Help with Generating MPAS Initial Files

[panting]

Hello!

I have run `init_atmosphere_model` according to the "MPAS-Atmosphere Model User’s Guide Version 7.0" and generated `x1.40962.init.20200101.nc` and `x1.40962.sfc_update.20200101-05.nc`. However, since there is no clear "successfully" or "complete" indicator in the log file, I'm not sure if the run was successful. Could you help me check if this run was successful?
I have uploaded my log file as an attachment. Additionally, here is a partial result of `ncdump -h`.


Additionally, it seems that the guide doesn't mention how to create the soil nudging file. Can you help me with that?
I look forward to your response!

Sincerely,
Pan.

 

[gdicker]

Hello, the messages you're looking for usually are written to a log.init_atmosphere.0000.out (sometimes .err for errors) instead of stdout or stderr. Could you please attach a (or any) log.init_atmosphere.* files that were produced with these runs?

A successful run of MPAS cores output a table with timing events (timer names, total time, num calls, min time, max time, etc) then followed by a summary of log messages. Your run likely succeeded if you see something like the following, with 0 error messages and especially with 0 critical error messages:
-----------------------------------------
Total log messages printed:
Output messages = 654
Warning messages = 3
Error messages = 0
Critical error messages = 0
-----------------------------------------

I'm unaware of the process for soil nudging files. @Ming Chen, would you be able to help?

 

[Ming Chen]

@panting:

I have a few concerns:

(1) Would you please update MPAS to new version (MPAS-v8.2.2 is the latest one) ? We are more focused on newer versions and it is not our top priority to debug issues in older version.

(2) As Dylan mentioned, helpful output information are saved in log.init_atmopshere.* files. Would you please upload your log.init_atmopshere.0000.out ( and log.init_atmopshere.0000.err if you have this file) for us to take a look?

Thanks.

 

[panting]

@panting:

I have a few concerns:

(1) Would you please update MPAS to new version (MPAS-v8.2.2 is the latest one) ? We are more focused on newer versions and it is not our top priority to debug issues in older version.

(2) As Dylan mentioned, helpful output information are saved in log.init_atmopshere.* files. Would you please upload your log.init_atmopshere.0000.out ( and log.init_atmopshere.0000.err if you have this file) for us to take a look?

Thanks.

Hello.Thank you for your prompt response and patient explanation!

(1) I apologize, but I am afraid I cannot update MPAS to the latest version at the moment, as I am attempting to run the MPAS-CMAQ model, which utilizes MPASv7.0. According to official information from the USEPA, they have not yet released a coupled model that uses MPASv8.2.2. Although this coupled model only compiles the MPAS core_atmosphere and CMAQ (as I mentioned in this thread Preparing the input files for the MPAS component in the MPAS-CMAQ model), it requires the use of MPAS's initialization module separately to generate input files such as 'init'. However, I am concerned that generating initialization files with MPASv8.2.2 and then running the atmosphere_model of v7.0 may not be feasible.
(2)I do have the log files you mentioned, and I have uploaded them as attachments.

Thanks!

 

[Ming Chen]

Hi,

Thank you for uploading the files.

(1) I looked at your log files in init log.zip, which I guess is for producing initial condition "x1.40962.init.20200101.nc", please let me know if I am wrong.

The log.init_atmosphere.0000.err gives the following error message:

ERROR: Writing to stream 'output' would clobber file 'x1.40962.init.20200101.nc',
ERROR: but clobber_mode is set to 'never_modify'.

This indicates that you already have the file 'x1.40962.init.20200101.nc' in your working directory. You can either delete it or rename it
(e.g. mv x1.40962.init.20200101.nc x1.40962.init.20200101.nc.old), then rerun this case.

(2) in your sfc_update log.zip, log.init_atmosphere.0000.out indicates that the run is successful. As Dylan pointed out, the end of this file shows that

-----------------------------------------
Total log messages printed:
Output messages = 129
Warning messages = 1
Error messages = 0
Critical error messages = 0
-----------------------------------------

This is what we expect if the case is done successfully.

Please let us know if you have more questions.

 

[panting]

Hi,

Thank you for uploading the files.

(1) I looked at your log files in init log.zip, which I guess is for producing initial condition "x1.40962.init.20200101.nc", please let me know if I am wrong.

The log.init_atmosphere.0000.err gives the following error message:

ERROR: Writing to stream 'output' would clobber file 'x1.40962.init.20200101.nc',
ERROR: but clobber_mode is set to 'never_modify'.

This indicates that you already have the file 'x1.40962.init.20200101.nc' in your working directory. You can either delete it or rename it
(e.g. mv x1.40962.init.20200101.nc x1.40962.init.20200101.nc.old), then rerun this case.

(2) in your sfc_update log.zip, log.init_atmosphere.0000.out indicates that the run is successful. As Dylan pointed out, the end of this file shows that

-----------------------------------------
Total log messages printed:
Output messages = 129
Warning messages = 1
Error messages = 0
Critical error messages = 0
-----------------------------------------

This is what we expect if the case is done successfully.

Please let us know if you have more questions.

Hello,

Thank you for your quick reply and patient explanation. I believe I can now successfully run the init and sfc_update files. I would also like to ask if the init_atmosphere core in MPAS v7.0 can generate the soil nudging file? I reviewed the guide but couldn't find any related operations.

Thanks,
Pan.

 

[Ming Chen]

Pan,

By saying 'soil nudging file', do you mean the surface update data? if so, then MPAS v7.0 works for sst_update option and you can produce sfc_update file by MPAS-v7.0.

 

[panting]

Pan,

By saying 'soil nudging file', do you mean the surface update data? if so, then MPAS v7.0 works for sst_update option and you can produce sfc_update file by MPAS-v7.0.

Hello！

I'm afraid that's not the case. By generating the sfc_update file, I have obtained the surface update data, and soil nudging is a separate file, as shown in the attached image in this post：Preparing the input files for the MPAS component in the MPAS-CMAQ model.

There is a thread in the CMAQ forum: Preparing for MPAS-CMAQ inputs. The questioner's statement made me think that the x1.40962.soilndg.2017.nc file is generated by the MPAS initialization module, so I came here to ask about its creation method. Perhaps my understanding is incorrect?

Thanks,
Pan.

 

[Ming Chen]

Hi Pan,

Thanks for the clarification. I believe the soil nudging feature is specific for MPAS-CMAQ, and it is not included in our official release of MPAS. Please talk to EPA people regarding this issue.

 

[panting]

Hi Pan,

Thanks for the clarification. I believe the soil nudging feature is specific for MPAS-CMAQ, and it is not included in our official release of MPAS. Please talk to EPA people regarding this issue.

Hello,

Thank you for your guidance and help! I will contact them as soon as possible.

Wishing you all the best,
Pan.