GWDO error when running a limited-area simulation

ntmanhvn181 · Aug 7, 2020

Hi everyone,
I've been running a limited-area simulation step by step followed the online tutorial (which is displayed in https://www2.mmm.ucar.edu/projects/mpas/tutorial).
I passed for interpolating regional lateral boundary conditions (LBCs) but when I running a regional simulation by atmosphere core it failed. The detail is described below:

Code:

WARNING: Variable qi not in input file.
WARNING: Variable qs not in input file.
WARNING: Variable qg not in input file.
ERROR: *******************************************************************************
ERROR: The GWDO scheme requires valid var2d, con, oa{1,2,3,4}, and ol{1,2,3,4} fields,
ERROR: but these fields appear to be zero everywhere in the model input.
ERROR: Either set config_gwdo_scheme = 'off' in the &physics namelist, or generate
ERROR: the GWDO static fields with the init_atmosphere core.
ERROR: *******************************************************************************
 
 Checking consistency of limited-area settings...
  - config_apply_lbcs = T
  - Maximum value in bdyMaskCell = 7
  - Input interval for 'lbc_in' stream = '0000000000_006:000:000'
  ----- done checking limited-area settings -----
 
ERROR: Please correct issues with the model input fields and/or namelist.
CRITICAL ERROR: Core init failed for core atmosphere

All materials, including namelist, streams file are attached in the attachments.
Please help me to address it.
Thank all,

mcurry · Aug 7, 2020

This problems usually occurs when your initialization file does not contain any GWDO fields. Are you using the mesh provided at the top of the tutorial page (found in the mpas_tutorial.tar.gz file)? The x1.163842.static.nc file provided in that tar file contains all the necessary static fields (including the GWDO fields) needed to run.

Can you confirm if you are using the provided static file another one?

ntmanhvn181 · Aug 7, 2020

Firstly, I used the x5.6488066.grid.nc file and my pts file (which is used to convert my region) to create the vietnam.grid.nc file by running ./create_region.
After that, the vietnam.grid.nc file was used as the input file to generate init file by running ./init_atmosphere.
Finally, I used that file which was created in the second stage as the input file for run a regional simualation.
That's all about my process. Please let me know if it has any errors.
Thank you!

mcurry · Aug 7, 2020

Thanks for the clarification on your process.

If you started your process from x5.6488066.grid.nc and not the provided x1.163842.static.nc then step 4 of the tutorial will not work correctly as it is written to start with a mesh that contains static terrestrial fields (These fields include: terrain (ter), land use category (lu_index), GWDO fields (oa and ol) and others). Step 4 skips the static interpolation of fields as it was covered in step 1.3 of the tutorial (and the static interpolation takes a while to run).

To confirm the above, you should notice that the 'ter' field of vietnam.init.nc is all 0? Is that correct?

If you started with the x.5.6488066.grid and followed the directions of step 4 then you'll need to run the static interpolation (with the init_atmosphere core as described in 1.3) on the x5.6488066.grid. Which will give you the static terrestrial fields and the GWDO fields (oa and ol) and then you can proceed with step 4.

ntmanhvn181 · Aug 8, 2020

I started with the x.5.6488066.grid on the input file to run the static interpolation (with the init_atmosphere core as described in 1.3) to create the x.5.6488066.static but it failed.
The log.init.out file reported that:

Code:

 Using default single-precision reals
  Reading namelist from file namelist.init_atmosphere
 Reading streams configuration from file streams.init_atmosphere
 Found mesh stream with filename template x5.6488066.grid.nc
 Using default io_type for mesh stream
  ** Attempting to bootstrap MPAS framework using stream: input
 Bootstrapping framework with mesh fields from input file 'x5.6488066.grid.nc'

Additionally, I changed my namelist.init file like:

Code:

&preproc_stages
    config_static_interp = true
    config_native_gwd_static = true
    config_vertical_grid = false
    config_met_interp = false
    config_input_sst = false
    config_frac_seaice = false
/

and my streams file was likely:

Code:

<immutable_stream name="input"
                  type="input"
                  filename_template="x5.6488066.grid.nc"
                  input_interval="initial_only" />

<immutable_stream name="output"
                  type="output"
                  filename_template="x5.6488066.static.nc"
                  packages="initial_conds"
                  output_interval="initial_only" />

mcurry · Aug 10, 2020

Looks like that is the correct setup for the interpolation of static and GWDO fields.

Does the 'ter' (terrain) field of vietnam.grid.nc contain all zeros when it should not? (i.e. your simulation is over land). Are you trying to run a simulation completely over water?

ntmanhvn181 · Aug 10, 2020

The stage I practiced in the last post is that I just used the x.5.6488066.grid file to run the static interpolation due to create the x.5.6488066.static file but it failed.
I didn't used the vietnam.grid file to create the x.5.6488066.static file.
Can you have any suggestions for it?

ntmanhvn181 · Aug 10, 2020

Besides, I practiced another way. First, I created the vietnam.pts file and ran ./create_region with the x5.6488066.grid.nc file in order to generate the vietnam.grid file. To test my domain, I used the regional_terrain.ncl script and the result was displayed in the attachment.
Next, I followed the 1.3 step in the online tutorial to begin processing of the static, terrestrial fields. My input file consists of the vietnam.static.nc file, the vietnam.graph.info file. In addition, my namelist.init_atmosphere file was edited like that:

Code:

