From 2840e990bc147a5b88aad9c3b3ec9fb938da3157 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 11:17:16 -0400
Subject: [PATCH 1/6] replace script_dir and top_dir with HOMEgfs in
 link_workflow

---
 sorc/link_workflow.sh | 128 ++++++++++++++++++++----------------------
 1 file changed, 60 insertions(+), 68 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 554b2d568a..f503e7e273 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -2,7 +2,8 @@
 
 #--make symbolic links for EMC installation and hardcopies for NCO delivery
 
-trap 'echo "${BASH_SOURCE[0]} encounted an error at line ${LINENO} (rc=$?)"' ERR
+declare -r HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/.." >/dev/null 2>&1 && pwd )"
+TRACE=NO source "${HOMEgfs}/ush/preamble.sh"
 
 function usage() {
   cat << EOF
@@ -18,8 +19,6 @@ EOF
   exit 1
 }
 
-set -eu
-
 RUN_ENVIR="emc"
 
 # Reset option counter in case this script is sourced
@@ -42,21 +41,16 @@ while getopts ":ho" option; do
 done
 shift $((OPTIND-1))
 
-script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
-top_dir=$(cd "$(dirname "${script_dir}")" &> /dev/null && pwd)
-cd "${script_dir}"
-
-export COMPILER="intel"
 # shellcheck disable=SC1091
-source gfs_utils.fd/ush/detect_machine.sh  # (sets MACHINE_ID)
+COMPILER="intel" source "${HOMEgfs}/sorc/gfs_utils.fd/ush/detect_machine.sh"  # (sets MACHINE_ID)
 # shellcheck disable=
 machine=$(echo "${MACHINE_ID}" | cut -d. -f1)
 
 #------------------------------
 #--Set up build.ver and run.ver
 #------------------------------
-cp "${top_dir}/versions/build.${machine}.ver" "${top_dir}/versions/build.ver"
-cp "${top_dir}/versions/run.${machine}.ver" "${top_dir}/versions/run.ver"
+cp "${HOMEgfs}/versions/build.${machine}.ver" "${HOMEgfs}/versions/build.ver"
+cp "${HOMEgfs}/versions/run.${machine}.ver" "${HOMEgfs}/versions/run.ver"
 
 #------------------------------
 #--model fix fields
@@ -74,7 +68,7 @@ case "${machine}" in
 esac
 
 # Source fix version file
-source "${top_dir}/versions/fix.ver"
+source "${HOMEgfs}/versions/fix.ver"
 
 # LINK is always ln, LINK_OR_COPY can be ln or cp depending on RUN_EVNVIR being emc or nco, respectively
 LINK="ln -fs"
@@ -87,22 +81,22 @@ fi
 
 # Link wxflow in ush/python, workflow and ci/scripts
 # TODO: This will be unnecessary when wxflow is part of the virtualenv
-cd "${top_dir}/ush/python" || exit 1
+cd "${HOMEgfs}/ush/python" || exit 1
 [[ -s "wxflow" ]] && rm -f wxflow
-${LINK} "${top_dir}/sorc/wxflow/src/wxflow" .
-cd "${top_dir}/workflow" || exit 1
+${LINK} "${HOMEgfs}/sorc/wxflow/src/wxflow" .
+cd "${HOMEgfs}/workflow" || exit 1
 [[ -s "wxflow" ]] && rm -f wxflow
-${LINK} "${top_dir}/sorc/wxflow/src/wxflow" .
-cd "${top_dir}/ci/scripts" || exit 1
+${LINK} "${HOMEgfs}/sorc/wxflow/src/wxflow" .
+cd "${HOMEgfs}/ci/scripts" || exit 1
 [[ -s "wxflow" ]] && rm -f wxflow
-${LINK} "${top_dir}/sorc/wxflow/src/wxflow" .
+${LINK} "${HOMEgfs}/sorc/wxflow/src/wxflow" .
 
 
 # Link fix directories
 if [[ -n "${FIX_DIR}" ]]; then
-  if [[ ! -d "${top_dir}/fix" ]]; then mkdir "${top_dir}/fix" || exit 1; fi
+  if [[ ! -d "${HOMEgfs}/fix" ]]; then mkdir "${HOMEgfs}/fix" || exit 1; fi
 fi
-cd "${top_dir}/fix" || exit 1
+cd "${HOMEgfs}/fix" || exit 1
 for dir in aer \
             am \
             chem \
@@ -128,8 +122,8 @@ do
 done
 
 
-if [[ -d "${script_dir}/ufs_utils.fd" ]]; then
-  cd "${script_dir}/ufs_utils.fd/fix" || exit 1
+if [[ -d "${HOMEgfs}/sorc/ufs_utils.fd" ]]; then
+  cd "${HOMEgfs}/sorc/ufs_utils.fd/fix" || exit 1
   ./link_fixdirs.sh "${RUN_ENVIR}" "${machine}" 2> /dev/null
 fi
 
@@ -137,7 +131,7 @@ fi
 #---------------------------------------
 #--add files from external repositories
 #---------------------------------------
-cd "${top_dir}/parm/post" || exit 1
+cd "${HOMEgfs}/parm/post" || exit 1
 for file in postxconfig-NT-GEFS-ANL.txt postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GFS-ANL.txt \
     postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt postxconfig-NT-GFS-FLUX.txt \
     postxconfig-NT-GFS-GOES.txt postxconfig-NT-GFS-TWO.txt \
@@ -145,26 +139,26 @@ for file in postxconfig-NT-GEFS-ANL.txt postxconfig-NT-GEFS-F00.txt postxconfig-
     post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat \
     AEROSOL_LUTS.dat optics_luts_DUST.dat optics_luts_SALT.dat optics_luts_SOOT.dat optics_luts_SUSO.dat optics_luts_WASO.dat
 do
-  ${LINK_OR_COPY} "${script_dir}/upp.fd/parm/${file}" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${file}" .
 done
 
-cd "${top_dir}/scripts" || exit 8
-${LINK_OR_COPY} "${script_dir}/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .
-cd "${top_dir}/ush" || exit 8
+cd "${HOMEgfs}/scripts" || exit 8
+${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_utils.fd/scripts/exemcsfc_global_sfc_prep.sh" .
+cd "${HOMEgfs}/ush" || exit 8
 for file in emcsfc_ice_blend.sh fv3gfs_driver_grid.sh fv3gfs_make_orog.sh global_cycle_driver.sh \
   emcsfc_snow.sh fv3gfs_filter_topo.sh global_cycle.sh fv3gfs_make_grid.sh
 do
-  ${LINK_OR_COPY} "${script_dir}/ufs_utils.fd/ush/${file}" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_utils.fd/ush/${file}" .
 done
 for file in finddate.sh make_ntc_bull.pl make_NTC_file.pl make_tif.sh month_name.sh ; do
-  ${LINK_OR_COPY} "${script_dir}/gfs_utils.fd/ush/${file}" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/ush/${file}" .
 done
 
