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-built recipes (Conda)
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. If MPI is enabled, HDF5 should be built with parallel support.
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. If MPI is enabled, then the underlying HDF5 dependency for NetCDF should have parallel support i.e., serial HDF5 dependency will not pass configuration checks.
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.
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 readingnc
files. If reading parallelh5m
files, we recommend using the offline partitioning tool withmbpart
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 (FY24Q3), we will deprecate the autotools configuration system and use the CMake-based approach instead. When this happens, the instructions will be updated accordingly.
For the autotools-based configuration, we recommend a minimum autoconf version of 2.69.
Autotools configuration
Run
autoreconf -fi
to generate theconfigure
scriptRun
./configure --help
script in the MOAB source directory to see the list of configure optionsUse
--prefix=INSTALL_DIR
to specify installation directory for MOABOverride 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
respectivelyIf 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 thebuild/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.