pymor 0.2.1

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pyMOR is a software library developed at the University of Münster for building model order reduction applications with the Python programming language. Its main focus lies on the reduction of parameterized partial differential equations using the reduced basis method. All algorithms in pyMOR are formulated in terms of abstract interfaces for seamless integration with external high-dimensional PDE-solver. Moreover, pure Python implementations of finite element and finite volume discretizations using the NumPy/SciPy scientific computing stack are provided for getting started quickly.

NOTE pyMOR is still in early development. Should you have any questions regarding pyMOR or wish to contribute, do not hesitate to contact us!

[Build Status]

License

Copyright (c) 2013, 2014, Rene Milk, Stephan Rave, Felix Schindler All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Distribution Packages

Packages for Ubuntu 12.04 and 13.10 are available via our PPA:

sudo apt-add-repository ppa:pymor/stable sudo apt-get update sudo apt-get install python-pymor

Demo applications and documentation are packaged separately:

sudo apt-get install python-pymor-demos sudo apt-get install python-pymor-doc

The latter makes a pymor-demo script available, which can be used to run all installed demos.

Installation into a virtualenv

When installing pyMOR manually, we recommend installation into a dedicated Python virtualenv. On Debian based systems, install virtualenv using

sudo apt-get install python-virtualenv

On Ubuntu systems, you may also wish to install pyMOR’s dependencies system-wide using

sudo apt-add-repository ppa:pymor/stable sudo apt-get update sudo apt-get build-dep python-pymor

Then create a new virtualenv and activate it:

virtualenv –system-site-packages $PATH_TO_VIRTUALENV source $PATH_TO_VIRTUALENV/bin/activate

The –system-site-packages flag makes Python packages installed by your distribution available inside the virtualenv. If you do not wish this behaviour, simply remove the flag.

On older distributions you will have to upgrade the distribute package. Moreover, if NumPy and Cython are not already available in the virtualenv, we will have to install them manually. (Automatic dependency resolution via pip fails for these packages. To build NumPy and, later, SciPy, you will need to have Fortran as well as BLAS and LAPACK headers installed on your system.)

pip install –upgrade distribute pip install cython pip install numpy

Finally install pyMOR itself with all missing dependencies:

pip install pymor

The installation script might recommend the installation of additional packages. (This is easy to miss, as pip will install dependencies after pyMOR itself has been installed, so search at the top of your console log!) You will most likely want to install IPython and, in particular, matplotlib, PyOpenGL, glumpy, and PySide. The latter packages are required for pyMOR’s visualization routines. At the time of writing, PySide fails to install with current Sphinx versions, so we have to install an old one:

pip install “sphinx==1.1.3” pip install ipython pyside matplotlib pyopengl glumpy

Documentation

Documentation is available online at Read the Docs or offline in the python-pymor-doc package.

To build the documentation yourself, execute

make doc

inside the root directory of the pyMOR source tree. This will generate HTML documentation in docs/_build/html.

Setting up an Environment for pyMOR Development

If you want to modify (or extend!) pyMOR itself, we recommend to setup a virtualenv for development (see above). The virtualenv should have all dependencies of pyMOR available. On Ubuntu machines, you can simply install pyMOR from our PPA and then create an empty virtualenv with system site-packages enabled. Otherwise, follow the above instructions for installing pyMOR inside a virtualenv. However, pyMOR itself should not be installed inside the virtualenv. If it is, use

pip uninstall pymor

to remove it. Then, clone the pyMOR git repository using

git clone https://github.com/pymor/pymor $PYMOR_SOURCE_DIR cd $PYMOR_SOURCE_DIR

and, optionally, switch to the branch you are interested in, e.g.

git checkout 0.2.x

Finally add pyMOR to the path of your virtualenv:

echo “$PYMOR_SOURCE_DIR/src” > $VIRTUAL_ENV/lib/python2.7/site-packages/pymor.pth

This will make pyMOR importable inside the virtualenv and will override any other pyMOR versions installed on the system.

Cython extension modules

pyMOR uses Cython extension modules to speed up numerical algorithms which cannot be efficiently expressed using NumPy idioms. To benefit from these optimizations, the modules’ source files (currently pymor/tools/inplace.pyx and pymor/tools/realations.pyx) have to be processed by Cython into a .c-file which then must be compiled into a shared object. These .so-files then take precedence over the non-optimized pure python modules. The whole build process is handeled automatically by setup.py.

If you want to develop Cython extensions modules for pyMOR yourself, you should add your module to the ext_modules list defined in the _setup method of setup.py. Calling

python setup.py build_ext –inplace

will then build the extension module and place it into your pyMOR source tree.

Tests

pyMOR uses pytest for unit testing. To run the test suite, simply execute make test in the base directory of the pyMOR repository. This will also create a test coverage report which can be found in the htmlcov directory. Alternatively, you can run make full-test which will also enable pyflakes and pep8 checks.

All tests are contained within the src/pymortests directory and can be run individually by executing py.test src/pymortests/the_module.py.

Contact

Should you have any questions regarding pyMOR or wish to contribute, do not hestitate to contact us via our development mailing list:

http://listserv.uni-muenster.de/mailman/listinfo/pymor-dev