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metgrid- produces different .nc files.

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these files has different num_ metgrid_ Levels and num_ sm_ Layers, which caused the real.exe cannont produce a complete boundary file. So how can I do to ensure the metgrid.exe generates the met files with same num_ metgrid_ Levels and num_ sm_ Layers.
What data did you ungrib? Can you check whether the vertical levels in these original data are same?
The datas are NCEP FNL Operational Model Global Tropospheric Analyses. The soil layers increased from 2 to 4 in May 31, 2005. And the met layers increased 32 to 34 in June 12, 2019.
What is your study period? I suppose that your period covers the time when the data is changed, please let me know if I am wrong.
For the soil levels, since WRF only needs soil information at the initial time, you can specify the information based on the data at the initial time of your study.
For upper air data, you need the same vertical levels at all the times. In this case, please take advantage of the WPS utility program mod_levs.exe, which can process the input data and make them to be located at the same levels. Please take a look at: