Dune 2.4.1

Download the Dune 2.4.1 module sources

DUNE 2.4.1 - Release Notes

DUNE 2.4.1 is mostly a bug fix release, but as DUNE 3.0.0 is still pretty far out, this release also contains a number of smaller new features and improvements. The following list of backported features and bug fixes is not exhaustive, for a complete list see the backport-tracking bugs for dune-common, dune-geometry, dune-grid, dune-istl and dune-localfunctions.

Release History

2.4.1

  • Fix Doxygen generation during make install when using CMake without a Doxylocal file.
  • Fix for using Scotch on Debian when using custom index type and static libraries.
  • Support for basis functions that are only bi-orthogonal on the faces for dualmortarbasis in dune-localfunctions.
  • Some small fixes to tarball generation.

2.4.1-rc2

  • Fix broken version signatures and tarball names in RC1.

2.4.1-rc1

  • Initial release.

Dependencies

In order to build this version of DUNE you need at least the following software:

  • CMake (>=2.8.6), preferably (>=2.8.12)
  • pkg-config
  • a standard compliant C++ compiler, tested are g++ (>=4.4) and Clang (>=3.4); recent versions of ICC (>= 15) should work, older versions like 14.0.3 needs patching of system headers and is discouraged

Build System

  • The CMake build system will now enable C++14 by default if your compiler supports it. You can change this by passing -DCXX_MAX_STANDARD=11 to CMake. Allowed values for this variable are currently 11, 14, 17. If you bypass the automatic C++ support detection with -DDISABLE_CXX_VERSION_CHECK, you need to tell the build system about the maximum supported C++ standard of your compiler by adding -DCXX_MAX_SUPPORTED_STANDARD=version to your CMake configuration, where version should be one of 11, 14, 17.
  • The CMake build system has a new function dune_require_cxx_standard(MODULE "name" VERSION version) that you can call in your own module if it needs a newer C++ standard than C++11. Valid values for the version version are 11, 14, 17.
  • UMFPack detection now uses a backported version of the new SuiteSparse test from the current master branch, which should work much more reliably for newer versions of SuiteSparse and UMFPACK.
  • The CMake build system now supports third-party grids for the Grid Type magic mechanism.
  • A larger number of dunecontrol subcommands now skip the version check, leading to faster run times and less spurious error messages.
  • The autotools build system should no longer fail when it cannot find a Fortran compiler.

dune-common

  • The DebugAllocator now works on OS X.
  • Reduced the number of warnings when using recent version versions of OpenMPI.

dune-geometry

  • GlobalGeometryTypeIndex now exports the per-dimension index offset via the static member function offset(std::size_t dim). This method is constexpr and can thus be used in compile-time context.

dune-grid

  • PartitionSet is now comparable.
  • New printGrid() function for visualizing topology and index structure of 2D grids.
  • The GmshWriter can now write out physical entities.
  • The VTKWriter now supports dune-functions style local functions.
  • The VTKSequenceWriter can now be constructed from a VTKWriter instead of a GridView, which is useful for dune-functions and makes the SubsamplingVTKSequenceWriter obsolete.
  • IntersectionIterator now complies to the forward iterator interface, which makes it more consistent with EntityIterator.

Bug Fixes

  • Replaced EntityPointer with Entity in a number of places.
  • Fixed a number of problems with very small parallel YaspGrid instances.
  • Tests for the deprecated ALUGrid 1.52 bindings compile again.
  • Added missing insertionIndex() for UG leaf intersections.
  • ParMetisGridPartitioner now works with ParMETIS 3.x.
  • Numerous smaller fixes.

dune-istl

  • Make ParMetis idx_t handling a little more robust.
  • Do not require BLAS when building with CMake.
  • The multi type containers now have operator[] implementations for std::integral_constant.
  • DynamicMatrix now supports MatLab output.
  • Numerous smaller fixes for using the solvers with complex-valued problems.

dune-localfunctions

  • Some documentation improvements.

dune-grid-howto

DUNE 2.4 - Release Notes

  • The minimal required compiler are GCC 4.4 (GCC 4.7 on OSX, see this bug) and Clang 3.4. We try to stay compatible to ICC 15, and newer. Older versions of Clang might work, ICC 14.0.3 needs patches to systems headers.

