Building MOAB

Posted by Vijay Mahadevan in MOAB

Note: If you are looking for building MOAB for E3SM, please refer to this link.

MOAB Pre-installed

MOAB comes pre-built in several different flavors and can be directly installed on several supported platforms.

• Docker image:
• Conda:

Optional Dependencies

There are several option dependencies for MOAB. Features and tools get automatically built based on the enabled dependencies when configuring MOAB library.

• 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.
• NetCDF: MOAB library optionally depends on the NetCDF libraries (C and C++) to compile the ExodusII reader/writer.
• 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 building from source

First, clone the sources from the repository using the command

git clone https://bitbucket.org/fathomteam/moab.git

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. Note that the autotools workflow may get deprecated in the future.

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 Eigen3 installed, use -DEIGEN3_DIR=$EIGEN3_INCLUDE_DIR
• If you have HDF5 installed, use -DENABLE_HDF5=ON -DHDF5_ROOT=$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
• If you have TempestRemap installed, use -DENABLE_TEMPESTREMAP=ON -DTEMPESTREMAP_DIR=$TEMPESTREMAP_DIR options

Once configuration with either autotools or the CMake workflow 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