Clean out non-gfs top level variables

[KateFriedman-NOAA]

What new functionality do you need?

Removal of duplicate variables that define the top level folder locations (e.g. PARMwave is the same as PARMgfs).

This is related to cleanup that happened in issue #2184 for the FIX* variables.

Remove the non-gfs versions of PARM*, USH*, UTIL*, EXEC*, SCR*. Also remove *gfs variables outside of configs including HOME* variables and EXPDIRs that aren't needed.

What are the requirements for the new functionality?

Functionality unimpacted.

Acceptance Criteria

The only top level path variables are now *gfs versions.

Suggest a solution (optional)

No response

[KateFriedman-NOAA]

@CoryMartin-NOAA @aerorahul While looking for PARM* variables to remove and replace with their ${PARMgfs}/SOMETHING alternative I see the IODAPARM parm file variable. Here are the two instances of it that I see in global-workflow:

-bash-4.2$ grep IODAPARM * -r                                                                                                            
jobs/JGLOBAL_ATM_PREP_IODA_OBS:${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
parm/config/gfs/config.prepatmiodaobs:export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"

While IODAPARM isn't a directory variable, it's a parm file being sourced from under the /sorc folder instead of via symlinks/copies within the top-level /parm folder. The ../sorc/gdas.cd/parm folder isn't currently included in the link step so it doesn't yet reside under the top level /parm folder after clone setup. It doesn't have to happen with this issue but perhaps the ../gdas.cd/parm/* folders should be added to the link step and references like IODAPARM updated? Asking now so this doesn't get forgotten until closer to ops handoff. Thoughts?

[KateFriedman-NOAA]

@JessicaMeixner-NOAA While working on this issue I noticed the wave_sys_var variable:

-bash-4.2$ grep wave_sys_ver * -r
parm/config/gefs/config.wave:export wave_sys_ver=v1.0.0
parm/config/gfs/config.wave:export wave_sys_ver=v1.0.0
ush/wave_grid_moddef.sh:  if [ -z "$grdID" ] || [ -z "$EXECwave" ] || [ -z "$wave_sys_ver" ]

The commit history shows it came with the creation of the config.wave back when Henrique and I committed changes to add waves 5yrs ago. I don't recall the history of the variable but it doesn't appear needed now. Do you know about the variable, if we still need it, or if we can remove it? Thanks!

[JessicaMeixner-NOAA]

I don't have any additional history. I agree with your assessment that it is not needed now and can be removed. Let me know if you have a PR you'll be adding that to or I can remove this in my open PR updating the model assuming testing hasn't started.

[KateFriedman-NOAA]

@JessicaMeixner-NOAA Great! If you can include it in your current open PR that works for me! Let me know if you aren't able to and I'll include it in the PR for this issue. Thanks!

[JessicaMeixner-NOAA]

@KateFriedman-NOAA - done - added to #2338

[KateFriedman-NOAA]

Perfect, thanks @JessicaMeixner-NOAA !

[RussTreadon-NOAA]

@KateFriedman-NOAA , thank you for bringing IODAPARM to our attention. I made your suggested change in a working copy of global-workflow on Hera. The following changes were made:

1. replace IODAPARM with PARMioda in jobs/JGLOBAL_ATM_PREP_IODA_OBS

@@ -6,7 +6,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prepatmiodaobs" -c "base prepatmiodao
 ##############################################
 # Set variables used in the script
 ##############################################
-
+PARMioda=${PARMioda:-${HOMEgfs}/parm/gdas/bufr2ioda}

 ##############################################
 # Begin JOB SPECIFIC work
@@ -18,7 +18,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 ###############################################################
 # Run relevant script
 EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.py}
-${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
+${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${PARMioda}" "${COM_OBS}/"
 status=$?

2. add a GDASApp parm section to sorc/link_workflow.sh

@@ -199,6 +199,14 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   done
 fi

+#------------------------------
+#--add GDASApp parm directory
+#------------------------------
+if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
+  cd "${HOMEgfs}/parm/gdas" || exit 1
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda" .
+fi
+
 #------------------------------
 #--add GDASApp files
 #------------------------------

3. Remove IODAPARM from parm/config/gfs/config.prepatmiodaobs. Also removed BUFR2IODASH from the same config file since jobs/JGLOBAL_ATM_PREP_IODA_OBS defaults to the correct path.

@@ -8,7 +8,4 @@ echo "BEGIN: config.prepatmiodaobs"
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepatmiodaobs

-export BUFR2IODASH="${HOMEgfs}/ush/run_bufr2ioda.py"
-export IODAPARM="${HOMEgfs}/sorc/gdas.cd/parm/ioda/bufr2ioda"
-
 echo "END: config.prepatmiodaobs"

Job gdasprepatmiodaobs was run with the above changes. The job successfully ran to completion.

[KateFriedman-NOAA]

@RussTreadon-NOAA Thanks for looking into this and providing tested changes to address it.

Changes 2 and 3 I can fold into my fork branch for this issue. I'll do that.

Change 1 goes in the opposite direction that this issue is going = remove non-gfs PARM* variables (e.g. remove PARMioda). For your suggested change 1 I would counter with replacing your suggested PARMioda with ${PARMgfs}/gdas/bufr2ioda and delete the line that sets PARMioda. Does that work for this job?

[RussTreadon-NOAA]

@KateFriedman-NOAA , do you mean

@@ -18,7 +18,7 @@ YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS
 ###############################################################
 # Run relevant script
 EXSCRIPT=${BUFR2IODASH:-${HOMEgfs}/ush/run_bufr2ioda.py}
-${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${IODAPARM}" "${COM_OBS}/"
+${EXSCRIPT} "${PDY}${cyc}" "${RUN}" "${DMPDIR}" "${PARMgfs}/gdas/bufr2ioda" "${COM_OBS}/"
 status=$?
 [[ ${status} -ne 0 ]] && (echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}")

in jobs/JGLOBAL_ATM_PREP_IODA_OBS?

I made this change and gdasprepatmiodaobs successfully ran to completion.