MPAS-A Segmentation Error

[yeamin47]

----------------------------------------------------------------------
Beginning MPAS-atmosphere Error Log File for task 0 of 1
Opened at 2025/02/28 22:13:23
----------------------------------------------------------------------

ERROR: Writing to stream 'output' would clobber file 'history.2014-09-10_00.00.00.nc',
ERROR: but clobber_mode is set to 'never_modify'.
ERROR: Writing to stream 'diagnostics' would clobber file 'diag.2014-09-10_00.00.00.nc',
ERROR: but clobber_mode is set to 'never_modify'.



I was doing variable mesh for simulation. In the last, in model integration we faced this issue in log file and in terminal we faced following text:

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 8770 RUNNING AT mpas-virtual-machine
= EXIT CODE: 139
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

 

[Ming Chen]

The error message indicates that history and diag files exist in your working directory and these files are not allowed to be overwritten.
Please either delete these files, or modify your streams.atmosphere by changing the cobber_mode from

clobber_mode="never_modify"

to

clobber_mode="overwrite"

Hope this is helpful you. Let us know if you still have problems.

 

[yeamin47]

In streams.atmosphere we could not find any clobber_mode line. Also, we have deleted the any history or diag file before running the exe.

 

[Ming Chen]

Please double check. Your log file clearly indicates that history and diag files exist in your working directory.

As for the clobber_mode, see the sample below:

<stream name="output"
        type="output"
        filename_template="history.noahmp.$Y-$M-$D_$h.$m.$s.nc"
        io_type = "pnetcdf,cdf5"
        clobber_mode="overwrite"
        output_interval="1:00:00" >
        <file name="stream_list.atmosphere.output"/>
</stream>

 

[gdicker]

Even if you don't find the line, you can add it. Some attributes are left out of the streams by default (I think io_type and clobber_mode). The default value for clobber_mode is "never_modify".

See Section 5.2 of the current (v8.2.0 ) MPAS User Guide: https://www2.mmm.ucar.edu/projects/mpas/mpas_atmosphere_users_guide_8.2.0.pdf

 

[Ming Chen]

@Dylan,

Thanks a lot for the follow-up, --- I didn't realize that the default value of clobber_mode is "never_modify".

Have a good weekend !

 

[gdicker]

You too @Ming Chen !

- Dylan

 

[yeamin47]

The problem has been solved but neither your solution worked. The problem was in config_lens_disp amount. In our file it was set to 240000. We found the solve in mpas tutorial 2019 where it was set to 48000. After giving that our problem solved.

But thank you for your response.

 

[Ming Chen]

@ yeamin47

This is weird and I am perplexed by the fix you reported....

Would you please upload your namelist.atmosphere for me to take a look? Also, which mesh did you use to run this case?

Thanks.

 

[yeamin47]

This is really unexpected. I know you guys are the best modeling and software engineer. The options of config_lens_Disp is removed from v8.2 for a reason. But when we try to run the ./atmoshere_model we faced MPI abort issue. No where we could not found the problem's solution. After we added config_lens_Disp option from your 2019 MPAS tutorial where for 240-48km mesh it was set to 48000.0.

We were using 240-48km mesh. Also in 240km mesh the config_lens_Disp needed to add. Below out namelist_atmosphere