vijaysm/moab-root

•Updated about 4 years ago

MOAB Docker image

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vijaysm/moab-root repository overview

⁠MOAB: Mesh-Oriented datABase

MOAB is a software component for representing for creating, storing and accessing mesh data. MOAB can describe structured and unstructured mesh, consisting of elements in the finite element "zoo". The functional interface to MOAB is simple yet powerful, allowing the representation of many types of metadata commonly found on the mesh. MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than through individual entities, while also versatile enough to support individual entity access. MOAB can be used in several ways:

A few highlights of the capabilities in MOAB include:

Representation of 0-3d elements in the finite element "zoo" (including support for quadratic elements), as well as support for polygon and polyhedron entities
Highly efficient storage and query of structured and unstructured mesh (e.g. a brick-shaped hex mesh requires approximately 25 and 55 MB per million hex elements in the structured and unstructured representations, respectively)
Powerful data model allowing representation of various metadata in the form of "sets" (arbitrary groupings of mesh entities and sets) and "tags" (annotation of entities, sets, and entire mesh)
Open source (LGPL) mesh readers/writers for Sandia ExodusII, CUBIT .cub save/restore, VTK, GMsh, and other mesh formats with capability to translate between them uniformly
Flexible access to MOAB routines from C and Fortran through iMesh and iMOAB interfaces are available
A high level Python interface (PyMOAB) based on Cython bindings can also be enabled

Several computational solvers in various scientific domains such as nuclear engineering, climate modeling, nonlinear thermo-mechanics, CFD, etc have been built on top of MOAB. Other common use-cases where MOAB is often applied are:

Unstructured mesh generation and manipulation for complex geometry
Mesh quality computation along with algorithms for smoothing and optimization
Solution field transfers for multi-physics problems
- High-order interpolation between unstructured grids in two and three dimensions
- Conservative remappng between meshes on the sphere for Climate problems

MOAB was developed originally as part of the CUBIT project at Sandia National Laboratories, and has been partially funded by the DOE SciDAC program (TSTT, ITAPS, FASTMath), ASCR (CESAR), and DOE-NE (NEAMS program). More recently, DOE-BER programs under the E3SM project have provided support for enabling scalable solution transfer techniques for climate applications.

MOAB is distributed under an open-source, GNU LGPL licensing agreement.

⁠Continuous Integration

There are several hooks to online continuous integration systems, nightly and commit-based Buildbot/Bitbucket builds that are constantly run during a development day to check the integrity and robustness of the library.

⁠Documentation

Detailed API documentation and user/development guides are available for the following repository branches, updated daily.

⁠MOAB Pre-installed

MOAB pre-installed docker image:
MOAB tools with anaconda:

⁠Optional Dependencies

MPI: MOAB supports usage of MPICH and OpenMPI libraries configured externally in order to enable scalable mesh manipulation algorithms.
HDF5: In order to manage the data dependencies and to natively support parallel I/O, MOAB uses a custom file format that can represent the entire MOAB data model in a native HDF5-based file format. Support for this file format requires version 5 of the HDF library, which can be obtained at HDF5⁠.
NetCDF: MOAB library optionally depends on the NetCDF libraries (C and C++) to compile the ExodusII reader/writer. To get netcdf, go to NetCDF⁠.
Metis/ParMetis: MOAB can use the Metis or ParMetis library for partitioning mesh files in serial and parallel respectively
Zoltan: Support for online partitioning through Zoltan (and its dependencies on Scotch, ParMetis etc) can be utilized through the partitioner tool
TempestRemap: Provide support for both offline and online remapping of Climate field data on unstructured spherical meshes
Eigen3: A substitute for BLAS/LAPACK interfaces. However if TempestRemap tools are to be built, this becomes a required dependency

⁠Configuration and Build from Source

Currently, both CMake and Autotools are maintained simultaneously in order to support all platforms (including Windows). Please choose your build system according to your needs and follow instructions below. Both of these workflows follow the same pattern of commands to build and install in your platform.

⁠Autotools based configuration workflow

Please ensure that the autotools toolchain is pre-installed locally. We recommend a minimum autoconf version of v2.69.
Run autoreconf -fi to generate the configure script
Run the configure --help script in the top source directory to see a list of available configure options.
- Use --prefix=INSTALL_DIR to specify installation directory
- Override default compilers with environment or user options: CC, CXX, FC, F77
- If you have MPI installed, use --with-mpi=$MPI_DIR
- If you have HDF5 and NetCDF installed, use --with-hdf5=$HDF5_DIR and --with-netcdf=$NETCDF_DIR to specify external dependencies.
- Similarly for Metis or ParMetis dependencies, use --with-metis=$METIS_DIR and --with-parmetis=$PARMETIS_DIR respectively
- If you have Zoltan installed, use --with-zoltan=$ZOLTAN_DIR
- In order to enable Python bindings (PyMOAB), you need to use --enable-shared --enable-pymoab options
- Auto-Download options: MOAB now supports automatic dependency download and configuration that has been tested on various platforms and architectures.
  - HDF5: Use --download-hdf5 OR --download-hdf5=TARBALL_PATH
  - NetCDF: Use --download-netcdf OR --download-netcdf=TARBALL_PATH
  - Metis: Use --download-metis OR --download-metis=TARBALL_PATH
  - TempestRemap: Use --download-tempestremap OR --download-tempestremap=master (to build from Git master)
Now run the configure script with desired configuration options either in-source or out-of-source (build) directory.

