Release Notes

pyMOR 0.4 (September 28, 2016)

With the pyMOR 0.4 release we have changed the copyright of pyMOR to

Copyright 2013-2016 pyMOR developers and contributors. All rights reserved.

Moreover, we have added a Contribution guideline to help new users with starting to contribute to pyMOR. Over 800 single commits have entered this release. For a full list of changes see here. pyMOR 0.4 contains contributions by Andreas Buhr, Michael Laier, Falk Meyer, Petar Mlinarić and Michael Schaefer. See here for more details.

Release highlights

FEniCS and deal.II support

pyMOR now includes wrapper classes for integrating PDE solvers written with the dolfin library of the FEniCS project. For a usage example, see pymordemos.thermalblock_simple.discretize_fenics. Experimental support for deal.II can be found in the pymor-deal.II repository of the pyMOR GitHub organization.

Parallelization of pyMOR’s reduction algorithms

We have added a parallelization framework to pyMOR which allows parallel execution of reduction algorithms based on a simple WorkerPool interface [#14]. The greedy [#155] and ei_greedy algorithms [#162] have been refactored to utilize this interface. Two WorkerPool implementations are shipped with pyMOR: IPythonPool utilizes the parallel computing features of IPython, allowing parallel algorithm execution in large heterogeneous clusters of computing nodes. MPIPool can be used to benefit from existing MPI-based parallel HPC computing architectures [#161].

Support classes for MPI distributed external PDE solvers

While pyMOR’s VectorArray, Operator and Discretization interfaces are agnostic to the concrete (parallel) implementation of the corresponding objects in the PDE solver, external solvers are often integrated by creating wrapper classes directly corresponding to the solvers data structures. However, when the solver is executed in an MPI distributed context, these wrapper classes will then only correspond to the rank-local data of a distributed VectorArray or Operator.

To facilitate the integration of MPI parallel solvers, we have added MPI helper classes [#163] in pymor.vectorarrays.mpi, pymor.operators.mpi and pymor.discretizations.mpi that allow an automatic wrapping of existing sequential bindings for MPI distributed use. These wrapper classes are based on a simple event loop provided by pymor.tools.mpi, which is used in the interface methods of the wrapper classes to dispatch into MPI distributed execution of the corresponding methods on the underlying MPI distributed objects.

The resulting objects can be used on MPI rank 0 (including interactive Python sessions) without any further changes to pyMOR or the user code. For an example, see pymordemos.thermalblock_simple.discretize_fenics.

New reduction algorithms

  • adaptive_greedy uses adaptive parameter training set refinement according to [HDO11] to prevent overfitting of the reduced model to the training set [#213].
  • reduce_parabolic reduces linear parabolic problems using reduce_generic_rb and assembles an error estimator similar to [GP05], [HO08]. The parabolic_mor demo contains a simple sample application using this reductor [#190].
  • The estimate_image and estimate_image_hierarchical algorithms can be used to find an as small as possible space in which the images of a given list of operators for a given source space are contained for all possible parameters mu. For possible applications, see reduce_residual which now uses estimate_image_hierarchical for Petrov-Galerkin projection of the residual operator [#223].

Copy-on-write semantics for VectorArrays

The copy method of the VectorArray interface is now assumed to have copy-on-write semantics. I.e., the returned VectorArray will contain a reference to the same data as the original array, and the actual data will only be copied when one of the arrays is changed. Both NumpyVectorArray and ListVectorArray have been updated accordingly [#55]. As a main benefit of this approach, immutable objects having a VectorArray as an attribute now can safely create copies of the passed VectorArrays (to ensure the immutability of their state) without having to worry about unnecessarily increased memory consumption.

Improvements to pyMOR’s discretizaion tookit

  • An unstructured triangular Grid is now provided by UnstructuredTriangleGrid. Such a Grid can be obtained using the discretize_gmsh method, which can parse Gmsh output files. Moreover, this method can generate Gmsh input files to create unstructured meshes for an arbitrary PolygonalDomain [#9].
  • Basic support for parabolic problems has been added. The discretize_parabolic_cg and discretize_parabolic_fv methods can be used to build continuous finite element or finite volume Discretizations from a given pymor.analyticalproblems.parabolic.ParabolicProblem. The parabolic demo demonstrates the use of these methods [#189].
  • The pymor.discretizers.disk module contains methods to create stationary and instationary affinely decomposed Discretizations from matrix data files and an .ini file defining the given problem.
  • EllipticProblems can now also contain advection and reaction terms in addition to the diffusion part. discretize_elliptic_cg has been extended accordingly [#211].
  • The continuous Galerkin module has been extended to support Robin boundary conditions [#110].
  • BitmapFunction allows to use grayscale image data as data Functions [#194].
  • For the visualization of time-dependent data, the colorbars can now be rescaled with each new frame [#91].

