onera / comma

Geometric agglomerator for unstructured grids

CoMMA (COarse Mesh Multigrid Agglomerator)

CoMMA is a suite of graph algorithms meant to operate on the graph representation of an unstructured computational mesh.

📐 Capabilities

The main features of CoMMA are:

• Support for any mesh (2- or 3D, polyhedral,...);
• Minimal knowledge of the mesh, only its graph representation;
• Sequential by zone (i.e. no coupling with graph partitioner);
• Optimization of the shape of the coarse cells w.r.t. their aspect ratio;
• Detection and treatment of anisotropic regions;
• Isotropic agglomeration with structured-like treatment of structured-like regions;
• Fine faces conservation for coarse levels;
• Connectivity of coarse cells.

📜 License

CoMMA is distributed under Mozilla Public License Version 2.0. It has been registered (more precisely, version 1.3) to the Agency for the Protection of Programs (APP), Paris, with IDDN identification number IDDN.FR.001.420013.000.S.X.2023.000.31235.

🔧 Building the library

CoMMA uses C++17 standards, hence a fairly recent compiler is needed, for instance, GNU > 8.1.9. For the configuration and building steps, it relies on cmake (>= 3.15).

CoMMA is a C++ header-only library hence it does not need compilation, per se, however a configuration step is necessary. A python module can be generated using pybind11: this is very convenient for testing and debugging purposes. Some tests relying on Catch2 have been written to check the soundness of CoMMA (for more details see the dedicated section below). In order to work, cmake should find pybind11 and Catch2 in the path, see below some tips on how to achieve this.

Both the python module and the tests need compilation. Finally, one can install the headers and, when applies, the python module in a given directory.

The pivotal part of the configuration step is the choice of the types used by CoMMA: one for indices (e.g., cell IDs), one for standard integers (e.g., cardinality of the coarse cells), and one for reals (e.g., graph weights). They can be chosen with configuration options, respectively, INDEX_T, INT_T, and REAL_T. If not set, the default values are, respectively, unsigned long, int, and double.

A typical flow for the configuration and installation of CoMMA usually relies on a standard out-of-source build and look like this:

cd path/to/CoMMA
mkdir build install
cd build
cmake -DINDEX_T="int" -DINT_T="int" -DREAL_T="double" -DCMAKE_INSTALL_PREFIX=../install ..
make
make install

Instead of -DCMAKE_INSTALL_PREFIX=, one could have used --install-prefix, although this later only accepts absolute paths.

If one wants to use CoMMA in their code, it is important to perform the installation step: indeed, during configuration an important header (including the type definitions) is generated and then added to the other headers during the installation phase. If one tries to build using only the files in the include directory, the additional configuration header won't be found and the process will fail.

The compilation of the tests and the generation of the python bindings are activated by default, but they can be switched off

cmake -DBUILD_TESTS=Off .. # No tests
cmake -DBUILD_PYTHON_BINDINGS=Off .. # No python bindings

An additional cmake option might be passed to build the tests with coverage support (default is off), in this case, the gcov library is needed:

cmake -DCOVERAGE=On ..

Support for pkg-config can be enabled by passing the related option to cmake:

cmake -DPKGCONFIG_SUPPORT=On -DCMAKE_INSTALL_PREFIX=../install ..

A template of such configuration file can be found in the repository; given the prefix provided in the example above, it will be installed in path/to/CoMMA/install/lib64/pkgconfig.

An option is available to use the flags usually considered when compiling the CODA-CFD library:

cmake -DCODAFLAGS=On ..

In order for CoMMA to be compatible with spack package manager, a configuration file and some patches are given in config_files/spack/comma. The spack configuration supports almost the same variants that cmake uses, e.g., +python, +doc, +pkgconfig, codaflags. They only two differences is that coverage option is not available, and the type choices are more limited. Indeed, one use 64 bit integer with +int64, otherwise 32 bit; and double reals with +real64, otherwise float.

🔗 Dependencies

If compiling CoMMA with tests, one needs to get Catch2. Being based on cmake, the flow is similar to CoMMA one:

git clone https://github.com/catchorg/Catch2
cd Catch2
mkdir build
cd build
cmake --install-prefix /path/to/Catch2/install ..
make -j4
make install

Once that is finished, in order for CoMMA to see Catch2, add the install directory to cmake path:

export CMAKE_PREFIX_PATH=/path/to/Catch2/install:$CMAKE_PREFIX_PATH

In order to get a python module of CoMMA, one has to compile it relying on pybind11. The easiest way to obtain it is to install it via pip (notice that we select the user installation, --user):

python3 -m pip --user pybind11

For cmake to find pybind one then has to give it the right path. Typically, assuming one has used the command above and was using python3.10, that is done by updating cmake path:

export CMAKE_PREFIX_PATH=${HOME}/.local/lib/python3.10/site-packages/pybind11:$CMAKE_PREFIX_PATH

The CLI utility pybind11-config, automatically installed with pybind, can help identifying the right path.