⁠CMake based configuration workflow

Please ensure you have CMake (>3.0) available locally.
Run ccmake visual configuration editor or cmake to get a bare configuration of MOAB
If you would like to override the compiler used by default, use the following variables to override
- C: -DCMAKE_C_COMPILER=mpicc
- C++: -DCMAKE_CXX_COMPILER=mpicxx
- Fortran: -DCMAKE_Fortran_COMPILER=mpif90
Specify your installation directory by using -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_PATH
If you have MPI installed, use -DENABLE_MPI=ON -DMPI_HOME=$MPI_DIR
If you have HDF5 installed, use -DENABLE_HDF5=ON -DHDF5_ROOT=$HDF5_DIR
If you have NetCDF installed, use -DENABLE_NETCDF=ON -DNETCDF_ROOT=$NETCDF_DIR.
Similarly for Metis or ParMetis dependencies, use -DENABLE_METIS=ON -DMETIS_DIR=$METIS_DIR and -DENABLE_PARMETIS=ON -DPARMETIS_DIR=$PARMETIS_DIR respectively
In order to enable Python bindings (PyMOAB), you need to use -DBUILD_SHARED_LIBS=ON -DENABLE_PYMOAB=ON options
If you have Zoltan installed, use -DENABLE_ZOLTAN=ON -DZOLTAN_DIR=$ZOLTAN_DIR options

Once configuration with autotools or CMake is complete in the build directory, run the following to build the library:
- Compile MOAB and supported tools: make -j4
- Verify configuration and build setup: make check
Next to install the compiled libraries, headers and tools, run make install
You can now use the makefile generated under the build/examples folder and modify it to compile downstream code with MOAB dependency

⁠Language Bindings

Even though the MOAB library is written in C++ language (conforming to C++11 standard), several partial bindings and interfaces are available for other languages.

C/Fortran: You can use the iMOAB interface to load, manipulate and query unstructured meshes in memory
- Supports both serial and parallel invocation under one interface. MOAB needs to be configured using --with-mpi option.
- Supports ability to migrate meshes and tags between processes
- Supports capability to compute remapping weights for Climate science applications
Note that the ITAPS iMesh interfaces are now deprecated and we encourage users to directly use MOAB or iMOAB interfaces if possible.
Python3: The Python bindings for MOAB can be enabled when configured with --enable-shared --enable-pymoab options.
- Supports access to the structured grid interfaces.
- Supports queries and access to Entities using a true-Pythonic implementation flavor.
- Utilizes Cython to provide flexible bindings without sacrificing runtime performance.
- Only supports serial computations for now. Parallel implementation using MPI4Py is underway.

⁠Third-party bindings

C#: This contributed source is developed and maintained by Qingfeng Xia, UKAEA 2021. It is distributed under the same LGPLv3 license as MOAB.
- The open-source repository containing C# interfaces are available in MOABSharp Bitbucket repository⁠.
- Supports builds on .NET Core 3.1 under Ubuntu 20.04, and .NET framework 4.x under Windows 10-64bit (target on "netstandard2").
- Detailed documentation and supported features are listed in the MOABSharp README file⁠.

⁠Bugs, Correspondence, Contributing

MOAB is distributed under LGPL(v3) licensing, and we encourage users to submit bug reports (and, if possible, fixes) directly on the Bitbucket interface. Optionally, users can email and discuss the issue with developers at [email protected]⁠. Also refer to FAQ⁠ for some commonly asked questions and their resolutions.

MOAB follows a fully transparent, open-source development workflow (refer to our Code of Conduct⁠ for further information), and we welcome all contributions that enhance the feature sets provided by MOAB. If you would like to contribute to MOAB, please submit your changes through pull request (PR) using a Bitbucket fork of MOAB (refer to CONTRIBUTING.md⁠ for more details), or send us patches that you would like merged upstream. Users are also encouraged to check SIGMA-MOAB⁠ documentation pages for news and updates.

⁠Citing MOAB

If you use MOAB for your research, please use the following bibtex entries for the software and the original report to cite us.

@techreport{moab_2004,
  author = {Tautges, T. J. and Meyers, R. and Merkley, K. and Stimpson, C. and Ernst, C.},
  type = {{SAND2004-1592}},
  title = {{MOAB:} A Mesh-Oriented Database},
  institution = {Sandia National Laboratories},
  month = apr,
  year = {2004},
  note = {Report}
}

@software{moab521_2020,
  author       = {Mahadevan, Vijay and
                  Grindeanu, Iulian and
                  Jain, Rajeev and
                  Shriwise, Patrick and
                  Wilson, Paul},
  title        = {MOAB v5.2.1},
  month        = aug,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {5.2.1},
  doi          = {10.5281/zenodo.2584862},
  url          = {https://doi.org/10.5281/zenodo.2584862}
}

Additionally, if you would like us to highlight your application, library or tool that uses MOAB, please contact the developers for more information.

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