 #------------------------------
 #--add GDASApp fix directory
 #------------------------------
-if [[ -d "${script_dir}/gdas.cd" ]]; then
-  cd "${top_dir}/fix" || exit 1
+if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
+  cd "${HOMEgfs}/fix" || exit 1
   [[ ! -d gdas ]] && mkdir -p gdas
   cd gdas || exit 1
   for gdas_sub in crtm fv3jedi gsibec; do
@@ -179,97 +173,97 @@ fi
 #------------------------------
 #--add GDASApp files
 #------------------------------
-if [[ -d "${script_dir}/gdas.cd" ]]; then
-  cd "${top_dir}/ush" || exit 1
-  ${LINK_OR_COPY} "${script_dir}/gdas.cd/ush/ufsda"                              .
-  ${LINK_OR_COPY} "${script_dir}/gdas.cd/ush/jediinc2fv3.py"                     .
-  ${LINK_OR_COPY} "${script_dir}/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
+if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
+  cd "${HOMEgfs}/ush" || exit 1
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
 fi
 
 
 #------------------------------
 #--add DA Monitor file (NOTE: ensure to use correct version)
 #------------------------------
-if [[ -d "${script_dir}/gsi_monitor.fd" ]]; then
+if [[ -d "${HOMEgfs}/sorc/gsi_monitor.fd" ]]; then
 
-  cd "${top_dir}/fix" || exit 1
+  cd "${HOMEgfs}/fix" || exit 1
   [[ ! -d gdas ]] && ( mkdir -p gdas || exit 1 )
   cd gdas || exit 1
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/fix/gdas_minmon_cost.txt" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/fix/gdas_minmon_gnorm.txt" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/fix/gdas_oznmon_base.tar" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/fix/gdas_oznmon_satype.txt" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_base.tar" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_satype.txt" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_scaninfo.txt" .
-  cd "${top_dir}/parm" || exit 1
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/fix/gdas_minmon_cost.txt" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/fix/gdas_minmon_gnorm.txt" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/fix/gdas_oznmon_base.tar" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/fix/gdas_oznmon_satype.txt" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_base.tar" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_satype.txt" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/fix/gdas_radmon_scaninfo.txt" .
+  cd "${HOMEgfs}/parm" || exit 1
   [[ -d mon ]] && rm -rf mon
   mkdir -p mon
   cd mon || exit 1
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/parm/gdas_radmon.parm" da_mon.parm
-  # ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/parm/gdas_minmon.parm" .
-  # ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gfs/parm/gfs_minmon.parm" .
-  ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/parm/gdas_oznmon.parm" .
-  # ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/parm/gdas_radmon.parm" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/parm/gdas_radmon.parm" da_mon.parm
+  # ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gdas/parm/gdas_minmon.parm" .
+  # ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Minimization_Monitor/nwprod/gfs/parm/gfs_minmon.parm" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Ozone_Monitor/nwprod/gdas_oznmon/parm/gdas_oznmon.parm" .
+  # ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/src/Radiance_Monitor/nwprod/gdas_radmon/parm/gdas_radmon.parm" .
 fi
 
 #------------------------------
 #--link executables
 #------------------------------
 
-if [[ ! -d "${top_dir}/exec" ]]; then mkdir "${top_dir}/exec" || exit 1 ; fi
-cd "${top_dir}/exec" || exit 1
+if [[ ! -d "${HOMEgfs}/exec" ]]; then mkdir "${HOMEgfs}/exec" || exit 1 ; fi
+cd "${HOMEgfs}/exec" || exit 1
 
 for utilexe in fbwndgfs.x gaussian_sfcanl.x gfs_bufr.x supvit.x syndat_getjtbul.x \
   syndat_maksynrc.x syndat_qctropcy.x tocsbufr.x overgridid.x \
   mkgfsawps.x enkf_chgres_recenter_nc.x tave.x vint.x reg2grb2.x
 do
   [[ -s "${utilexe}" ]] && rm -f "${utilexe}"
-  ${LINK_OR_COPY} "${script_dir}/gfs_utils.fd/install/bin/${utilexe}" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/install/bin/${utilexe}" .
 done
 
 [[ -s "ufs_model.x" ]] && rm -f ufs_model.x
-${LINK_OR_COPY} "${script_dir}/ufs_model.fd/tests/ufs_model.x" .
+${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/ufs_model.x" .
 
 [[ -s "upp.x" ]] && rm -f upp.x
-${LINK_OR_COPY} "${script_dir}/upp.fd/exec/upp.x" .
+${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/exec/upp.x" .
 
 for ufs_utilsexe in emcsfc_ice_blend emcsfc_snow2mdl global_cycle; do
     [[ -s "${ufs_utilsexe}" ]] && rm -f "${ufs_utilsexe}"
-    ${LINK_OR_COPY} "${script_dir}/ufs_utils.fd/exec/${ufs_utilsexe}" .
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_utils.fd/exec/${ufs_utilsexe}" .
 done
 
 # GSI
-if [[ -d "${script_dir}/gsi_enkf.fd" ]]; then
+if [[ -d "${HOMEgfs}/sorc/gsi_enkf.fd" ]]; then
   for gsiexe in enkf.x gsi.x; do
     [[ -s "${gsiexe}" ]] && rm -f "${gsiexe}"
-    ${LINK_OR_COPY} "${script_dir}/gsi_enkf.fd/install/bin/${gsiexe}" .
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_enkf.fd/install/bin/${gsiexe}" .
   done
 fi
 
 # GSI Utils
-if [[ -d "${script_dir}/gsi_utils.fd" ]]; then
+if [[ -d "${HOMEgfs}/sorc/gsi_utils.fd" ]]; then
   for exe in calc_analysis.x calc_increment_ens_ncio.x calc_increment_ens.x \
     getsfcensmeanp.x getsigensmeanp_smooth.x getsigensstatp.x \
     interp_inc.x recentersigp.x
   do
     [[ -s "${exe}" ]] && rm -f "${exe}"
-    ${LINK_OR_COPY} "${script_dir}/gsi_utils.fd/install/bin/${exe}" .
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_utils.fd/install/bin/${exe}" .
   done
 fi
 
 # GSI Monitor
-if [[ -d "${script_dir}/gsi_monitor.fd" ]]; then
+if [[ -d "${HOMEgfs}/sorc/gsi_monitor.fd" ]]; then
   for exe in oznmon_horiz.x oznmon_time.x radmon_angle.x \
     radmon_bcoef.x radmon_bcor.x radmon_time.x
   do
     [[ -s "${exe}" ]] && rm -f "${exe}"
-    ${LINK_OR_COPY} "${script_dir}/gsi_monitor.fd/install/bin/${exe}" .
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gsi_monitor.fd/install/bin/${exe}" .
   done
 fi
 
