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To use the MOAB-based coupler (E3SM/driver-moab), you will need to install MOAB and some of its dependencies on your machine to get started. Some instructions are provided below to install the dependencies directly on a new machine other than the ones officially supported for E3SM, where MOAB will be pre-built and installed.

Pre-installed recipes

MOAB comes pre-built as part of a conda package to test and experiment with the capabilities. Note that we do not recommend using the conda installation for MOAB for the online coupler workflows as often the preinstalled package will be suboptimal for the cluster or machine in use. However, such installations are useful for offline remapping and computational analysis workflows (with Python interfaces) using MOAB.

Once you have a conda environment setup, use the command below to install MOAB with TempestRemap enabled (with or without MPI).

With MPI: conda install -c conda-forge moab=*=mpi_mpich_tempest*

Without MPI: conda install -c conda-forge moab=*=nompi_tempest*

This method is useful for quickly getting started with MOAB and TempestRemap interfaces, as the build is consistent with all third-party libraries (TPLs) available prebuilt with MPI enabled or disabled. For more extensive TPL support in Conda, use the E3SM-Unified conda package.

Building MOAB library with TPL dependencies

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

  • MPI: MOAB supports both MPICH and OpenMPI based libraries configured externally to enable scalable mesh manipulation algorithms.

  • HDF5: To manage the data dependencies and to natively support parallel I/O, MOAB uses a native HDF5-based file format to represent the entire MOAB data model.

  • NetCDF: MOAB library optionally depends on the NetCDF libraries (C) to compile the ExodusII reader/writer. NetCDF is also required to process NetCDF4 format nc files for E3SM.

  • Parallel-NetCDF: MOAB library optionally depends on the parallel-NetCDF (pnetcdf) libraries to compile the support for parallel  reader and writer of NetCDF meshes and linear map weight files. This is a required dependency to enable parallel I/O of MPAS, SCRIP, ESMF and Exodus meshes as well.

  • Metis/ParMetis: MOAB can optionally use the Metis or ParMetis library for partitioning mesh files in an offline form through the mbpart tool. This may be useful to pre-partition the mesh apriori in offline remapping workflows.

  • Zoltan: Support for both offline and online partitioning through Zoltan (and its dependencies on Scotch, ParMetis etc) can be utilized through the partitioner tool and at runtime with appropriate file read options (PARTITION_METHOD=RCBZOLTAN;). This dynamic rebalancing is important to achieve good scalability when reading nc files. If reading parallel h5m files, we recommend using the offline partitioning tool with mbpart with -z RCB to use the Recursive Bisection geometric partitioner implementation in Zoltan.

  • TempestRemap: Provides support for both offline and online remapping of Climate field data on unstructured spherical meshes. Required dependency for all E3SM workflows.

  • Eigen3: A substitute for BLAS/LAPACK interfaces. However, if TempestRemap tools are to be built, this becomes a required dependency as we store the SparseMatrix internally on every task using the Eigen3 data-structures.

Configuring and building MOAB 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 to support all platforms (including Windows). In this section, we will focus only on the autotools configuration system as this remains the most tested configuration approach for now. In the future, we will be deprecating the autotools configuration system and use the CMake-based approach.

For the autotools-based configuration, we recommend a minimum autoconf version of 2.69.

Autotools configuration

  • Run autoreconf -fi to generate the configure script

  • Run ./configure --help script in the MOAB source directory to see the list of configure options

  • Use --prefix=INSTALL_DIR to specify installation directory for MOAB

  • Override default compilers with environment variables or configure-time options: CC, CXX, FC, F77

  • If you have MPI installed, use --with-mpi=$MPI_DIR

  • If you have HDF5, NetCDF, PNetCDF installed, use --with-hdf5=$HDF5_DIR --with-netcdf=$NETCDF_DIR --with-pnetcdf=$PNETCDF_DIR to specify these 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

  • If you have TempestRemap pre-installed, then use --with-tempestremap=$TEMPESTREMAP_DIR during configuration, or you can use the auto-download option to let MOAB automatically build the dependency with the configure option --download-tempestremap(to download the latest release) OR --download-tempestremap=master (to build from TempestRemap git repository, master branch).

  • Now execute the configure script with desired configuration options either in-source or out-of-source (recommended) directory. A typical MOAB configuration command with all TPLs enabled might look like the one shown below, where $PACKAGE_DIR indicates the location of the installation prefix for the particular TPL.

    $MOAB_SRC/configure CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 \
                    --prefix=$MOAB_INSTALL_DIR \
                    --enable-debug --enable-optimize \
                    --with-mpi=$MPI_DIR \
                    --with-eigen3=$EIGEN3_INCLUDE_DIR \
                    --with-hdf5=$HDF5_DIR \
                    --with-netcdf=$NETCDF_DIR \
                    --with-pnetcdf=$PNETCDF_DIR \
                    --with-tempestremap=$TEMPESTREMAP_DIR \
                    --with-zoltan=$ZOLTAN_DIR

Once configuration with the autotools workflow is complete in the build directory, run the following commands to build the library and verify the build.

  • 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

After this step, the MOAB installation with TempestRemap should be usable for all E3SM online and offline workflows. If you experience any issues during configuration or linking phases of MOAB, please email the mailing list: moab-dev@mcs.anl.gov , or contact Vijay M , Iulian Grindeanu for additional help.

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