Correct all syntax errors in output logs

[CarlosMDiaz-NCO]

All output logs should be free of warnings and errors such as 'No such file or directory', 'Cannot stat', etc.
For cases where the file/directory isn't found, there should be logic to check for the file first

For these jobs I'll add what I think the fixes are:

nwps_chs_prep.o267398467:1344:/lfs/h1/ops/para/packages/nwps.v1.5.1/ush/run_nwps_wcoss.sh: line 164: [: ==: unary operator expected
needs quotes around $COLDSTART: if [ "$COLDSTART" == "YES" ]; then

nwps_gyx_post_cg1.o267398462:2959:/lfs/f1/ops/para/tmp/pnwps_gyx_para/parm/templates/gyx/GYX: line 82: NEST: command not found
line missing # to make it a comment fix/domains/GYX

nwps_aer_post_cg1.o267467111:/lfs/h1/ops/para/packages/nwps.v1.5.1/ush/shiproutes/plot_shiproutes.sh: line 319: 18: command not found
missing $(( ... ))` around logic

Others from post_cg1 jobs. Tried to just leave 1 example of each type, but there could be multiple for each job:

nwps_tbw_post_cg1.o267398475:5081490:cp: cannot stat '/lfs/f1/ops/para/tmp/pnwps_tbw_para/run/PE0095/20260608.1200*': No such file or directory

nwps_aer_post_cg1.o267399725:3379:ERROR - /lfs/f1/ops/para/tmp/pnwps_aer_para/run/SHIPRT1.YY26.MO06.DD08.HH18 file does not exist

nwps_aer_post_cg1.o267399725:7070:cp: cannot stat '/lfs/f1/ops/para/tmp/pnwps_aer_para/var/shiproutes/route*/swan*hr*.png': No such file or directory
nwps_aer_post_cg1.o267399725:7072:chmod: cannot access '/lfs/f1/ops/para/tmp/pnwps_aer_para/output/figures/aer/shiproutes/swan*hr*.png': No such file or directory
nwps_aer_post_cg1.o267399725:7076:tar: *.png: Cannot stat: No such file or directory`

nwps_tbw_post_cg1.o267398475:4845694:cp: cannot stat '/riphist/TBW/5*CG1*TBW': No such file or directory
nwps_bro_post_cg1.o267398469:1550282:cp: cannot stat '/lfs/h1/ops/para/com/nwps/v1.5/nwps.20260605/nwges/riphist/BRO/5*CG1*BRO': No such file or directory

nwps_bro_post_cg1.o267398469:1819051:cat: /lfs/f1/ops/para/tmp/pnwps_bro_para/run/nests.flag: No such file or directory

nwps_key_post_cg1.o267398476:270472:ERROR - /lfs/f1/ops/para/tmp/pnwps_key_para/run/SHIPRT4.YY26.MO06.DD08.HH12 file does not exist

and errors from wavetrack_cg1 jobs:
nwps_key_wavetrack_cg1.o267399021:3285:mv: cannot stat '/lfs/f1/ops/para/tmp/pnwps_key_para/run/PRT.SHIPRT5.CG1.TAB.YY26.MO06.DD08.HH12': No such file or directory

[JessicaMeixner-NOAA]

Updates are being added to: https://github.com/JessicaMeixner-NOAA/nwps/tree/v1.5/issue83

[JessicaMeixner-NOAA]

@CarlosMDiaz-NCO - I've been looking at the log files and making sure we find all syntax issues and ran across:

nwps_tbw_forecast_cgn.o272246387:2382:++ 0 /lfs/h1/ops/para/packages/nwps.v1.5.4/scripts/exnwps_forecast.sh + echo 'WARNING - This is a production workstation with debugging on'
nwps_tbw_forecast_cgn.o272246387:2383:WARNING - This is a production workstation with debugging on
nwps_tbw_forecast_cgn.o272246387:2384:++ 0 /lfs/h1/ops/para/packages/nwps.v1.5.4/scripts/exnwps_forecast.sh + echo 'WARNING - Check your DEBUGGING setting'

This is coming from this block of code:
https://github.com/NOAA-EMC/nwps/blob/prod/v1.5/ush/nwps_config.sh#L281-L285

We default to debugging=true in jobs/JNWPS* and in https://github.com/NOAA-EMC/nwps/blob/prod/v1.5/ush/nwps_config.sh#L50

This warning is also in prod, so I'm hesitant to change the DEBUGGING defaults/settings at this stage of the process. That being said, should we just disable the "WARNING" message about this?

[JessicaMeixner-NOAA]

@CarlosMDiaz-NCO - Any thoughts on the "WARNING - Check your DEBUGGING setting" mentioned in the last comment?

[CarlosMDiaz-NCO]

Since it will always be on it doesn't seem helpful so I think those messages should be disabled.
What do the variables ISPRODUCTION and DEBUGGING do other than print out these warning messages? There is a standard checklist item "Have all development blocks of code been removed or minimized?" so I'm now wondering if any sections other than the ISPRODUCTION and DEBUGGING = TRUE blocks need to be removed

[JessicaMeixner-NOAA]

The DEBUGGING outputs a few extra lines in the log files (0(10)) and given that is how we currently run in production, our preference would just be to keep that as true and disable the WARNING message. The ISPRODUCTION line outputs a line saying it is for production, and we can also disable that write message. Otherwise we do not see major dev lines of code.

I disabled the warning message in PR #111

[CarlosMDiaz-NCO]

ok I think for the purposes of this issue removing the "WARNING" messages is good. I may open up a separate one about development blocks of code after taking a closer look

[CarlosMDiaz-NCO]

I found a couple more syntax errors. Can you investigate?

The nwps_stofs_prep jobs occasionally output a FATAL ERROR message but seem to continue fine.
/lfs/h1/ops/para/output/20260805/nwps_stofs_prep_18.o280204441
*** FATAL ERROR: rd_grib2_msg_seq_file, read outside of file, bad grib file ***

Showing up in eka, pwr, and sew outputs. e.g. /lfs/h1/ops/para/output/20260805/nwps_sew_prep.o280376442
/lfs/h1/ops/para/packages/nwps.v1.5.8/ush/get_ncep_initfiles.sh: line 298: [: 00_2026080: integer expression expected
It looks like init_time is getting the wrong value when the files are wave_stofs_uv_*.dat instead of wave_stofs_waterlevel_*.dat . I think the cut -c23-32 command needs to be modified on line 298.

[sbanihash]

Looking at it right now.

[CarlosMDiaz-NCO]

Just for tracking, the latest errors for this issue were:
in nwps_stofs_prep jobs, lots of cannot create regular file: ... File exists errors. It was said this was caused by multiple processes trying to copy the same file in. The solution was to create a subdirectory for each process to work in