 # GDASApp
-if [[ -d "${script_dir}/gdas.cd" ]]; then
+if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   declare -a JEDI_EXE=("fv3jedi_addincrement.x" \
                        "fv3jedi_diffstates.x" \
                        "fv3jedi_ensvariance.x" \
@@ -296,14 +290,14 @@ if [[ -d "${script_dir}/gdas.cd" ]]; then
                        "apply_incr.exe" )
   for gdasexe in "${JEDI_EXE[@]}"; do
     [[ -s "${gdasexe}" ]] && rm -f "${gdasexe}"
-    ${LINK_OR_COPY} "${script_dir}/gdas.cd/build/bin/${gdasexe}" .
+    ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/${gdasexe}" .
   done
 fi
 
 #------------------------------
 #--link source code directories
 #------------------------------
-cd "${script_dir}" || exit 8
+cd "${HOMEgfs}/sorc" || exit 8
 if [[ -d ufs_model.fd ]]; then
   [[ -d upp.fd ]] && rm -rf upp.fd
   ${LINK} ufs_model.fd/FV3/upp upp.fd
@@ -389,6 +383,4 @@ do
   ${LINK_OR_COPY} "gfs_utils.fd/src/${prog}" .
 done
 
-echo "${BASH_SOURCE[0]} completed successfully"
-
 exit 0

From 81792f91f40daed7cc1c3d4031162387f19dac0b Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 15:05:47 -0400
Subject: [PATCH 2/6] move nems.configure.*.IN from ush to parm/ufs/

---
 {ush => parm/ufs}/nems.configure.atm.IN                 | 0
 {ush => parm/ufs}/nems.configure.atm_aero.IN            | 0
 {ush => parm/ufs}/nems.configure.blocked_atm_wav.IN     | 0
 {ush => parm/ufs}/nems.configure.cpld.IN                | 0
 {ush => parm/ufs}/nems.configure.cpld_aero.IN           | 0
 {ush => parm/ufs}/nems.configure.cpld_aero_outerwave.IN | 0
 {ush => parm/ufs}/nems.configure.cpld_aero_wave.IN      | 0
 {ush => parm/ufs}/nems.configure.cpld_outerwave.IN      | 0
 {ush => parm/ufs}/nems.configure.cpld_wave.IN           | 0
 {ush => parm/ufs}/nems.configure.leapfrog_atm_wav.IN    | 0
 10 files changed, 0 insertions(+), 0 deletions(-)
 rename {ush => parm/ufs}/nems.configure.atm.IN (100%)
 rename {ush => parm/ufs}/nems.configure.atm_aero.IN (100%)
 rename {ush => parm/ufs}/nems.configure.blocked_atm_wav.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld_aero.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld_aero_outerwave.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld_aero_wave.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld_outerwave.IN (100%)
 rename {ush => parm/ufs}/nems.configure.cpld_wave.IN (100%)
 rename {ush => parm/ufs}/nems.configure.leapfrog_atm_wav.IN (100%)

diff --git a/ush/nems.configure.atm.IN b/parm/ufs/nems.configure.atm.IN
similarity index 100%
rename from ush/nems.configure.atm.IN
rename to parm/ufs/nems.configure.atm.IN
diff --git a/ush/nems.configure.atm_aero.IN b/parm/ufs/nems.configure.atm_aero.IN
similarity index 100%
rename from ush/nems.configure.atm_aero.IN
rename to parm/ufs/nems.configure.atm_aero.IN
diff --git a/ush/nems.configure.blocked_atm_wav.IN b/parm/ufs/nems.configure.blocked_atm_wav.IN
similarity index 100%
rename from ush/nems.configure.blocked_atm_wav.IN
rename to parm/ufs/nems.configure.blocked_atm_wav.IN
diff --git a/ush/nems.configure.cpld.IN b/parm/ufs/nems.configure.cpld.IN
similarity index 100%
rename from ush/nems.configure.cpld.IN
rename to parm/ufs/nems.configure.cpld.IN
diff --git a/ush/nems.configure.cpld_aero.IN b/parm/ufs/nems.configure.cpld_aero.IN
similarity index 100%
rename from ush/nems.configure.cpld_aero.IN
rename to parm/ufs/nems.configure.cpld_aero.IN
diff --git a/ush/nems.configure.cpld_aero_outerwave.IN b/parm/ufs/nems.configure.cpld_aero_outerwave.IN
similarity index 100%
rename from ush/nems.configure.cpld_aero_outerwave.IN
rename to parm/ufs/nems.configure.cpld_aero_outerwave.IN
diff --git a/ush/nems.configure.cpld_aero_wave.IN b/parm/ufs/nems.configure.cpld_aero_wave.IN
similarity index 100%
rename from ush/nems.configure.cpld_aero_wave.IN
rename to parm/ufs/nems.configure.cpld_aero_wave.IN
diff --git a/ush/nems.configure.cpld_outerwave.IN b/parm/ufs/nems.configure.cpld_outerwave.IN
similarity index 100%
rename from ush/nems.configure.cpld_outerwave.IN
rename to parm/ufs/nems.configure.cpld_outerwave.IN
diff --git a/ush/nems.configure.cpld_wave.IN b/parm/ufs/nems.configure.cpld_wave.IN
similarity index 100%
rename from ush/nems.configure.cpld_wave.IN
rename to parm/ufs/nems.configure.cpld_wave.IN
diff --git a/ush/nems.configure.leapfrog_atm_wav.IN b/parm/ufs/nems.configure.leapfrog_atm_wav.IN
similarity index 100%
rename from ush/nems.configure.leapfrog_atm_wav.IN
rename to parm/ufs/nems.configure.leapfrog_atm_wav.IN

From 03f8f60e4cf03ca8c9e222293ef00508e53a45b9 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 15:16:38 -0400
Subject: [PATCH 3/6] replace SCRIPTSDIR with HOMEgfs/ush

---
 scripts/exglobal_forecast.sh | 15 ++++++---------
 ush/forecast_postdet.sh      |  8 ++++----
 ush/nems_configure.sh        |  7 ++-----
 3 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/scripts/exglobal_forecast.sh b/scripts/exglobal_forecast.sh
index d2cc11617a..076c635c17 100755
--- a/scripts/exglobal_forecast.sh
+++ b/scripts/exglobal_forecast.sh
@@ -79,16 +79,13 @@
 
 source "${HOMEgfs}/ush/preamble.sh"
 
