As part of the efforts in the CMDV project, interfaces to integrate the MOAB unstructured mesh library with the TempestRemap remapping tool have been undertaken. Detailed information on the algorithmic and implementation aspects of this effort have been written in a manuscript submitted to Geoscientific Model Development [1]. This work has led to the development of a new offline remapping tool called mbtempest, which exposes the functionality to compute the supermesh or intersection mesh between two unstructured source and target component grids, in addition to using this supermesh for computing the remapping weights to project solutions between the grids. This functionality is part of the critical worflow with E3SM, where the generated remapping weights in the offline step are consumed by MCT at runtime to seamlessly transfer solution data between components (atm↔ocn, atm↔lnd, etc).
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1. mpiexec -n 1 tools/mbtempest -t 5 -l outputCSMesh.exo -l outputICOMesh.exo -i moab_intx_cs_ico.exoh5m 2. mpiexec -n 16 tools/mbtempest -t 5 -l $MOAB_SRC_DIR/MeshFiles/unittest/wholeATM_T.h5m -l outputICOMesh.exo -i moab_intx_atm_ico.h5m 3. mpiexec -n 128 tools/mbtempest -t 5 -l $MOAB_SRC_DIR/MeshFiles/unittest/wholeATM_T.h5m -l $MOAB_SRC_DIR/MeshFiles/unittest/recMeshOcn.h5m -i moab_intx_atm_ocn.h5m |
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Once we have a source and target grid that is to be used to compute the remapping weights, mbtempest can be used in a similar fashion to GenerateOverlapMesh/GenerateOfflineMap in TempestRemap or the ESMF_RegridWeightGen tool with ESMF to create the field projection weights. Note that unlike ESMF, there is no need to create a dual of the higher-order Spectral Element (SE) mesh using the TempestRemap workflow. Some examples with different options are provided below. Note that to enable generation of weights in addition to computing the intersection mesh, the only main option to enable is -w.
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1. Serial: mpiexec -n 1 tools/mbtempest -t 5 -l outputCSMesh.exo -l outputICOMesh.exo -f moab_mbtempest_remap_csico_fvfv.h5mnc -i moab_intx_file2.exo -w 2. Parallel: mpiexec -n 64 tools/mbtempest -t 5 -l $MOAB_SRC_DIR/MeshFiles/unittest/wholeATM_T.h5m -l $MOAB_SRC_DIR/MeshFiles/unittest/recMeshOcn.h5m -f moab_mbtempest_remap_fvfv.h5mnc -i moab_intx_file2.exo -w -m fv -m fv 3. Parallel: mpiexec -n 128 tools/mbtempest -t 5 -l $MOAB_SRC_DIR/MeshFiles/unittest/wholeATM_T.h5m -l $MOAB_SRC_DIR/MeshFiles/unittest/recMeshOcn.h5m -f moab_mbtempest_remap_sefv.h5mnc -i moab_intx_file2.exo -w -m cgll -m fv -o 4 -o 1 -g GLOBAL_DOFS -g GLOBAL_ID |
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Converting parallel h5m file to SCRIP file for E3SM
To complete the offline map generation workflow, a converter tool from the parallel MOAB h5m file to a SCRIP file to be consumed in E3SM directly is available. This h5mtoscrip converter tool takes the output file from mbtempest and produces the mapping weights and attributes in SCRIP nc file based on the metadata generated during the remapping process. The downside to this extra step in conversion is that this process is only run in serial and is limited to the memory constraints on the node. As a future task, we will also be investing effort into writing a SCRIP file in parallel through a custom I/O interface using PNetCDF.
Typical usage of the tool takes the mapping file (h5m) as input and writes out the SCRIP (nc) file as output.
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tools/h5mtoscrip -d 2 -w mapSEFV-NE30.h5m -s mapSEFV-NE30.nc |
NOTE: In the latest version of MOAB (5.2.1+ or master branch), we now have a parallel SCRIP writer for map files. So you can just use .nc extension when writing out the map file with the -f argument for mbtempestNOTE: In older versions of MOAB (< 5.2.1), you have to write out the map file in parallel using h5m format and then use the h5mtoscrip tool to convert to .nc file.
Machines with mbtempest tool pre-installed
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If steps (a)-(g) pass successfully, the MOAB libraries and tools, along with interfaces for TempestRemap will be installed in $INSTALL_PREFIX/moab directory. The offline remapping weight computation tool, mbtempest, will also be installed during this process and can then be used standalone to generate the weight files as needed.
References
1 Mahadevan, V. S., Grindeanu, I., Jacob, R., and Sarich, J.: Improving climate model coupling through a complete mesh representation: a case study with E3SM (v1) and MOAB (v5.x), Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2018-280, in review, 2018.