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Atmosphere Failing at Physics (solved)

R

rasaba

New member
Hello,

I am attempting to run MPAS-A using ERA5 initial conditions and a limited area grid. I have downlaoded the ERA 5 data using the era5_to_init python script and the steps provided in the github repo. I have also generated my limited_area grid successfully using the steps and README provided in that github repo. My steps thus far:
  1. interpolated initial conditions using the init module --> successfully created my init.nc file (central_ok.init.nc)
  2. interpolated lateral boundary conditions using the init module --> successfully created my lbc.*.nc files
  3. Edited my streams.atmoshere namelist:
    1. defined my init.nc file as the input in the top section
    2. changed my lbc in interval to match the interval of my lbc.*.nc files
  4. Edited my namelist.atmoshere:
    1. config_dt = 18.0 --> six times my grids spacing in km (recommended by tutorial)
    2. added my start time and run time
    3. added by limited area graph file to config_block_decomp_file_prefix
When I submit the job to run the simulation, I receive the following info:
  • --- time to calculate additional physics_diagnostics = F --> last line of my log.atmosphere.0000.out file before the job ended
  • dec1923.hsn.de.hpc.ucar.edu: rank 64 exited with code 174 --> last line of my job pbs error output file (mpas_run.e*)
It was suggested to me that maybe my init file didn't contain all necessary information to calculate the physics diagnostics. I converted my init.nc file to a latlon grid using the provided steps in that github repo and the variables appeared to all by the correct shapes and no issues were made apparent.

The directory to all MPAS files references can be found in /glade/work/rasaba/MPAS_NWP/ and the converted init file is in /glade/u/home/rasaba/convert_mpas/latlon.nc, thanks in advance for any assistance!
 
Hi Rasaba,

Thank you for posting the issues in the Forum.

Would you please tell me where your case is located? How did you create the regional mesh for your regional MPAS run?

Thanks.
 
Hi Ming,

Thanks so much for your timely response. My case is located in /glade/work/rasaba/MPAS_NWP/ but on the off chance that you meant geographically it is a limited area grid over central Oklahoma. I also created this mesh using the MPAS limited-area provided on GitHub. That implementation and associated points file on be found in /glade/u/home/rasaba/MPAS-Limited-Area/

Thanks again,
Bobby
 
Hi Bobby,

I looked at your input data. Both your initial and lateral boundary data contain many invalid values NaN. This is why the model crashed immediately after it started.

Would you please check your data? Let me know if you have trouble during the process.
 
Hi Ming,

Thank you for getting back to me. Assuming that the init file is generated from the ERA5 files contained in my directory, is there any particular reason there are empty variables (e.g., surface pressure, rho, theta upon further investigation)? I created these files via the era5_to_init repo on GitHub with the following command:

python era5_to_int.py -i 2023-02-26_23 2023-02-27_04 1

Which seemed to work effortlessly, although I imagine this is the source of error? Your insight here is appreciated.

Thanks again,
Bobby
 
Hi Ming,

I just wanted to let you know that I have figured out the issue. In my namelist.init_atmoshere, I was previously using:

config_blend_bdy_terrain = true

per the MMM example. However I kept it as 'true' during both init and lbc creation. Once I changed that to:

config_blend_bdy_terrain = false

during the lbc creation, things seemed to progress as you would expect and the atmosphere component ran without error. I am checking my output, but if any errors persist at this point, I'll equate it to user error.

Thanks again,
Bobby
 
Last edited:
Hi Bobby,

Thank you for the update and I am glad the regional MPAS works for you. Please confirm that

(1) when you create initial condition, you set config_blend_bdy_terrain = true

(2) when you create lateral boundary condition, you set config_blend_bdy_terrain = false

And MPAS runs successfully.

However, in your previous run that failed with NaN values in your input data, you set config_blend_bdy_terrain = true., is this correct?

Thanks.
 
Correct, Ming! I have updated my previous message to make that more clear for future viewing.

Thanks
 
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