-SCRIPTDIR="${HOMEgfs}/ush"
-echo "MAIN: environment loaded for ${machine} platform,Current Script locates in ${SCRIPTDIR}."
-
 # include all subroutines. Executions later.
-source "${SCRIPTDIR}/cplvalidate.sh"	# validation of cpl*
-source "${SCRIPTDIR}/forecast_predet.sh"	# include functions for variable definition
-source "${SCRIPTDIR}/forecast_det.sh"  # include functions for run type determination
-source "${SCRIPTDIR}/forecast_postdet.sh"	# include functions for variables after run type determination
-source "${SCRIPTDIR}/nems_configure.sh"	# include functions for nems_configure processing
-source "${SCRIPTDIR}/parsing_model_configure_FV3.sh"
+source "${HOMEgfs}/ush/cplvalidate.sh"	# validation of cpl*
+source "${HOMEgfs}/ush/forecast_predet.sh"	# include functions for variable definition
+source "${HOMEgfs}/ush/forecast_det.sh"  # include functions for run type determination
+source "${HOMEgfs}/ush/forecast_postdet.sh"	# include functions for variables after run type determination
+source "${HOMEgfs}/ush/nems_configure.sh"	# include functions for nems_configure processing
+source "${HOMEgfs}/ush/parsing_model_configure_FV3.sh"
 
 # Compset string. For nems.configure.* template selection. Default ATM only
 confignamevarfornems=${confignamevarfornems:-'atm'}
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index d3fd5c2a97..a251a44e83 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -483,7 +483,7 @@ FV3_nml(){
   # namelist output for a certain component
   echo "SUB ${FUNCNAME[0]}: Creating name lists and model configure file for FV3"
   # Call child scripts in current script directory
-  source "${SCRIPTDIR}/parsing_namelists_FV3.sh"
+  source "${HOMEgfs}/ush/parsing_namelists_FV3.sh"
   FV3_namelists
   echo "SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created"
 }
@@ -648,7 +648,7 @@ WW3_nml() {
       exit 4
     fi
   fi
-  source "${SCRIPTDIR}/parsing_namelists_WW3.sh"
+  source "${HOMEgfs}/ush/parsing_namelists_WW3.sh"
   WW3_namelists
 }
 
@@ -835,7 +835,7 @@ MOM6_postdet() {
 
 MOM6_nml() {
   echo "SUB ${FUNCNAME[0]}: Creating name list for MOM6"
-  source "${SCRIPTDIR}/parsing_namelists_MOM6.sh"
+  source "${HOMEgfs}/ush/parsing_namelists_MOM6.sh"
   MOM6_namelists
 }
 
@@ -975,7 +975,7 @@ CICE_postdet() {
 
 CICE_nml() {
   echo "SUB ${FUNCNAME[0]}: Creating name list for CICE"
-  source "${SCRIPTDIR}/parsing_namelists_CICE.sh"
+  source "${HOMEgfs}/ush/parsing_namelists_CICE.sh"
   CICE_namelists
 }
 
diff --git a/ush/nems_configure.sh b/ush/nems_configure.sh
index 7393d346a7..c51e500d5d 100755
--- a/ush/nems_configure.sh
+++ b/ush/nems_configure.sh
@@ -11,10 +11,7 @@
 #####
 writing_nems_configure()
 {
-echo "SUB ${FUNCNAME[0]}: parsing_nems_configure begins"
-if [[ -e "${SCRIPTDIR}/nems.configure" ]]; then
-  rm -f "${SCRIPTDIR}/nems.configure"
-fi
+echo "SUB ${FUNCNAME[0]}: nems.configure.sh begins"
 
 # Setup nems.configure
 local DumpFields=${NEMSDumpFields:-false}
@@ -34,7 +31,7 @@ rm -f "${DATA}/nems.configure"
 local esmf_logkind=${esmf_logkind:-"ESMF_LOGKIND_MULTI"} #options: ESMF_LOGKIND_MULTI_ON_ERROR, ESMF_LOGKIND_MULTI, ESMF_LOGKIND_NONE
 
 # Copy the selected template into run directory
-infile="${SCRIPTDIR}/nems.configure.${confignamevarfornems}.IN"
+infile="${HOMEgfs}/parm/ufs/nems.configure.${confignamevarfornems}.IN"
 if [[ -s ${infile} ]]; then
   cp "${infile}" tmp1
 else

From 932be4408507cf9265afb30d985c538b6b69b14e Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 16:39:30 -0400
Subject: [PATCH 4/6] gfs and gefs resources are the same

---
 .gitignore                        |   1 +
 parm/config/gefs/config.resources |  12 ++-
 parm/config/gefs/config.ufs       |  14 ++-
 parm/config/gfs/config.resources  |  12 ++-
 parm/config/gfs/config.ufs        |   8 +-
 sorc/link_workflow.sh             |  24 +++++
 ush/nems_configure.sh             | 147 +++++++-----------------------
 7 files changed, 90 insertions(+), 128 deletions(-)

diff --git a/.gitignore b/.gitignore
index 3eb6853c19..3abc6e6449 100644
--- a/.gitignore
+++ b/.gitignore
@@ -142,6 +142,7 @@ ush/make_ntc_bull.pl
 ush/make_tif.sh
 ush/month_name.sh
 ush/imsfv3_scf2ioda.py
+ush/atparse.bash
 
 # version files
 versions/build.ver
diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
index e5995b3cf2..6f1db0007b 100644
--- a/parm/config/gefs/config.resources
+++ b/parm/config/gefs/config.resources
@@ -550,38 +550,42 @@ elif [[ "${step}" = "fcst" || "${step}" = "efcs" ]]; then
         export MEDPETS MEDTHREADS
         echo "MEDIATOR using (threads, PETS) = (${MEDTHREADS}, ${MEDPETS})"
 
+        CHMPETS=0; CHMTHREADS=0
         if [[ "${DO_AERO}" = "YES" ]]; then
           # GOCART shares the same grid and forecast tasks as FV3 (do not add write grid component tasks).
           (( CHMTHREADS = ATMTHREADS ))
           (( CHMPETS = FV3PETS ))
           # Do not add to NTASKS_TOT
-          export CHMPETS CHMTHREADS
           echo "GOCART using (threads, PETS) = (${CHMTHREADS}, ${CHMPETS})"
         fi
+        export CHMPETS CHMTHREADS
 
+        WAVPETS=0; WAVTHREADS=0
         if [[ "${DO_WAVE}" = "YES" ]]; then
           (( WAVPETS = ntasks_ww3 * nthreads_ww3 ))
           (( WAVTHREADS = nthreads_ww3 ))
-          export WAVPETS WAVTHREADS
           echo "WW3 using (threads, PETS) = (${WAVTHREADS}, ${WAVPETS})"
           (( NTASKS_TOT = NTASKS_TOT + WAVPETS ))
         fi
+        export WAVPETS WAVTHREADS
 