&nhyd_model
    config_init_case = 7
    config_start_time = '2019-09-01_00:00:00'
    config_stop_time = '2019-09-04_00:00:00'
    config_theta_adv_order = 3
    config_coef_3rd_order = 0.25
/
&dimensions
    config_nvertlevels = 55
    config_nsoillevels = 4
    config_nfglevels = 38
    config_nfgsoillevels = 4
/
&data_sources
    config_geog_data_path = '/work/users/agpc/share/geog/'
    config_met_prefix = 'CFSV2'
    config_sfc_prefix = 'SST'
    config_fg_interval = 21600
    config_landuse_data = 'MODIFIED_IGBP_MODIS_NOAH'
    config_topo_data = 'GMTED2010'
    config_vegfrac_data = 'MODIS'
    config_albedo_data = 'MODIS'
    config_maxsnowalbedo_data = 'MODIS'
    config_supersample_factor = 3
    config_use_spechumd = false
/
&vertical_grid
    config_ztop = 30000.0
    config_nsmterrain = 1
    config_smooth_surfaces = true
    config_dzmin = 0.3
    config_nsm = 30
    config_tc_vertical_grid = true
    config_blend_bdy_terrain = true
/
&interpolation_control
    config_extrap_airtemp = 'linear'
/
&preproc_stages
    config_static_interp = true
    config_native_gwd_static = true
    config_vertical_grid = false
    config_met_interp = false
    config_input_sst = false
    config_frac_seaice = false
/
&io
    config_pio_num_iotasks = 0
    config_pio_stride = 1
/
&decomposition
    config_block_decomp_file_prefix = 'vietnam.graph.info.part.'
/

and my streams.init_atmosphere also was edited like:

Code:

<streams>
<immutable_stream name="input"
                  type="input"
                  filename_template="vietnam.grid.nc"
                  input_interval="initial_only" />

<immutable_stream name="output"
                  type="output"
                  filename_template="vietnam.static.nc"
                  packages="initial_conds"
                  clobber_mode="overwrite"
                  output_interval="initial_only" />

<immutable_stream name="surface"
                  type="output"
                  filename_template="x1.163842.sfc_update.nc"
                  filename_interval="none"
                  packages="sfc_update"
                  output_interval="86400" />

<immutable_stream name="lbc"
                  type="output"
                  filename_template="lbc.$Y-$M-$D_$h.$m.$s.nc"
                  filename_interval="output_interval"
                  packages="lbcs"
                  output_interval="6:00:00" />

</streams>

The model ran successfully:

Code:

 -----------------------------------------
 Total log messages printed:
    Output messages =                 3621
    Warning messages =                   7
    Error messages =                     0
    Critical error messages =            0
 -----------------------------------------
 Logging complete.  Closing file at 2020/08/11 10:47:39

In the next step, I interpolated regional initial conditions with the CFSV2 data. The namelist file was set-up similarly with the send step except:

Code:

&preproc_stages
    config_static_interp = false
    config_native_gwd_static = false
    config_vertical_grid = true
    config_met_interp = true
    config_input_sst = false
    config_frac_seaice = true

and the streams.init file was like:

Code:

<immutable_stream name="input"
                  type="input"
                  filename_template="vietnam.static.nc"
                  input_interval="initial_only" />

<immutable_stream name="output"
                  type="output"
                  filename_template="vietnam.init.nc"
                  packages="initial_conds"
                  clobber_mode="overwrite"
                  output_interval="initial_only" />

After running, it worked.

Code:

 -----------------------------------------
 Total log messages printed:
    Output messages =                  230
    Warning messages =                   1
    Error messages =                     0
    Critical error messages =            0
 -----------------------------------------
 Logging complete.  Closing file at 2020/08/11 10:57:03

In the next step (LBCs), I modified the namelist.init_atmosphere file:

Code:

config_init_case = 9

and the streams.init file was likely:

Code:

<immutable_stream name="input"
                  type="input"
                  filename_template="vietnam.init.nc"
                  input_interval="initial_only" />

<immutable_stream name="output"
                  type="output"
                  filename_template="foo.nc"
                  packages="initial_conds"
                  clobber_mode="append"
                  output_interval="initial_only" />

There were no errors reported at the end of the log.init_atmosphere.0000.out file:

Code:

 -----------------------------------------
 Total log messages printed:
    Output messages =                 2742
    Warning messages =                   0
    Error messages =                     0
    Critical error messages =            0
 -----------------------------------------

Finally, I ran a regional simulation followed by the 4.4 step in the online toturials, the details of the namelist and streams files were attached in the attachments.
My process is right, doestn't it?
Thank!

mcurry · Aug 11, 2020

Your setup process looks correct and the `ter` field of vietnam.static.nc is present and looks correct so I can see that it has been interpolated with static fields (as you noted you did).

Did you still get the GWDO error that you received in your first post when running on this vietnam.static.nc mesh?

mcurry · Aug 12, 2020

Glad to see that you are no longer getting the GWDO error you were getting, ntmanhvn181. I have moved your last post in this thread into a new topic in the post-processing forum as its more related to post processing rather than running. You can see the new topic here:

https://forum.mmm.ucar.edu/phpBB3/viewtopic.php?f=62&t=9442

mcurry · Sep 1, 2020

I have updated the title of this post to better represent the nature of the error that occurred so that it may be easier to find by other users with the same problem.

GWDO error when running a limited-area simulation

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