pymor 0.5.1

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pyMOR - Model Order Reduction with Python

pyMOR is a software library for building model order reduction applications with the Python programming language. Implemented algorithms include reduced basis methods for parametric linear and non-linear problems, as well as system-theoretic methods such as balanced truncation or IRKA. All algorithms in pyMOR are formulated in terms of abstract interfaces for seamless integration with external PDE solver packages. Moreover, pure Python implementations of finite element and finite volume discretizations using the NumPy/SciPy scientific computing stack are provided for getting started quickly.

License

Copyright 2013-2018 pyMOR developers and contributors. 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.

The following files contain source code originating from other open source software projects:

• docs/source/pymordocstring.py (sphinxcontrib-napoleon)
• src/pymor/algorithms/genericsolvers.py (SciPy)

See these files for more information.

Citing

If you use pyMOR for academic work, please consider citing our publication:

R. Milk, S. Rave, F. Schindler
pyMOR - Generic Algorithms and Interfaces for Model Order Reduction
SIAM J. Sci. Comput., 38(5), pp. S194-S216

Installation via pip

We recommend installation of pyMOR in a virtual environment.

pyMOR can easily be installed with the pip command:

pip install --upgrade pip  # make sure that pip is reasonably new
pip install pymor[full]

This will install the latest release of pyMOR on your system with most optional dependencies. For Linux we provide binary wheels, so no further system packages should be required. Use

pip install pymor

for an installation with minimal dependencies. There are some optional packages not included with pymor[full] because they need additional setup on your system:

# for support of MPI distributed models and parallelization of
# greedy algorithms (requires MPI development headers and a C compiler)
pip install mpi4py

# dense matrix equation solver for system-theoretic MOR methods,
# required for H-infinity norm calculation (requires OpenBLAS headers and a Fortran compiler)
pip install slycot

# sparse matrix equation solver for system-theoretic MOR methods
# (other backends available)
open https://www.mpi-magdeburg.mpg.de/projects/mess
# download and install pymess wheel for your architecture

If you are not operating in a virtual environment, you can pass the optional --user argument to pip. pyMOR will then only be installed for your local user, not requiring administrator privileges.

To install the latest development version of pyMOR, execute

pip install git+https://github.com/pymor/pymor#egg=pymor[full]

which will require that the git version control system is installed on your system.

From time to time, the master branch of pyMOR undergoes major changes and things might break (this is usually announced on our mailing list), so you might prefer to install pyMOR from the current release branch:

pip install git+https://github.com/pymor/pymor@0.5.x#egg=pymor[full]

Release branches will always stay stable and will only receive bugfix commits after the corresponding release has been made.

Documentation

Documentation is available online at Read the Docs or you can build it yourself from inside the root directory of the pyMOR source tree by executing:

make doc

This will generate HTML documentation in docs/_build/html.

External PDE solvers

pyMOR has been designed with easy integration of external PDE solvers in mind.

A basic approach is to use the solver only to generate high-dimensional system matrices which are then read by pyMOR from disk (pymor.discretizers.disk). Another possibility is to steer the solver via an appropriate network protocol.

Whenever possible, we recommend to recompile the solver as a Python extension module which gives pyMOR direct access to the solver without any communication overhead. A basic example using pybindgen can be found in src/pymordemos/minimal_cpp_demo. A more elaborate nonlinear example using Boost.Python can be found here. Moreover, we provide bindings for the following solver libraries:

• FEniCS

  MPI-compatible wrapper classes for dolfin linear algebra data structures are shipped with pyMOR (pymor.bindings.fenics). For an example see pymordemos.thermalbock, pymordemos.thermalblock_simple.

• deal.II

  Python bindings and pyMOR wrapper classes can be found here.

• NGSolve

  Wrapper classes for the NGSolve finite element library are shipped with pyMOR (pymor.bindings.ngsolve). For an example see pymordemos.thermalblock_simple.

Do not hesitate to contact us if you need help with the integration of your PDE solver.

Setting up an Environment for pyMOR Development

If you already installed a pyMOR release version, please uninstall it

pip uninstall pyMOR

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 0.5.x

Then, make an editable installation of pyMOR with

pip install -e .

and pull in all optional dependencies by using

pip install -r requirements-optional.txt

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