+        OCNPETS=0; OCNTHREADS=0
         if [[ "${DO_OCN}" = "YES" ]]; then
           (( OCNPETS = ntasks_mom6 * nthreads_mom6 ))
           (( OCNTHREADS = nthreads_mom6 ))
-          export OCNPETS OCNTHREADS
           echo "MOM6 using (threads, PETS) = (${OCNTHREADS}, ${OCNPETS})"
           (( NTASKS_TOT = NTASKS_TOT + OCNPETS ))
         fi
+        export OCNPETS OCNTHREADS
 
+        ICEPETS=0; ICETHREADS=0
         if [[ "${DO_ICE}" = "YES" ]]; then
           (( ICEPETS = ntasks_cice6 * nthreads_cice6 ))
           (( ICETHREADS = nthreads_cice6 ))
-          export ICEPETS ICETHREADS
           echo "CICE6 using (threads, PETS) = (${ICETHREADS}, ${ICEPETS})"
           (( NTASKS_TOT = NTASKS_TOT + ICEPETS ))
         fi
+        export ICEPETS ICETHREADS
 
         echo "Total PETS for ${_CDUMP} = ${NTASKS_TOT}"
 
diff --git a/parm/config/gefs/config.ufs b/parm/config/gefs/config.ufs
index c23ccf2abd..bfbb0a12cb 100644
--- a/parm/config/gefs/config.ufs
+++ b/parm/config/gefs/config.ufs
@@ -255,6 +255,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs_1998-2006_smoothed_2X.nc"
       MOM6_RESTART_SETTING='r'
       MOM6_RIVER_RUNOFF='False'
+      eps_imesh="4.0e-1"
       ;;
     "100")
       ntasks_mom6=20
@@ -267,6 +268,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs_1998-2006_smoothed_2X.nc"
       MOM6_RESTART_SETTING='n'
       MOM6_RIVER_RUNOFF='False'
+      eps_imesh="2.5e-1"
       ;;
     "50")
       ntasks_mom6=60
@@ -279,7 +281,8 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs-clim-1997-2010.${NX_GLB}x${NY_GLB}.v20180328.nc"
       MOM6_RESTART_SETTING='n'
       MOM6_RIVER_RUNOFF='True'
-        ;;
+      eps_imesh="1.0e-1"
+      ;;
     "025")
       ntasks_mom6=220
       OCNTIM=1800
@@ -291,12 +294,14 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs-clim-1997-2010.${NX_GLB}x${NY_GLB}.v20180328.nc"
       MOM6_RIVER_RUNOFF='True'
       MOM6_RESTART_SETTING="r"
+      eps_imesh="1.0e-1"
       ;;
     *)
       echo "FATAL ERROR: Unsupported MOM6 resolution = ${mom6_res}, ABORT!"
       exit 1
       ;;
   esac
+
   export nthreads_mom6 ntasks_mom6
   export OCNTIM
   export NX_GLB NY_GLB
@@ -305,6 +310,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
   export CHLCLIM
   export MOM6_RIVER_RUNOFF
   export MOM6_RESTART_SETTING
+  export eps_imesh
 fi
 
 # CICE6 specific settings
@@ -357,10 +363,12 @@ if [[ "${skip_ww3}" == "false" ]]; then
       ntasks_ww3=262
       ;;
     "glo_200")
-      ntasks_ww3=40
+      ntasks_ww3=30
+      nthreads_ww3=1
       ;;
     "glo_500")
-      ntasks_ww3=10
+      ntasks_ww3=12
+      nthreads_ww3=1
       ;;
     "mx025")
       ntasks_ww3=80
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 2cc8b2426f..bc9edfcb7e 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -544,38 +544,42 @@ elif [[ "${step}" = "fcst" || "${step}" = "efcs" ]]; then
         export MEDPETS MEDTHREADS
         echo "MEDIATOR using (threads, PETS) = (${MEDTHREADS}, ${MEDPETS})"
 
+        CHMPETS=0; CHMTHREADS=0
         if [[ "${DO_AERO}" = "YES" ]]; then
           # GOCART shares the same grid and forecast tasks as FV3 (do not add write grid component tasks).
           (( CHMTHREADS = ATMTHREADS ))
           (( CHMPETS = FV3PETS ))
           # Do not add to NTASKS_TOT
-          export CHMPETS CHMTHREADS
           echo "GOCART using (threads, PETS) = (${CHMTHREADS}, ${CHMPETS})"
         fi
+        export CHMPETS CHMTHREADS
 
+        WAVPETS=0; WAVTHREADS=0
         if [[ "${DO_WAVE}" = "YES" ]]; then
           (( WAVPETS = ntasks_ww3 * nthreads_ww3 ))
           (( WAVTHREADS = nthreads_ww3 ))
-          export WAVPETS WAVTHREADS
           echo "WW3 using (threads, PETS) = (${WAVTHREADS}, ${WAVPETS})"
           (( NTASKS_TOT = NTASKS_TOT + WAVPETS ))
         fi
+        export WAVPETS WAVTHREADS
 
+        OCNPETS=0; OCNTHREADS=0
         if [[ "${DO_OCN}" = "YES" ]]; then
           (( OCNPETS = ntasks_mom6 * nthreads_mom6 ))
           (( OCNTHREADS = nthreads_mom6 ))
-          export OCNPETS OCNTHREADS
           echo "MOM6 using (threads, PETS) = (${OCNTHREADS}, ${OCNPETS})"
           (( NTASKS_TOT = NTASKS_TOT + OCNPETS ))
         fi
+        export OCNPETS OCNTHREADS
 
+        ICEPETS=0; ICETHREADS=0
         if [[ "${DO_ICE}" = "YES" ]]; then
           (( ICEPETS = ntasks_cice6 * nthreads_cice6 ))
           (( ICETHREADS = nthreads_cice6 ))
-          export ICEPETS ICETHREADS
           echo "CICE6 using (threads, PETS) = (${ICETHREADS}, ${ICEPETS})"
           (( NTASKS_TOT = NTASKS_TOT + ICEPETS ))
         fi
+        export ICEPETS ICETHREADS
 
         echo "Total PETS for ${_CDUMP} = ${NTASKS_TOT}"
 