buildsystem

  • The default buildsystem has been switched from Autotools to CMake. For Dune 2.4 you can use Autotools by adding --no-cmake to dunecontrol. (see our CMake documentation, this bug).
  • If MPI is found, the build is parallel. It is no longer necessary to explicitly enable its support. It can still be disabled by passing -DCMAKE_DISABLE_FIND_PACKAGE_MPI=TRUE for CMake and --disable-parallel for Autotools.
  • Some convenience macros for automatically copying or symlinking files from the source tree to the build tree are provided in dune-common/cmake/modules/DuneSymlinkOrCopy.cmake
  • With CMake headercheck is disabled by default as it creates a host of files in the build directory. You can re-enable it by adding -DENABLE_HEADERCHECK=1 to the CMake flags.

Deprecated and removed features

  • The use of Autotools is deprecated and will be removed after Dune 2.4. Use CMake instead.
  • The macros HAVE_DUNE_HASH, HAVE_INTEGRAL_CONSTANT, HAVE_RVALUE_REFERENCES, HAVE_STD_HASH, HAVE_TYPE_TRAITS, HAVE_VARIADIC_CONSTRUCTOR_SFINAE and, HAVE_VARIADIC_TEMPLATES, defined in config.hh, are deprecated and will be removed after Dune 2.4. This applies to various HAVE_TR1_*, too. The variables are always true for the minimal required compiler versions.

dune-common

  • dune-common now provides a (simple) implementation of bash-completion for the dunecontrol command.
  • FieldMatrix and FieldVector now offer construction from initializer lists.
  • CollectiveCommunication is now default-constructible.
  • Objects of type DiagonalMatrix can now be constructed from initializer_lists.

Deprecated and removed features

  • The class SelectType (from typetraits.hh), deprecated in Dune 2.3, has been removed. Use conditional instead.
  • The deprecated file misc.hh has been removed. Most math-related stuff has moved to math.hh. The two methods hasPrefix and hasSuffix are now in the new header stringutility.hh. The methods SQR and genFilename disappear with no replacement.
  • Support for very old MPI implementations, specifically implementations without support for the MPI-2.1 standard, has been removed. It was deprecated in Dune 2.3. This should affect very few users because all common MPI packages have been compatible with that standard since 2009.
  • Support for compilers that lack std::thread. Thread support is needed to implement a thread-safe quadrature rule cache, see this bug. All compilers officially supported by dune have std::thread. Note however that support on OS X for GCC < 4.7 was dropped because of the lacking support for std::thread.

dune-geometry

  • The quadrature rule cache QuadratureRules is now thread safe, see this bug.
  • There are new types Codim<cd> and Dim<d> that can be used to encapsulate a (co)dimension. They inherit from std::integral_constant<int> and are useful when an interface should accept both a dimension and a codimension.

Deprecated and removed features

  • The 1d quadrature rules Gauss, Jacobian_1_0, and Jacobian_2_0 have been removed. Please use the rules GaussLegendre, GaussJacobi_1_0, and GaussJacobi_2_0.
  • The class QuadraturePoint does not export the variable d and the type CoordType anymore. Please use dimension and Field instead.
  • The methods global, mapping, volumeOuterNormal, and initializeTopology have been removed from the ReferenceElement class.
  • The methods ReferenceElement::global have been removed; use ReferenceElement::geometry<codim>(i).global instead. The non-interface method ReferenceElement::mapping, which is superseded by the geometry method, has been deprecated, too.
  • The classes GenericReferenceElement* were renamed as ReferenceElement* in Dune 2.3. The old, deprecated names have been removed.
  • The class MockGeometry, deprecated in Dune 2.3, has been removed. In most cases, replacing it by MultiLinearGeometry and adapting the includes will do.
  • The header genericgeometry/geometry.hh and its containing classes Geometry, GenericGeometry, and LocalGeometry, which were all deprecated in Dune 2.3, have been removed.