Caching improvements

  • state id generation is now based on deterministic pickling. In previous version of pyMOR, the state id of immutable objects was computed from the state ids of the parameters passed to the object’s __init__ method. This approach was complicated and error-prone. Instead, we now compute the state id as a hash of a deterministic serialization of the object’s state. While this approach is more robust, it is also slightly more expensive. However, due to the object’s immutability, the state id only has to be computed once, and state ids are now only required for storing results in persistent cache regions (see below). Computing such results will usually be much more expensive than the state id calculation [#106].
  • CacheRegions now have a persistent attribute indicating whether the cache data will be kept between program runs. For persistent cache regions the state id of the object for which the cached method is called has to be computed to obtain a unique persistent id for the given object. For non-persistent regions the object’s uid can be used instead. pymor.core.cache_regions now by default contains 'memory', 'disk' and 'persistent' cache regions [#182], [#121] .
  • defaults can now be marked to not affect state id computation. In previous version of pyMOR, changing any default value caused a change of the state id pyMOR’s defaults dictionary, leading to cache misses. While this in general is desirable, as, for instance, changed linear solver default error tolerances might lead to different solutions for the same Discretization object, it is clear for many I/O related defaults, that these will not affect the outcome of any computation. For these defaults, the defaults decorator now accepts a sid_ignore parameter, to exclude these defaults from state id computation, preventing changes of these defaults causing cache misses [#81].
  • As an alternative to using the @cached decorator, cached_method_call can be used to cache the results of a function call. This is now used in solve to enable parsing of the input parameter before it enters the cache key calculation [#231].

Additional new features

Backward incompatible changes

  • VectorArray implementations have been moved to the pymor.vectorarrays sub-package [#89].

  • The dot method of the VectorArray interface has been split into dot and pairwise_dot [#76].

    The pairwise parameter of dot has been removed, always assuming pairwise == False. The method pairwise_dot corresponds to the pairwise == True case. Similarly the pariwise parameter of the apply2 method of the Operator interface has been removed and a pairwise_apply2 method has been added.

  • almost_equal has been removed from the VectorArray interface [#143].

    As a replacement, the new method pymor.algorithms.basic.almost_equal can be used to compare VectorArrays for almost equality by the norm of their difference.

  • lincomb has been removed from the Operator interface [#83].

    Instead, a LincombOperator should be directly instantiated.

  • Removal of the options parameter of apply_inverse in favor of solver_options attribute [#122].

    The options parameter of OperatorInterface.apply_inverse has been replaced by the solver_options attribute. This attribute controls which fixed (linear) solver options are used when apply_inverse is called. See here <https://github.com/pymor/pymor/pull/184> for more details.

  • Renaming of reductors for coercive problems [#224].

    pymor.reductors.linear.reduce_stationary_affine_linear and pymor.reductors.stationary.reduce_stationary_coercive have been renamed to pymor.reductors.coercive.reduce_coercive and pymor.reductors.coercive.reduce_coercive_simple. The old names are deprecated and will be removed in pyMOR 0.5.

  • Non-parametric objects have now parameter_type {} instead of None [#84].

  • Sampling methods of ParameterSpaces now return iterables instead of iterators [#108].

  • Caching of solve is now disabled by default [#178].

    Caching of solve must now be explicitly enabled by using pymor.core.cache.CacheableInterface.enable_caching.

  • The default value for extension_algorithm parameter of greedy has been removed [#82].

  • Changes to ei_greedy [#159], [#160].

    The default for the projection parameter has been changed from 'orthogonal' to 'ei' to let the default algorithm agree with literature. In addition a copy parameter with default True has been added. When copy is True, the input data is copied before executing the algorithm, ensuring, that the original VectorArray is left unchanged. When possible, copy should be set to False in order to reduce memory consumption.

  • The copy parameter of pymor.algorithms.gram_schmidt.gram_schmidt now defaults to True [#123].

  • with_ has been moved from BasicInterface to ImmutableInterface [#154].

  • BasicInterface.add_attributes has been removed [#158].

  • Auto-generated names no longer contain the uid [#198].

    The auto-generated name of pyMOR objects no longer contains their uid. Instead, the name is now simply set to the class name.

  • Python fallbacks to Cython functions have been removed [#145].

    In order to use pyMOR’s discretization toolkit, building of the _unstructured, inplace, relations Cython extension modules is now required.

pyMOR 0.3 (March 2, 2015)

  • Introduction of the vector space concept for even simpler integration with external solvers.
  • Addition of a generic Newton algorithm.
  • Support for Jacobian evaluation of empirically interpolated operators.
  • Greatly improved performance of the EI-Greedy algorithm. Addition of the DEIM algorithm.
  • A new algorithm for residual operator projection and a new, numerically stable a posteriori error estimator for stationary coercive problems based on this algorithm. (cf. A. Buhr, C. Engwer, M. Ohlberger, S. Rave, ‘A numerically stable a posteriori error estimator for reduced basis approximations of elliptic equations’, proceedings of WCCM 2014, Barcelona, 2014.)
  • A new, easy to use mechanism for setting and accessing default values.
  • Serialization via the pickle module is now possible for each class in pyMOR. (See the new ‘analyze_pickle’ demo.)
  • Addition of generic iterative linear solvers which can be used in conjunction with any operator satisfying pyMOR’s operator interface. Support for least squares solvers and PyAMG (http://www.pyamg.org/).
  • An improved SQLite-based cache backend.
  • Improvements to the built-in discretizations: support for bilinear finite elements and addition of a finite volume diffusion operator.
  • Test coverage has been raised from 46% to 75%.

Over 500 single commits have entered this release. A full list of all changes can be obtained under the following address: https://github.com/pymor/pymor/compare/0.2.2...0.3.0