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index 1ec419b822..bfbb0a12cb 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -255,6 +255,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs_1998-2006_smoothed_2X.nc"
       MOM6_RESTART_SETTING='r'
       MOM6_RIVER_RUNOFF='False'
+      eps_imesh="4.0e-1"
       ;;
     "100")
       ntasks_mom6=20
@@ -267,6 +268,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs_1998-2006_smoothed_2X.nc"
       MOM6_RESTART_SETTING='n'
       MOM6_RIVER_RUNOFF='False'
+      eps_imesh="2.5e-1"
       ;;
     "50")
       ntasks_mom6=60
@@ -279,7 +281,8 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs-clim-1997-2010.${NX_GLB}x${NY_GLB}.v20180328.nc"
       MOM6_RESTART_SETTING='n'
       MOM6_RIVER_RUNOFF='True'
-        ;;
+      eps_imesh="1.0e-1"
+      ;;
     "025")
       ntasks_mom6=220
       OCNTIM=1800
@@ -291,12 +294,14 @@ if [[ "${skip_mom6}" == "false" ]]; then
       CHLCLIM="seawifs-clim-1997-2010.${NX_GLB}x${NY_GLB}.v20180328.nc"
       MOM6_RIVER_RUNOFF='True'
       MOM6_RESTART_SETTING="r"
+      eps_imesh="1.0e-1"
       ;;
     *)
       echo "FATAL ERROR: Unsupported MOM6 resolution = ${mom6_res}, ABORT!"
       exit 1
       ;;
   esac
+
   export nthreads_mom6 ntasks_mom6
   export OCNTIM
   export NX_GLB NY_GLB
@@ -305,6 +310,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
   export CHLCLIM
   export MOM6_RIVER_RUNOFF
   export MOM6_RESTART_SETTING
+  export eps_imesh
 fi
 
 # CICE6 specific settings
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index f503e7e273..36afb4d4c1 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -154,6 +154,30 @@ for file in finddate.sh make_ntc_bull.pl make_NTC_file.pl make_tif.sh month_name
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/ush/${file}" .
 done
 
+# TODO: Link these nems.configure templates from ufs-weather-model
+#cd "${HOMEgfs}/parm/ufs" || exit 1
+#declare -a nems_configure_files=("nems.configure.atm.IN" \
+#                                 "nems.configure.atm_aero.IN" \
+#                                 "nems.configure.atmw.IN" \
+#                                 "nems.configure.blocked_atm_wav_2way.IN" \
+#                                 "nems.configure.blocked_atm_wav.IN" \
+#                                 "nems.configure.cpld_agrid.IN" \
+#                                 "nems.configure.cpld_esmfthreads.IN" \
+#                                 "nems.configure.cpld.IN" \
+#                                 "nems.configure.cpld_noaero.IN" \
+#                                 "nems.configure.cpld_noaero_nowave.IN" \
+#                                 "nems.configure.cpld_noaero_outwav.IN" \
+#                                 "nems.configure.leapfrog_atm_wav.IN")
+#for file in "${nems_configure_files[@]}"; do
+#  [[ -s "${file}" ]] && rm -f "${file}"
+#  ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/${file}" .
+#done
+
+cd "${HOMEgfs}/ush" || exit 1
+[[ -s "atparse.bash" ]] && rm -f "atparse.bash"
+${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/atparse.bash" .
+
+
 #------------------------------
 #--add GDASApp fix directory
 #------------------------------
diff --git a/ush/nems_configure.sh b/ush/nems_configure.sh
index c51e500d5d..1c62cdfd25 100755
--- a/ush/nems_configure.sh
+++ b/ush/nems_configure.sh
@@ -39,153 +39,68 @@ else
   exit 1
 fi
 
+local atm_model="fv3"
 local atm_petlist_bounds="0 $(( ${ATMPETS}-1 ))"
-local med_petlist_bounds="0 $(( ${MEDPETS}-1 ))"
+local atm_omp_num_threads="${ATMTHREADS}"
 
-sed -i -e "s;@\[atm_model\];fv3;g" tmp1
-sed -i -e "s;@\[atm_petlist_bounds\];${atm_petlist_bounds};g" tmp1
-sed -i -e "s;@\[atm_omp_num_threads\];${ATMTHREADS};g" tmp1
-sed -i -e "s;@\[med_model\];cmeps;g" tmp1
-sed -i -e "s;@\[med_petlist_bounds\];${med_petlist_bounds};g" tmp1
-sed -i -e "s;@\[med_omp_num_threads\];${MEDTHREADS};g" tmp1
-sed -i -e "s;@\[esmf_logkind\];${esmf_logkind};g" tmp1
+local med_model="cmeps"
+local med_petlist_bounds="0 $(( ${MEDPETS}-1 ))"
+local med_omp_num_threads="${MEDTHREADS}"
 
 if [[ "${cpl}" = ".true." ]]; then
-  sed -i -e "s;@\[coupling_interval_slow_sec\];${CPL_SLOW};g" tmp1
+  local coupling_interval_slow_sec="${CPL_SLOW}"
 fi
 
 if [[ "${cplflx}" = ".true." ]]; then
-  # TODO: Should this be raised up to config.ufs or config.ocn?
-  case "${OCNRES}" in
-    "500") local eps_imesh="4.0e-1";;
-    "100") local eps_imesh="2.5e-1";;
-    *) local eps_imesh="1.0e-1";;
-  esac
 
   local use_coldstart=${use_coldstart:-".false."}
   local use_mommesh=${USE_MOMMESH:-"true"}
-  local restile=$(echo "${CASE}" |cut -c2-)
-
-  local start="${ATMPETS}"
-  local end="$(( ${start}+${OCNPETS}-1 ))"
-  local ocn_petlist_bounds="${start} ${end}"
-
-  sed -i -e "s;@\[ocn_model\];mom6;g" tmp1
-  sed -i -e "s;@\[ocn_petlist_bounds\];${ocn_petlist_bounds};g" tmp1
-  sed -i -e "s;@\[ocn_omp_num_threads\];${OCNTHREADS};g" tmp1
-  sed -i -e "s;@\[DumpFields\];${DumpFields};g" tmp1
-  sed -i -e "s;@\[cap_dbug_flag\];${cap_dbug_flag};g" tmp1
-  sed -i -e "s;@\[use_coldstart\];${use_coldstart};g" tmp1
-  sed -i -e "s;@\[RUNTYPE\];${cmeps_run_type};g" tmp1
-  sed -i -e "s;@\[CPLMODE\];${cplmode};g" tmp1
-  sed -i -e "s;@\[coupling_interval_fast_sec\];${CPL_FAST};g" tmp1
-  sed -i -e "s;@\[RESTART_N\];${restart_interval};g" tmp1
-  sed -i -e "s;@\[use_mommesh\];${use_mommesh};g" tmp1
-  sed -i -e "s;@\[eps_imesh\];${eps_imesh};g" tmp1
-  sed -i -e "s;@\[ATMTILESIZE\];${restile};g" tmp1
+
+  local ocn_model="mom6"
+  local ocn_petlist_bounds="${ATMPETS} $(( ${ATMPETS}+${OCNPETS}-1 ))"
+  local ocn_omp_num_threads="${OCNTHREADS}"
+  local RUNTYPE="${cmeps_run_type}"
+  local CPLMODE="${cplmode}"
+  local coupling_interval_fast_sec="${CPL_FAST}"
+  local RESTART_N="${restart_interval}"
+  local ATMTILESIZE="${CASE:2:}"
 fi
 