dune-grid

  • The minimum required version of UG is now UG-3.11.0. Note that you need a bugfix provided by UG-3.11.1 if you want to build UG on your own with Clang.
  • UGGrid now allows to do load balancing with the element partitioning being provided by third-party software. There is no restriction on what software to use here. All you need to do is to set up a std::vector which for each element contains the rank where this element is supposed to be sent to. Everything else happens automatically.
  • The results of Geometry::jacobianTransposed and Geometry::jacobianInverseTransposed are now returned by value rather than by reference. The result types are guaranteed to be copyable and assignable. In the unlikely event that you store references or pointers to these returned values, this change might break your code without a word of warning.
  • The class Entity<0> has a new method subEntities(uint codim), which returns the number of subentities of the given codimension. It has the same functionality as the method count, but the codim argument of the new method is normal parameter, rather than a template parameter. Also, we believe that the new name is more telling. The count method is deprecated.
  • IdentityGrid has been moved from dune-grid-dev-howto to dune-grid.
  • Support for the external Grid Alberta older then the current release 3 has been abandoned without deprecation.
  • The mapper classes SingleCodimSingleGeometryMapper and MultipleCodimMultipleGeometryMapper now use the number type used by the grid index set to return indices. Previously, int was hard-wired.
  • It is now possible to use C++11 range-based for loops to iterate over entities and intersections. See the new section Iterating over grid entities and intersections in the Doxygen documentation for further details. This feature is not available on all supported compilers, it requires GCC 4.6 or greater (or another compiler that supports range-based for loops).
  • All iterators over entities are now forward iterators in the sense of the standard library. In particular, they can now be default-constructed and postfix-incremented, which wasn’t possible previously. The usual caveat concerning postfix increments applies: postfix incrementing may be noticeably slower than prefix incrementing.
  • The various Mapper classes in dune/grid/common now have methods index and subIndex, which do the same thing as the map methods. With this renaming the Mapper interface is more consistent with the conceptually similar IndexSet interface. The old map methods are still there, but they are marked as deprecated and will be removed after the 2.4 release.
  • There is a new method types on index sets that returns an iterator range visiting all geometry types of a given codimension contained in the domain of the index set. Its type is implementation defined and exported as typedef Types.
  • A new helper class ParMetisGridPartitioner allows to use ParMetis to compute partitionings for arbitrary Dune grids. Currently, UGGrid can handle such partitionings.
  • Entities can now be compared with each other.
  • TensorGridFactory, a factory class for tensor product grids can be found in dune/grid/utility/tensorgridfactory.hh. It is implemented through the GridFactory for all unstructured grids and has a specialization for YaspGrid. The factory class provides a multitude methods to fill coordinate ranges. Check the doxygen documentation for details.

Copyable entities and intersections

Entitys and Intersections can now be copied and default-constructed. This will allow us to remove the EntityPointer, which has been deprecated in DUNE 2.4. User-visible changes include:

  • Most obviously: Instead of storing an EntityPointer or an IntersectionIterator, it is now possible to directly store a copy of an Entity or an Intersection.
  • Iterators are now allowed to return temporary Entity or Intersection objects instead of references. Code that captures the result in a const reference will still work in both cases, because the life time of the temporary is bound to this reference. Important interface change: Code that forwards such references may fail due to dangling references. In order to avoid this you can forward with the correct return type using decltype(*it). I.e. you have to change const Entity& foo(const Iterator& it) { return *it;} to auto foo(const Iterator& it) -> decltype(*it) { return *it;} .
  • Important: Keep in mind that Entity and Intersection objects are expensive. Don’t try to store lots of them! If you need to keep around a list of entities, use EntitySeed instead.
  • All interface methods that used to return an EntityPointer now return an Entity instead. This change applies to the following methods:
    • Entity::father() for entities of codimension 0.
    • Entity::subEntity<codim>() for entities of codimension 0.
    • Intersection::inside()
    • Intersection::outside()
    • Grid::entityPointer(const EntitySeed&). This method has been deprecated, please use the new method Grid::entity(const EntitySeed&) instead, which returns an Entity
  • Entity and EntityPointer have a certain amount of interoperability code to ease the transition. In particular, you can dereference an entity with *entity and call member methods with entity->foo() so that your code works with both grids that have been ported to the new interfaces as well as unported grids. All of the compatibility methods do however raise deprecation warnings.
  • All grid implementations in dune-grid have been ported to the new interface, except for the deprecated bindings for ALUGrid 1.52. If you use ALUGrid, you should switch to the new dune-alugrid module.
  • While ported and unported grids are mostly interoperable, there is one important exception: You cannot use meta grids that use the new interface (like GeometryGrid with host grids that still use the old interface.

