Installing MOAB and TempestRemap for E3SM

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.

MOAB will be pre-built and installed on officially supported machines.

Building MOAB library with TPL dependencies needed for E3SM

These instructions assume you have already ported E3SM to your machine (you have it defined in config_machines.xml and can build and run cases.)

To build the MOAB library specifically for E3SM, the following dependencies are required and mandatory for scalable coupler workflows. MOAB has to be configured with these TPLs to work consistently with E3SM and to support both online and offline workflows. The appropriate features and tools needed within MOAB will get automatically built and enabled based on the dependencies during MOAB configuration.

• MPI: MOAB supports both MPICH- and OpenMPI-based libraries configured externally to enable scalable mesh manipulation algorithms. Required dependency for the MOAB-coupler. (Without MPI, only a serial version of MOAB will be built.) Use the same MPI library/wrappers as E3SM.

• HDF5: MOAB uses a native HDF5-based file format to represent the entire MOAB data model and this is the recommended interface and format for scalable I/O of MOAB meshes and associated data. If MPI is enabled, HDF5 should be built with parallel support. HDF5 support allows you to output any E3SM state maintained by MOAB in h5m files that are tremendously useful in debugging as they can be directly visualized with VisIt using the MOAB plugin (on a sphere and with the exact mesh). If you built HDF5 for E3SM (with parallel support), use that to enable HDF5 support in MOAB configuration. For MOAB-E3SM workflows, this is an optional dependency unless you expect to develop and debug MOAB driver.

• Parallel-NetCDF: MOAB library uses parallel-NetCDF (pnetcdf) library directly for reading NetCDF (v3) meshes in parallel and linear map weight files (for instance the r2o map). All other component maps are generally calculated online by the MOAB coupler. Use the same PNetCDF library as E3SM. For MOAB-E3SM workflows, this is a required dependency.

• Zoltan: Support for online or offline partitioning through Zoltan (optionally configured with dependency on ParMetis/Metis) can be utilized with the MOAB partitioner tool (mbpart). The runtime partitioning can be invoked with appropriate file read options (PARTITION_METHOD=RCBZOLTAN;). This dynamic rebalancing is important to achieve good scalability when reading nc files in parallel. For MOAB-E3SM workflows, this is a required dependency.

• TempestRemap: Provides support for both offline and online remapping of Climate field data on unstructured spherical meshes. The offline remapping weights can be generated using the mbtempest tool. Refer to https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/932380820 for more details. For MOAB-E3SM workflows, this is a required dependency.

• Eigen3: A substitute for BLAS/LAPACK interfaces (if not available locally). This is a required dependency for MOAB when calculating weights with TempestRemap as we store the SparseMatrix linear map internally on every task and perform SpMV using the Eigen3 interfaces. For MOAB-E3SM workflows, this is a required dependency.

Optional dependencies (not needed to run the default MOAB coupler)

• Metis/ParMetis: MOAB can optionally use the Metis or ParMetis library for partitioning mesh files in an offline form through MOAB’s mbpart tool. This may be useful to pre-partition the mesh apriori in offline remapping workflows, especially when using Metis KWAY graph partitioning algorithm (MPAS).

• NetCDF: MOAB library optionally depends on the NetCDF(-C) libraries to compile the ExodusII reader/writer. If MPI is enabled, then the underlying HDF5 dependency for NetCDF should have parallel support i.e., serial HDF5 dependency will not pass internal configuration checks. If you built the NetCDF library for E3SM, consistently use that installation to enable NetCDF support in MOAB.

Configuring and building MOAB from source

First, clone the sources from the repository using the command

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 at the moment. In the future (FY24Q3/4), we will deprecate the autotools configuration system and use the CMake-based approach instead as the default. 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 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

(Below use the same compiler, MPI and I/O libraries you have set up for E3SM. If you have multiple compiler-MPI options, you will need to build MOAB for each compiler family with corresponding TPL dependencies.)

• Override default compilers with environment variables or configure-time options with the compilers you use for E3SM: CC, CXX, FC, F77

• For the MPI installed for E3SM, use --with-mpi=$MPI_DIR

• For the PNetCDF installed, use --with-pnetcdf=$PNETCDF_DIR

• To simplify the process of building MOAB TPLs that are not used directly by E3SM, we currently offer a workflow to automatically pull the TPL sources and build it on the machine. These packages will be installed in the same location as the specified MOAB prefix (INSTALL_DIR).

• If you built NetCDF4 and HDF5, add --with-hdf5=$HDF5_DIR --with-netcdf=$NETCDF_DIR

• Execute the configure script with desired configuration options out-of-source (recommended) build directory. A typical MOAB configuration command with all TPLs pre-built for your machine might look like the one shown below, where $PACKAGE_DIR indicates the location of the installation prefix for the particular TPL package.

  $MOAB_SRC/configure CC=$E3SM_MPI_DIR/bin/mpicc \ CXX=$E3SM_MPI_DIR/bin/mpicxx \ FC=$E3SM_MPI_DIR/bin/mpif90 \ F77=$E3SM_MPI_DIR/bin/mpif77 \ --prefix=$MOAB_INSTALL_DIR \ --enable-debug --enable-optimize \ --with-mpi=$E3SM_MPI_DIR \ --with-hdf5=$E3SM_HDF5_DIR \ --with-netcdf=$E3SM_NETCDF_DIR \ --with-pnetcdf=$E3SM_PNETCDF_DIR \ --with-eigen3=$EIGEN3_INCLUDE_DIR \ --with-tempestremap=$TEMPESTREMAP_DIR \ --with-zoltan=$ZOLTAN_DIR

However, if external libraries like Eigen3, TempestRemap, and Zoltan are to be auto-downloaded and configured dynamically, then one can use the following command.

Once configuration with the autotools configuration 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 (Some checks may not pass without HDF5. Ignore those).

• Note: If running on machines that require a job submission, request an interactive node before you run make check

• To install the compiled libraries, headers, and tools in the prefix directory, run: make install

If you experience any issues during the configuration or linking phases of MOAB, please email the mailing list: moab-dev@mcs.anl.gov , or contact @Vijay M , @Iulian Grindeanu or #coupler on Slack for additional help.

Once you have verified MOAB has been built correctly, you need to update the CIME machine configuration to specify the MOAB_ROOT (point to the installation prefix).

Edit the entry for your machine in config_machines.xml and make changes like below (example from pm-cpu configuration)

In the above example, replace the MOAB_ROOT path with your MOAB installation prefix directory. In the above case, MOAB was built for multiple compilers so “intel” is in the path and there’s another entry for “gnu” on Perlmutter.

After you’ve built MOAB and modified config_machines.xml, you can try building and running a case.

A simple create_newcase line is:

You can add --driver moab to any B or F case at this time.

For create_test, a command like the following:

You can add “Vmoab” to any watercycle or F case test.

Pre-built recipes (Conda)

MOAB comes pre-built as part of a conda package to use offline tools like mbtempest. DO NOT use the conda installation of MOAB for the MOAB coupler in E3SM as often the preinstalled package will be suboptimal for the cluster or machine in use. However, such installations are useful for offline remapping (mbtempest) and computational analysis workflows (with Python interfaces) using MOAB (and PyMOAB).

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.