 if [[ "${cplice}" = ".true." ]]; then
 
-  local mesh_ocn_ice=${MESH_OCN_ICE:-"mesh.mx${ICERES}.nc"}
-
-  local start="$(( ${ATMPETS}+${OCNPETS} ))"
-  local end="$(( ${start}+${ICEPETS}-1 ))"
-  local ice_petlist_bounds="${start} ${end}"
-
-  sed -i -e "s;@\[ice_model\];cice6;g" tmp1
-  sed -i -e "s;@\[ice_petlist_bounds\];${ice_petlist_bounds};g" tmp1
-  sed -i -e "s;@\[ice_omp_num_threads\];${ICETHREADS};g" tmp1
-  sed -i -e "s;@\[MESH_OCN_ICE\];${mesh_ocn_ice};g" tmp1
-  sed -i -e "s;@\[FHMAX\];${FHMAX_GFS};g" tmp1
+  local ice_model="cice6"
+  local ice_petlist_bounds="$(( ${ATMPETS}+${OCNPETS} )) $(( ${ATMPETS}+${OCNPETS}+${ICEPETS}-1 ))"
+  local ice_omp_num_threads="${ICETHREADS}"
+  local MESH_OCN_ICE=${MESH_OCN_ICE:-"mesh.mx${ICERES}.nc"}
+  local FHMAX="${FHMAX_GFS}"  # TODO:  How did this get in here hard-wired to FHMAX_GFS?
 fi
 
 if [[ "${cplwav}" = ".true." ]]; then
 
-  local start="$(( ${ATMPETS}+${OCNPETS:-0}+${ICEPETS:-0} ))"
-  local end="$(( ${start}+${WAVPETS}-1 ))"
-  local wav_petlist_bounds="${start} ${end}"
+  local wav_model="ww3"
+  local wav_petlist_bounds="$(( ${ATMPETS}+${OCNPETS}+${ICEPETS} )) $(( ${ATMPETS}+${OCNPETS}+${ICEPETS}+${WAVPETS}-1 ))"
+  local wav_omp_num_threads="${WAVTHREADS}"
+  local MULTIGRID="${waveMULTIGRID}"
 
-  sed -i -e "s;@\[wav_model\];ww3;g" tmp1
-  sed -i -e "s;@\[wav_petlist_bounds\];${wav_petlist_bounds};g" tmp1
-  sed -i -e "s;@\[wav_omp_num_threads\];${WAVTHREADS};g" tmp1
-  sed -i -e "s;@\[MESH_WAV\];${MESH_WAV};g" tmp1
-  sed -i -e "s;@\[MULTIGRID\];${waveMULTIGRID};g" tmp1
 fi
 
 if [[ "${cplchm}" = ".true." ]]; then
 
+  local chm_model="gocart"
   local chm_petlist_bounds="0 $(( ${CHMPETS}-1 ))"
+  local chm_omp_num_threads="${CHMTHREADS}"
+  local coupling_interval_fast_sec="${CPL_FAST}"
 
-  sed -i -e "s;@\[chm_model\];gocart;g" tmp1
-  sed -i -e "s;@\[chm_petlist_bounds\];${chm_petlist_bounds};g" tmp1
-  sed -i -e "s;@\[chm_omp_num_threads\];${CHMTHREADS};g" tmp1
-  sed -i -e "s;@\[coupling_interval_fast_sec\];${CPL_FAST};g" tmp1
 fi
 
-mv tmp1 nems.configure
+source "${HOMEgfs}/ush/atparse.bash"
+rm -f "${DATA}/nems.configure"
+atparse < "${infile}" >> "${DATA}/nems.configure"
 
 echo "$(cat nems.configure)"
 
-if [[ "${cplflx}" = ".true." ]]; then
-
-#Create other CMEPS mediator related files
-cat > pio_in << EOF
-&papi_inparm
-  papi_ctr1_str = "PAPI_FP_OPS"
-  papi_ctr2_str = "PAPI_NO_CTR"
-  papi_ctr3_str = "PAPI_NO_CTR"
-  papi_ctr4_str = "PAPI_NO_CTR"
-/
-&pio_default_inparm
-  pio_async_interface = .false.
-  pio_blocksize = -1
-  pio_buffer_size_limit = -1
-  pio_debug_level = 0
-  pio_rearr_comm_enable_hs_comp2io = .true.
-  pio_rearr_comm_enable_hs_io2comp = .false.
-  pio_rearr_comm_enable_isend_comp2io = .false.
-  pio_rearr_comm_enable_isend_io2comp = .true.
-  pio_rearr_comm_fcd = "2denable"
-  pio_rearr_comm_max_pend_req_comp2io = 0
-  pio_rearr_comm_max_pend_req_io2comp = 64
-  pio_rearr_comm_type = "p2p"
-/
-&prof_inparm
-  profile_add_detail = .false.
-  profile_barrier = .false.
-  profile_depth_limit = 4
-  profile_detail_limit = 2
-  profile_disable = .false.
-  profile_global_stats = .true.
-  profile_outpe_num = 1
-  profile_outpe_stride = 0
-  profile_ovhd_measurement = .false.
-  profile_papi_enable = .false.
-  profile_single_file = .false.
-  profile_timer = 4
-/
-EOF
-
-echo "$(cat pio_in)"
-
-cat > med_modelio.nml << EOF
-&pio_inparm
-  pio_netcdf_format = "64bit_offset"
-  pio_numiotasks = -99
-  pio_rearranger = 1
-  pio_root = 1
-  pio_stride = 36
-  pio_typename = "netcdf"
-/
-EOF
-
-echo "$(cat med_modelio.nml)"
-
-fi
-
 ${NCP} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/fd_nems.yaml" fd_nems.yaml
 
-echo "SUB ${FUNCNAME[0]}: Nems configured for ${confignamevarfornems}"
+echo "SUB ${FUNCNAME[0]}: nems.configure.sh ends for ${confignamevarfornems}"
 
 }

From ea91d12e88a91e47f2d93afe79b6c38dfcbdc698 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 17:02:59 -0400
Subject: [PATCH 5/6] disable shellcheck on external sources in this function

---
 sorc/link_workflow.sh |  2 +-
 ush/nems_configure.sh | 19 ++++++++++---------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 36afb4d4c1..b88fd664e2 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -2,7 +2,7 @@
 