YaspGrid

The YaspGrid grid manager has received an important overhaul. Changes include:

  • YaspGrid now has a second template parameter, which specifies how coordinates are stored. This parameter defaults to EquidistantCoordinates<ctype, dim> which mimics the old behavior.
  • As a new feature, YaspGrid now has the capabilities of a tensor-product grid. This can be enabled via the second template parameter TensorProductCoordinates<ctype, dim>. Constructor calls for a tensor-product grid use Dune::array<std::vector<ctype>, dim> as a data structure for the coordinates of the grid.
  • Changing the coordinate type of YaspGrid can now be done by switching the template parameter of the coordinate container.
  • YaspGrid is (again) working for arbitrary dimension.
  • YaspGrid implements entities of arbitrary codimension and can communication on these entities. With this addition, YaspGrid fulfills all requirements of a DUNE grid (as decided upon in Aachen 2013).
  • You can obtain an equidistant YaspGrid with non-trivial origin by using EquidistantOffsetCoordinates<ctype, dim> as the second template parameter. This feature can also be used through StructuredGridFactory
  • There are only three constructors for a Yaspgrid: One for equidistant grids, one for equidistant grids with non-trivial origin and one for tensorproduct grids. All other constructors are either deprecated or can still be used due to proper default values on the new constructors.
  • YaspGrid now makes consequent use of CollectiveCommunication. As these classes have just been made default-constructible, the communicator parameter can usually be omitted on the constructor call.
  • A BackupRestoreFacility for YaspGrid is implemented in the header <dune/grid/yaspgrid/backuprestore.hh>. Equidistant grids write a single file for all processes, tensorproduct grids write one file per processor, that only contains the coordinate range relevant to that processor. The output format is a self-defined ascii format which is readable by the human eye.
  • All partitioning code is now located in dune/grid/yaspgrid/partitioning.hh. Note that if you previously implemented your own partitioner, you need to update its signature to use std::array<int, dim> instead of Dune::FieldVector<int, dim>. YaspFixedSizePartitioner is a new implementation of a partitioner with a predefined number of processors per direction.
  • YaspGrid now provides a native implementation of PersistentContainer.

Deprecated and removed features

  • The SGrid grid manager has been marked as deprecated, and will be removed after the 2.4 release. YaspGrid now supports all features of SGrid, so there is no reason left to have two structured grid managers in dune-grid. To suppress the SGrid deprecation warning define the macro DUNE_AVOID_SGRID_DEPRE_WARNING_BECAUSE_I_KNOW_WHAT_IM_DOING.
  • The class Geometry does not export the type Jacobian anymore. Please use the type JacobianInverseTransposed instead.
  • The class Entity does not export the type ctype anymore. Please use the type Entity::Geometry::ctype instead.
  • The class Entity does not export the number dimensionworld anymore. Please use Entity::Geometry::dimensionworld instead.
  • The methods EntityIterator::level and EntityPointer::level have been deprecated. To obtain the level of an entity pointed to by an iterator or EntityPointer, please dereference the iterator/pointer and call the method level on the entity directly.
  • The class EntityPointer does not export codim anymore. Please use the type codimension instead (see this bug).
  • The method Entity<0>::count<codim> is deprecated. Please use Entity<0>::subEntities(uint codim) instead.
  • The values Geometry::dimension and Geometry::dimensionworld are deprecated, and will be removed after the release of dune-grid-2.4.
  • The constructors of YaspGrid, that take a communicator as its first argument are deprecated. Please use the new constructors instead. The old ones will be removed after the release of dune-grid-2.4.
  • The capability class Dune::Capabilities<GridType>::isParallel is deprecated because its meaning was never well-defined. It will be removed after the 2.4 release. To suppress the deprecation warning define the macro DUNE_AVOID_CAPABILITIES_IS_PARALLEL_DEPRECATION_WARNING.
  • The map methods on mappers are deprecated and will be removed after the 2.4 release. They are replaced by the index and subIndex method (see above).
  • The method geomTypes on index sets is deprecated and will be removed after the 2.4 release. It is replaced by the new types method (see above).
  • The methods lbegin, lend, leafbegin, and leafend on grids are deprecated and will be removed after the 2.4 release. Use instead the methods begin and end from the grid’s level and leaf grid view.
  • The EntityPointer is deprecated and will be removed after the 2.4 release. Instead, it is now possible to store and copy entities directly. All interface methods that used to return an EntityPointer now return an Entity instead. In order to ease the transition, entities can be used like an EntityPointer, but doing so will also raise deprecation warnings.
  • In line with the EntityPointer removal, the method entityPointer(const EntitySeed&) on grids has been deprecated. Please use the new method entity(const EntitySeed&) instead, which returns an Entity.
  • Comparisons between different types of entity iterators (level vs. leaf) and EntityPointer have been deprecated. Those kinds of comparisons should be replaced by comparisons between the entities pointed at by the iterators, so leaf_it == level_it becomes *leaf_it == *level_it. Iterators of a single type can of course still be compared with each other.
  • Support for Grape has been deprecated and will be removed after the 2.4 release. Use the Dune module dune-grape instead.