👷 Usage

CoMMA provides a namespace with the same name, but in lowercase: comma. Its interface is very simple and consists in only one function, comma::agglomerate_one_level. This functions needs several arguments: some define the graph representation of the mesh (e.g., connectivities, weights) in Compressed Row Storage (CRS) format; others set the parametrization of the coarsening algorithm (e.g., anisotropy, goal cardinality of the coarse cells); others are modified by CoMMA to store the results. No special classes or containers are needed since CoMMA itself relies on containers of the standard library. CoMMA does have some custom types though, which, as seen above, are chosen during the configuration phase. For more details, about the arguments, the reader is referred to the Doxygen page of the function and section 2 of the user manual.

A typical C++ file using CoMMA will look like the following:

#include <vector>

#include "CoMMA/CoMMA.h"

// Graph representation
std::vector<comma::CoMMAIndexT> graph_CRS_rows, graph_CRS_cols;
std::vector<comma::CoMMAWeightT> graph_CRS_weights;
// ...

// Algorithm parametrization
comma::CoMMAIntT min_card, goal_card, max_card;
// ...

// Output storage
std::vector<comma::CoMMAIndexT> fc2cc;
// ...

// Agglomerate
comma::agglomerate_one_level(
  // ...args...
)

📖 Documentation

CoMMA is documented via doxygen. If you have it and wish to have the full documentation, just run from the main directory:

doxygen Documentation/Doxyfile

and related html pages will be built in documentation. Otherwise, the documentation can be activated during the configuration phase of the compilation, then built and installed:

cmake -DBUILD_DOC=On -DCMAKE_INSTALL_PREFIX=../install ..
make
make install

An online version of the doc is available.

A user manual is also available, see Documentation/CoMMA_user_manual.pdf. The goal of this document is to clearly state and explain how CoMMA works, that applies both to algorithms and their actual implementation (e.g., which data structures have been used). After having read this document, the user should be able to understand what CoMMA actually does under the hood and should have the essential insights to use it (e.g., which input parameters should one provides, how they will impact the final results...).

Finally, a brief note dedicated to the aspect-ratio computation can be found in the repository as well.

💡 Examples

Here are two animations about the agglomeration on a 2D mesh of a ring for two different option settings:

• Seeds pool with full initialization and boundary priority

• Seeds pool with one-point initialization and neighbourhood priority

🔍 Testing CoMMA

A set of tests to verify code and algorithm integrity has been set up, see the related file. The tests rely on the Catch2 framework. To run the tests, start by building the library (see above. The cmake commands related to the tests are already part of the reference CMakeLists.txt), this will generate an executable CoMMA_test in the building directory, simply run it.

cmake -DBUILD_TESTS=On ..
make CoMMA_test # or simply make
./CoMMA_test  # or simply: make test

🐍 A python interface to CoMMA

A python module which interfaces to CoMMA can be obtained using pybind11 (a submodule of CoMMA). To have it, just "build", see above.

cmake -DBUILD_PYTHON_BINDINGS=On ..
make CoMMA # or simply make

A library called CoMMA.cpython-310-x86_64-linux-gnu.so (or similar depending on the python version and the architecture) is installed in ${CMAKE_INSTALL_LIBDIR}/python3.X/site-packages, which, supposing one has given install as prefix in the cmake configuration step and using python3.10, will develop to install/lib64/python3.10/site-packages. To use it, add that directory to your python path:

export PYTHONPATH:/path/to/CoMMA/install/lib64/python3.10/site-packages:$PYTHONPATH

then just load CoMMA module in a python session:

import CoMMA

# Do python stuff

Like standard C++ CoMMA, the python module contains only one function, the counterpart of agglomerate_one_level. It has just the very same input arguments, only, all arguments are necessary (no defaulted parameters). However, differently from the C++ version, it returns three lists:

• fc_to_cc: list telling the ID of the coarse cell to which a fine cell belongs after agglomeration
• aggloLines_Idx: connectivity for the agglomeration lines: each element points to a particular element in the list aggloLines
• aggloLines: list storing all the elements of the anisotropic lines.

import CoMMA
fc_to_cc, aggloLines_Idx, aggloLines = CoMMA.agglomerate_one_level(*args)

Several python scripts showcasing the CoMMA package (as well as its two main dependencies, meshio and dualGPy) are available.

🤝 Cite CoMMA

If you have found CoMMA useful, do not hesitate to cite it in your paper:

@techreport{CoMMA23,
    author = {Milani, Riccardo},
    title = {{CoMMA}, a geometric unstructured agglomerator},
    institution = {ONERA},
    number = {RT 7/30485},
    year = {2023},
    month = {November},
    url = {https://github.com/onera/CoMMA/blob/main/Documentation/CoMMA_user_manual.pdf},
}

🙏 Acknowledgements

The development of CoMMA was financially supported by the European Union's Horizon 2020 research and innovation program under grant agreement number 956104 ("NextSim") and the French Directorate General for Civil Aviation (DGAC) project "LAMA".