Page Comparison

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• MPI: MOAB supports the usage of MPICH and OpenMPI 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 a-priori 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 datastructuresdata-structures.

Configuration and building MOAB from source

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• Run autoreconf -fi to generate the configure script

• Run the ./configure --help script in the top MOAB source directory to see a the list of available 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 (build) directory.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.

  Code Block
  $MOAB_SRC/configure CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 \ --prefix=$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.

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