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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Converting parallel h5m file to SCRIP file for E3SM
We are currently working on a Python script to convert the 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.
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 |
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.
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Cori: Updated sources of TempestRemap and MOAB have been pre-installed along with all required dependencies on some of the standard machines. The MOAB installation is available on Cori within the E3SM project space: /project/projectdirs/acme/software/moab and the corresponding TempestRemap installation is at /project/projectdirs/acme/software/tempestremap. The workflow for generating the offline maps using these installed tools is described below.
Note that for the mbtempest stack to run cleanly on Cori, you may have to set the following environment variable:
csh:
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setenv HDF5_USE_FILE_LOCKING FALSE |
bash:
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export HDF5_USE_FILE_LOCKING=FALSE |
Anvil: Soon..
Compy:
After several iterations to get the dependency stack correct with respect to compatible parallel HDF5 and NetCDF installations by sysadmins on Compy, the other required dependencies were installed successfully and verified/tested to run without issues. Now mbtempest tool is accessible from $MOAB_DIR (see below).
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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.