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Installation

hIPPYlib-MUQ builds on hIPPYlib version 3.1.0 with FEniCS version 2019.1 and MUQ version 0.4.0. Installations of these packages are summarized here, but please see the detailed installation guides given in each github/bitbucket page.

Additional dependencies are

  • jupyter, matplotlib (for tutorial notebooks)
  • seaborn, statsmodels (for postprocessing)

Docker

We highly recommend to use our prebuilt Docker image, which is the easiest way to run hIPPYlib-MUQ. The docker image with the installation of all the dependencies is available here.

With Docker installed on your system, type:

docker run -ti --rm ktkimyu/hippylib2muq

Then, hIPPYlib-MUQ is available within the generated Docker container.

If you want to run hIPPYlib-MUQ using interactive notebooks, please type

docker run -ti --rm -p 8888:8888 ktkimyu/hippylib2muq 'jupyter-notebook --ip=0.0.0.0'

The notebook will be available at the following address in your web-browser. If you want to mount your local directory on docker container, add it with -v options, e.g., to mount your current directory on /home/fenics/shared/ in docker container, type

docker run -ti --rm -v $(pwd):/home/fenics/shared \
           -p 8888:8888 ktkimyu/hippylib2muq 'jupyter-notebook --ip=0.0.0.0'

Conda

Conda is also a very convenient way to set up an enviroment to use hIPPYlib-MUQ. The script below builds a conda enviroment with FEniCS 2019 and MUQ. hIPPYlib 3.1.0 is also downloaded and installed via pip.

conda create -q -n hippylib2muq -c conda-forge fenics==2019.1.0 muq seaborn statsmodels
conda activate hippylib2muq
git clone --depth 1 --branch 3.1.0 https://github.com/hippylib/hippylib.git
python hippylib/setup.py install

Installation of MUQ from source codes (Expert user/MUQ developers)

This requires cmake, the GNU Compiler Collection or Clang, and pybind11. On macOS, you can have these by installing Xcode Command Line Tools.

To compile and install MUQ, type

git clone https://bitbucket.org/mituq/muq2
cd muq2/build
cmake -DCMAKE_INSTALL_PREFIX=/your/muq2/install/directory -DMUQ_USE_PYTHON=ON ..
make
make install

Then Python static libraries are generated in /your/muq2/install/directory/lib folder.

You may append the path to this library folder, for example,

export PYTHONPATH=/your/muq2/install/directory/python:$PYTHONPATH

Build the hIPPYlib-MUQ documentation using Sphinx

You can build the documentation on your local machine by using sphinx (tested on version 2.3.0). Additional required packages are

  • m2r
  • sphinx_rtd_theme (current HTML theme)

If you want to use other HTML themes, install the corresponding package and modify the following line in conf.py in doc/source folder accordingly:

html_theme = 'name_of_the_theme'

All the packages above can be installed via pip or conda.

Once the required packages are installed, run make html from doc folder to build the documentation, then the document is available at doc/build/html/.