Changes for maintainers of grid implementations

  • All grid implementations not using the DefaultGridView must rename their implementations from leafView / levelView to leafGridView / levelGridView.
  • Grid must be ported to the new copyable entities and intersections. See this How-To for some pointers.
  • Grids are now allowed to return temporary objects from their entity and intersection iterators. This is mostly interesting for meta grid developers, as it allows for a much more straightforward implementation.

dune-istl

Deprecated and removed features

  • The transition header <dune/istl/diagonalmatrix.hh> has been removed. The original header was moved to dune-common in Dune 2.2, use this instead.

dune-localfunctions

  • All LocalFiniteElement classes now have a method size, which returns the number of shape functions of the finite element. This method is for convenience: previously, the localBasis had to be fetched to get the same information.
  • The MonomLocalFiniteElement class has been renamed to MonomialLocalFiniteElement. Correspondingly, its header monom.hh has been renamed to monomial.hh. The old class and header are still there for backward-compatibility.
  • New Raviart-Thomas elements were added but only for interpolation as the Jabobians are missing. The new elements are Raviart-Thomas 3 and 4 for 2d quadrilaterals. Thanks to Jizhou Li.
  • You can now get second derivatives of the shape functions of the Pk2DLocalFiniteElement. Thanks to Elisa Friebel.

Deprecated and removed features

  • The class Q2LocalFiniteElement, deprecated in Dune 2.3 has been removed. Please use the more general QkLocalFiniteElement instead.
  • The class RannacherTurek2DLocalFiniteElement<D, R>, deprecated in Dune 2.3, has been removed. Please use RannacherTurekLocalFiniteElement<D, R, 2> instead.
  • Most of the Raviart-Thomas and Brezzi-Douglas-Marini elements not following the new naming scheme have been removed.

dune-grid-howto

dune-grid-dev-howto

  • The whole module was deprecated with DUNE 2.3 and has been abandoned. IdentityGrid has been moved to dune-grid.

Known Bugs

  • The pseudo inverse used in the generic geometries might fail for nearly singular matrices. This is not really a problem unless the grid is nearly degenerate.
  • The parallel UGGrid may return wrong ids on very complex adaptively refined and load-balanced grids. The reason is that the Dune grid interface mandates that two entities on different levels have the same id if they are copies. Therefore the UGGrid id/subId methods look through the ancestry of a given entity to see if there are copies. However, UG does so-called vertical load-balancing, which means that the ancestry may be distributed across different processors. Since the current code does not take that into account, wrong ids will be returned in the presence of vertical load-balancing. This is a potentially severe issue, because users do not get error messages, only ids that are tacitly wrong.
  • Building shared libraries with CMake might break if you are using external static libraries compiled without support for position independent code (g++ -fpic).
  • Dune-grid fails to build with GCC 4.4 when configured with UGGrid. This is due to an overload resolution failure in GCC 4.4 that is no longer present in newer compilers. (See this bug.)
  • You can only build dune with GCC 4.9 without the -pedantic flag because it will otherwise reject some compatibility code needed to support GCC 4.4. (See this bug.)
  • Dune-istl does not work with METIS 5, see this bug.
  • Dune does not build on debian-ish systems if all the following conditions are satisfied: The system uses GCC 4.9 or newer as default compiler, you are building with GCC 4.8 or below, and you are using MPICH. The reason is this bug which makes mpi propose flags from the newer default compiler also for older compilers where they are not supported.

A list of all bugs can be found online in our bug-tracker http://www.dune-project.org/flyspray/.

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