From PyPi

By far the easiest way to get access to Dune is by installing into a virtual environment using pip. In some folder e.g. Dune setup a virtual environment and activate it

python3 -m venv dune-env
source dune-env/bin/activate

Then download and build Dune (note that this takes some time to have coffee/tea at hand):

pip install dune-fem

To test that everything works you can download all the scripts described in this tutorial and try them out

python -m dune.fem
cd fem_tutorial
python concepts.py

All examples are available as Python scripts or IPython notebooks - for this jupyter is needed

pip install jupyter
jupyter notebook

This has been tested with different Linux distributions, MacOS, and using the Windows Linux Subsystem.

Note

the current installation requires MPI to be available.

From Source

Note

We strongly encourage the use of a python virtual environment and the following instructions are written assuming that a virtual environment is activated.

Requirements

The following dependencies are needed for Dune-Fem python binding:

Building the Required Dune Modules

Read the instructions on how to build Dune with Python support which also links to general instructions on how to build Dune modules.

Test your completed installation by opening a Python terminal and running

import math
from dune.grid import structuredGrid
from dune.fem.function import gridFunction
grid = structuredGrid([0,0],[1,1],[10,10])
@gridFunction(grid,name="test",order=2)
def f(x):
   return math.sin(x.two_norm*2*math.pi)
f.plot()

If you have everything set up correctly (and have matplotlib) you should get a colored figure and are hopefully ready to go…

Note

The first time you construct an object of a specific realization of one of the Dune interfaces (e.g. here a structured grid), the just in time compiler needs to be invoked. This can take quite some time - especially for grid realizations. This needs to be done only once so rerunning the above code a second time (even using other parameters in the structuredGrid function) should execute almost instantaniously.

Troubleshooting

  • The compiler version needs to be 7 or later. This can be checked in terminal with

    $ g++ --version
    

    If your version is out of date, you will need to upgrade your system to use Dune

  • It is possible that the python version may be an issue. The scripts require python3 including the development package being installed. If during the Dune installation you get the error

    fatal error: pyconfig.h: No such file or directory
    

    This can probably be fixed by installing additional python3.5 libraries with e.g.

    $ sudo apt-get install libpython3-dev
    
  • One other problem is that a default version of Open MPI may already be installed. This will lead to errors where Dune appears to be looking in the wrong directory for Open MPI (e.g. usr/lib/openmpi instead of the home directory where the script installs it). This can be solved by running

    $ make uninstall
    

    in the original MPI install directory, followed by removing the folder. It will then be necessary to reinstall Open MPI and Dune. It may also be necessary to direct mpi4py to the new MPI installation. It is possible to check whether this is a problem by running python and trying out

    from mpi4py import MPI
    

    If it comes up with an error, this can be fixed by installing mpi4py manually using the following commands

    $ git clone https://bitbucket.org/mpi4py/mpi4py.git
    $ cd mpi4py
    $ python setup.py build --mpicc=/path/to/openmpi/bin/mpicc
    $ python setup.py install --user
    
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