Removes no such file or directory messages

[HenryRWinterbottom]

Description

This PR addresses issue #1252. The following is accomplished:

• A check for the existence of a specified file is made prior to attempting to use it in the respective GSI ncdiag file concatenation;
• The issues raised by the shellcheck test are resolved; where exceptions are made but no relevant, the respective check is disabled.

Type of change

• Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

• Is this a breaking change (a change in existing functionality)? NO
• Does this change require a documentation update? NO

How has this been tested?

A set of files, replicating the respective GSI ncdiag files, is created. The respective files are listed here. Files were selectively removed and the script sub-section was executed to verify that the erroneous messages, raising issue #1252 no longer raised the specified messages.

Checklist

• Any dependent changes have been merged and published
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• New and existing tests pass with my changes
• I have made corresponding changes to the documentation if necessary

[KateFriedman-NOAA]

Update to address No such file or directory in scripts/exglobal_diag.sh is taken care of, as well as some additional shellcheck warning fixes (good). Surprised this script hasn't been touched earlier and had shellcheck stuff taken care of...oh well, fun for you!

Left a few comments, one of which involves even more shellcheck warning fixes. Thanks for working on this @HenryWinterbottom-NOAA !

[KateFriedman-NOAA]

@HenryWinterbottom-NOAA Have all of the scripts referenced in the main bugzilla description of #1252 been examined for "No such" statements and resolved if they still have them? If not (totally fine btw!), then please remove the "Resolves" statement so this PR doesn't close the associated issue just yet. Yourself or another developer will need to check the other jobs and confirm the issue is resolved before closing it...which will be a bit tricky for some jobs like the MOS jobs since we can't run them in our rocoto mesh (even after PR #2148 goes in). Thanks!

[emcbot]

CI Update on Hera at 12/20/23 08:00:53 PM
============================================
Cloning and Building global-workflow PR: 2146
with PID: 288108 on host: hfe05

[emcbot]

CI Update on Orion at 12/20/23 02:00:55 PM
============================================
Cloning and Building global-workflow PR: 2146
with PID: 209328 on host: Orion-login-1

[emcbot]

Automated global-workflow Testing Results:

Machine: Hera
Start: Wed Dec 20 20:05:42 UTC 2023 on hfe05
---------------------------------------------------
Build: Completed at 12/20/23 08:55:56 PM
Case setup: Completed for experiment C48_ATM_c24df27d
Case setup: Completed for experiment C48_S2SW_c24df27d
Case setup: Completed for experiment C48_S2SWA_gefs_c24df27d
Case setup: Completed for experiment C96C48_hybatmDA_c24df27d
Case setup: Completed for experiment C96_atm3DVar_c24df27d

[emcbot]

Automated global-workflow Testing Results:

Machine: Orion
Start: Wed Dec 20 14:03:31 CST 2023 on Orion-login-1.HPC.MsState.Edu
---------------------------------------------------
Build: Completed at 12/20/23 02:57:13 PM
Case setup: Completed for experiment C48_ATM_c24df27d
Case setup: Completed for experiment C48_S2SWA_gefs_c24df27d
Case setup: Completed for experiment C48_S2SW_c24df27d
Case setup: Completed for experiment C96_atm3DVar_c24df27d
Case setup: Completed for experiment C96C48_hybatmDA_c24df27d

[emcbot]

Experiment C96C48_hybatmDA_c24df27d  *** FAILED *** on Hera
Experiment C96C48_hybatmDA_c24df27d  with 1 tasks failed at 12/20/23 09:36:17 PM
Error logs:
/scratch1/NCEPDEV/global/Terry.McGuinness/GFS_CI_ROOT/PR/2146/RUNTESTS/COMROT/C96C48_hybatmDA_c24df27d/logs/2021122100/enkfgdasediag.log

[emcbot]

Experiment C96C48_hybatmDA_c24df27d  *** FAILED *** on Orion
Experiment C96C48_hybatmDA_c24df27d  with 1 tasks failed at 12/20/23 03:42:19 PM
Error logs:
/work2/noaa/stmp/GFS_CI_ROOT/ORION/PR/2146/RUNTESTS/COMROT/C96C48_hybatmDA_c24df27d/logs/2021122100/enkfgdasediag.log

[WalterKolczynski-NOAA]

@HenryWinterbottom-NOAA Please test this on your own on at least one machine before we run CI again. I don't want to do an iterative back-and-forth if there are more issues.

[WalterKolczynski-NOAA]

@HenryWinterbottom-NOAA Have you successfully tested this so I can try the CI on it?

[HenryRWinterbottom]

@WalterKolczynski-NOAA I am working on it now.

[WalterKolczynski-NOAA]

Will revisit this later