 #--make symbolic links for EMC installation and hardcopies for NCO delivery
 
-declare -r HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/.." >/dev/null 2>&1 && pwd )"
+HOMEgfs="$(cd "$(dirname  "${BASH_SOURCE[0]}")/.." >/dev/null 2>&1 && pwd )"
 TRACE=NO source "${HOMEgfs}/ush/preamble.sh"
 
 function usage() {
diff --git a/ush/nems_configure.sh b/ush/nems_configure.sh
index 1c62cdfd25..df825eeea3 100755
--- a/ush/nems_configure.sh
+++ b/ush/nems_configure.sh
@@ -9,8 +9,9 @@
 ## This is a child script of modular
 ## forecast script. This script is definition only (Is it? There is nothing defined here being used outside this script.)
 #####
-writing_nems_configure()
-{
+# shellcheck disable=SC2034
+writing_nems_configure() {
+
 echo "SUB ${FUNCNAME[0]}: nems.configure.sh begins"
 
 # Setup nems.configure
@@ -40,11 +41,11 @@ else
 fi
 
 local atm_model="fv3"
-local atm_petlist_bounds="0 $(( ${ATMPETS}-1 ))"
+local atm_petlist_bounds="0 $(( ATMPETS-1 ))"
 local atm_omp_num_threads="${ATMTHREADS}"
 
 local med_model="cmeps"
-local med_petlist_bounds="0 $(( ${MEDPETS}-1 ))"
+local med_petlist_bounds="0 $(( MEDPETS-1 ))"
 local med_omp_num_threads="${MEDTHREADS}"
 
 if [[ "${cpl}" = ".true." ]]; then
@@ -57,7 +58,7 @@ if [[ "${cplflx}" = ".true." ]]; then
   local use_mommesh=${USE_MOMMESH:-"true"}
 
   local ocn_model="mom6"
-  local ocn_petlist_bounds="${ATMPETS} $(( ${ATMPETS}+${OCNPETS}-1 ))"
+  local ocn_petlist_bounds="${ATMPETS} $(( ATMPETS+OCNPETS-1 ))"
   local ocn_omp_num_threads="${OCNTHREADS}"
   local RUNTYPE="${cmeps_run_type}"
   local CPLMODE="${cplmode}"
@@ -69,7 +70,7 @@ fi
 if [[ "${cplice}" = ".true." ]]; then
 
   local ice_model="cice6"
-  local ice_petlist_bounds="$(( ${ATMPETS}+${OCNPETS} )) $(( ${ATMPETS}+${OCNPETS}+${ICEPETS}-1 ))"
+  local ice_petlist_bounds="$(( ATMPETS+OCNPETS )) $(( ATMPETS+OCNPETS+ICEPETS-1 ))"
   local ice_omp_num_threads="${ICETHREADS}"
   local MESH_OCN_ICE=${MESH_OCN_ICE:-"mesh.mx${ICERES}.nc"}
   local FHMAX="${FHMAX_GFS}"  # TODO:  How did this get in here hard-wired to FHMAX_GFS?
@@ -78,7 +79,7 @@ fi
 if [[ "${cplwav}" = ".true." ]]; then
 
   local wav_model="ww3"
-  local wav_petlist_bounds="$(( ${ATMPETS}+${OCNPETS}+${ICEPETS} )) $(( ${ATMPETS}+${OCNPETS}+${ICEPETS}+${WAVPETS}-1 ))"
+  local wav_petlist_bounds="$(( ATMPETS+OCNPETS+ICEPETS )) $(( ATMPETS+OCNPETS+ICEPETS+WAVPETS-1 ))"
   local wav_omp_num_threads="${WAVTHREADS}"
   local MULTIGRID="${waveMULTIGRID}"
 
@@ -87,7 +88,7 @@ fi
 if [[ "${cplchm}" = ".true." ]]; then
 
   local chm_model="gocart"
-  local chm_petlist_bounds="0 $(( ${CHMPETS}-1 ))"
+  local chm_petlist_bounds="0 $(( CHMPETS-1 ))"
   local chm_omp_num_threads="${CHMTHREADS}"
   local coupling_interval_fast_sec="${CPL_FAST}"
 
@@ -97,7 +98,7 @@ source "${HOMEgfs}/ush/atparse.bash"
 rm -f "${DATA}/nems.configure"
 atparse < "${infile}" >> "${DATA}/nems.configure"
 
-echo "$(cat nems.configure)"
+cat nems.configure
 
 ${NCP} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/fd_nems.yaml" fd_nems.yaml
 

From e0bd484cbff57d12738085cf87b43ae0953eafe8 Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Thu, 13 Jul 2023 17:10:04 -0400
Subject: [PATCH 6/6] no need for tmp1

---
 ush/nems_configure.sh | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/ush/nems_configure.sh b/ush/nems_configure.sh
index df825eeea3..5de127bb31 100755
--- a/ush/nems_configure.sh
+++ b/ush/nems_configure.sh
@@ -9,6 +9,8 @@
 ## This is a child script of modular
 ## forecast script. This script is definition only (Is it? There is nothing defined here being used outside this script.)
 #####
+
+# Disable variable not used warnings
 # shellcheck disable=SC2034
 writing_nems_configure() {
 
@@ -27,19 +29,9 @@ else
   local cmeps_run_type='startup'
 fi
 
-rm -f "${DATA}/nems.configure"
-
 local esmf_logkind=${esmf_logkind:-"ESMF_LOGKIND_MULTI"} #options: ESMF_LOGKIND_MULTI_ON_ERROR, ESMF_LOGKIND_MULTI, ESMF_LOGKIND_NONE
 
-# Copy the selected template into run directory
-infile="${HOMEgfs}/parm/ufs/nems.configure.${confignamevarfornems}.IN"
-if [[ -s ${infile} ]]; then
-  cp "${infile}" tmp1
-else
-  echo "FATAL ERROR: nem.configure template '${infile}' does not exist!"
-  exit 1
-fi
-
+# Atm-related
 local atm_model="fv3"
 local atm_petlist_bounds="0 $(( ATMPETS-1 ))"
 local atm_omp_num_threads="${ATMTHREADS}"
@@ -94,10 +86,17 @@ if [[ "${cplchm}" = ".true." ]]; then
 
 fi
 
+# Ensure the template exists
+template="${HOMEgfs}/parm/ufs/nems.configure.${confignamevarfornems}.IN"
+if [[ ! -f ${template} ]]; then
+  echo "FATAL ERROR: template '${template}' does not exist, ABORT!"
+  exit 1
+fi
+
 source "${HOMEgfs}/ush/atparse.bash"
 rm -f "${DATA}/nems.configure"
-atparse < "${infile}" >> "${DATA}/nems.configure"
-
+atparse < "${template}" >> "${DATA}/nems.configure"
+echo "Rendered nems.configure:"
 cat nems.configure
 
 ${NCP} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/fd_nems.yaml" fd_nems.yaml