:**
Dion Haefner's avatar
Dion Haefner committed
111
    
Dion Haefner's avatar
Dion Haefner committed
112
        apt update 
Dion Haefner's avatar
Dion Haefner committed
113
        apt install autoconf bison cmake flex gcc-5 g++-5 gfortran-5 \
Dion Haefner's avatar
Dion Haefner committed
114 115
                    git libatlas-base-dev libfftw3-dev libfftw3-mpi-dev \
                    libfreetype6-dev libhdf5-mpi-dev libopenmpi-dev libpng-dev \
Dion Haefner's avatar
Dion Haefner committed
116 117
                    libsuperlu-dev libxft-dev python-dev python-pip python-sphinx \
                    python-breathe doxygen
118

119 120 121 122
    **Mac OS X:**

        brew update
        brew install automake cmake doxygen gcc libtool libpng open-mpi \
123
                    pkg-config python3 superlu
124 125 126
        brew install hdf5 --with-mpi
        brew install fftw --with-mpi

127
2. Install the necessary Python packages using `pip`:
128 129

    **Ubuntu:**
130
        
Dion Haefner's avatar
Dion Haefner committed
131
        python -m pip install virtualenv
132

133 134
    **Mac OS X:**

135
        sudo -H python3 -m pip install virtualenv sphinx breathe
136

137
3. **Mac OS X** only: 
138
    The Apple Clang compiler shipped with CMake is not suitable for compiling DUNE and UG. Before proceeding, call
139

140 141
        export CC=gcc-6
        export CXX=g++-6
142

143
    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.
144

145
4. Clone the DUNE modules and DORiE into a suitable folder on your machine. Make sure that you check out the correct branches (see above). Enter the parent folder, and call
146 147
    
    **Ubuntu:**
Dion Haefner's avatar
Dion Haefner committed
148

149
        MAKE_FLAGS="-j <N>" ./dune-common/bin/dunecontrol all
150

151 152 153 154
    **Mac OS X:**

        CMAKE_FLAGS="-DDUNE_FORCE_PYTHON3=True" MAKE_FLAGS="-j <N>" ./dune-common/bin/dunecontrol all

155
    to build all DUNE modules in parallel on `N` processes. 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.
Dion Haefner's avatar
Dion Haefner committed
156 157
 
5. To install all DUNE packages into system locations (so you can call `dunecontrol` and `dorie` from anywhere), you can run
158

159
        ./dune-common/bin/dunecontrol make install
160

161
    which may require `sudo` rights on your machine. This action is **optional and not required to run DORiE**. If you choose not to install DORiE, make sure to append the location of `dunecontrol` (`dune-common/bin`) and `dorie` (`dorie/build-cmake/bin`) to your search path.
162

163

164 165 166
## 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:
Dion Haefner's avatar
Dion Haefner committed
167 168 169 170

* [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.

171
# Usage
Dion Haefner's avatar
Dion Haefner committed
172

173 174
## Start an interactive Docker session

175
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:
176 177 178 179 180

    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`.

181
## Documentation
Dion Haefner's avatar
Dion Haefner committed
182

183
The documentation of the current `master` branch can be found [online](http://dorie-docs.gitballoon.com) (password: `richards`).
Dion Haefner's avatar
Dion Haefner committed
184

185
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
Dion Haefner's avatar
Dion Haefner committed
186

Dion Haefner's avatar
Dion Haefner committed
187
    dunecontrol --only=dorie make doc
Dion Haefner's avatar
Dion Haefner committed
188

189
The documentation files can now be found in the subfolder `dorie/build-cmake/doc`.
Dion Haefner's avatar
Dion Haefner committed
190

191
## Run, DORiE, Run!
Dion Haefner's avatar
Dion Haefner committed
192
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
193 194

    dorie <command>
195

Dion Haefner's avatar
Dion Haefner committed
196
If you did not run `dunecontrol make install`, you can find the wrapper in the `dorie/build-cmake/bin` folder of your installation.
197

198
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
199 200 201

    dorie create

202 203
DORiE encapsulates two routines, the Parameter Field Generator (PFG) and the main program routine. Each takes a single `.ini` configuration file as arguments.

204 205
Tweak the paramters to your liking and then call

206 207 208 209
    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

210
    dorie run <inifile>
Dion Haefner's avatar
Dion Haefner committed
211

212
to execute the main program.
Dion Haefner's avatar
Dion Haefner committed
213

214
List all available commands and find further help by executing
Dion Haefner's avatar
Dion Haefner committed
215

Dion Häfner's avatar
Dion Häfner committed
216
    dorie --help
Dion Haefner's avatar
Dion Haefner committed
217

218 219
or

Dion Häfner's avatar
Dion Häfner committed
220
    dorie <command> --help
221

222
## Troubleshooting
Dion Haefner's avatar
Dion Haefner committed
223 224
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`.

225
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.
Dion Haefner's avatar
Dion Haefner committed
226

227
### Debugging
Dion Haefner's avatar
Dion Haefner committed
228
DORiE can be built with debugging flags via CMake. To do so, run
229

Dion Haefner's avatar
Dion Haefner committed
230
    CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Debug" dunecontrol --only=dorie all
231

Dion Haefner's avatar
Dion Haefner committed
232
After building, a debugger can hook into the executables.
233

Dion Haefner's avatar
Dion Haefner committed
234
**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.
235

Dion Haefner's avatar
Dion Haefner committed
236
To re-create a release build, configure DORiE with the release build type by executing
237

Dion Haefner's avatar
Dion Haefner committed
238
    CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Release" dunecontrol --only=dorie all
239

240 241 242 243 244
#### 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

Dion Häfner's avatar
Dion Häfner committed
245
The debugger `gdb` is pre-installed in the Docker container.
246

Dion Haefner's avatar
Dion Haefner committed
247
### DORiE is running, but I suspect that something is wrong
Dion Haefner's avatar
Dion Haefner committed
248
You can execute system tests in order to ensure that DORiE is running correctly and producing the expected results:
Dion Haefner's avatar
Dion Haefner committed
249

Dion Haefner's avatar
Dion Haefner committed
250
    ARGS="--output-on-failure" dunecontrol --only=dorie make test
Dion Haefner's avatar
Dion Haefner committed
251 252 253

You will be informed whether each test has been passed or failed, and you may find additional output in the DORiE build directory.

254
### Further Help
255
[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).