From c98474a7076a3419a93e63cf8609901e02979ccc Mon Sep 17 00:00:00 2001
From: Jessica Meixner <jessica.meixner@noaa.gov>
Date: Wed, 12 Jun 2024 11:03:13 -0400
Subject: [PATCH] Update ufs-weather-model  (#2663)

Updates ufs-weather-model, this updates RDHPCS to the newer spack-stack
allowing some temporary fixes to be reverted.
* removes upp submodule
* uses upp from the ufs-weather-model
* restores the build and link that were hacked during the Hera Rocky 8
transition to allow for UPP submodule
* Removes forecast directories in clean-up

Resolves #2617
Resolves #2437

---------

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 .gitmodules                 |  4 ----
 scripts/exglobal_cleanup.sh |  7 +++++++
 sorc/build_upp.sh           |  2 +-
 sorc/link_workflow.sh       |  9 ++++-----
 sorc/ufs_model.fd           |  2 +-
 sorc/upp.fd                 |  1 -
 ush/forecast_postdet.sh     | 11 +++++------
 7 files changed, 18 insertions(+), 18 deletions(-)
 delete mode 160000 sorc/upp.fd

diff --git a/.gitmodules b/.gitmodules
index ea1b5c06af..1c3b7acfa5 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -26,10 +26,6 @@
 [submodule "sorc/gsi_monitor.fd"]
   path = sorc/gsi_monitor.fd
   url = https://github.com/NOAA-EMC/GSI-Monitor.git
-[submodule "sorc/upp.fd"]
-  path = sorc/upp.fd
-  url = https://github.com/NOAA-EMC/UPP.git
-  ignore = dirty
 [submodule "sorc/jcb"]
   path = sorc/jcb
   url = https://github.com/noaa-emc/jcb
diff --git a/scripts/exglobal_cleanup.sh b/scripts/exglobal_cleanup.sh
index c2b748f696..7c3dfafbad 100755
--- a/scripts/exglobal_cleanup.sh
+++ b/scripts/exglobal_cleanup.sh
@@ -2,6 +2,13 @@
 
 source "${USHgfs}/preamble.sh"
 
+# Remove DATAoutput from the forecast model run
+# TODO: Handle this better
+DATAfcst="${DATAROOT}/${RUN}fcst.${PDY:-}${cyc}"
+if [[ -d "${DATAfcst}" ]]; then rm -rf "${DATAfcst}"; fi
+#DATAefcs="${DATAROOT}/${RUN}efcs???${PDY:-}${cyc}"
+rm -rf "${DATAROOT}/${RUN}efcs"*"${PDY:-}${cyc}"
+
 ###############################################################
 # Clean up previous cycles; various depths
 # PRIOR CYCLE: Leave the prior cycle alone
diff --git a/sorc/build_upp.sh b/sorc/build_upp.sh
index 1dca0035fd..e217e171db 100755
--- a/sorc/build_upp.sh
+++ b/sorc/build_upp.sh
@@ -26,6 +26,6 @@ if [[ ! -d "../exec" ]]; then
   mkdir -p ../exec
 fi
 
-cd upp.fd/tests
+cd ufs_model.fd/FV3/upp/tests
 # shellcheck disable=SC2086
 BUILD_JOBS=${BUILD_JOBS:-8} ./compile_upp.sh ${_opts}
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index f338f2bad3..593a4694c1 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -370,11 +370,10 @@ fi
 #--link source code directories
 #------------------------------
 cd "${HOMEgfs}/sorc" || exit 8
-# TODO: Commenting out until UPP is up-to-date with Rocky-8.
-#if [[ -d ufs_model.fd ]]; then
-#  [[ -d upp.fd ]] && rm -rf upp.fd
-#  ${LINK} ufs_model.fd/FV3/upp upp.fd
-#fi
+if [[ -d ufs_model.fd ]]; then
+  [[ -d upp.fd ]] && rm -rf upp.fd
+  ${LINK} ufs_model.fd/FV3/upp upp.fd
+fi
 
 if [[ -d gsi_enkf.fd ]]; then
   [[ -d gsi.fd ]] && rm -rf gsi.fd
diff --git a/sorc/ufs_model.fd b/sorc/ufs_model.fd
index 5bec704243..485ccdfc4a 160000
--- a/sorc/ufs_model.fd
+++ b/sorc/ufs_model.fd
@@ -1 +1 @@
-Subproject commit 5bec704243286421fc613838fc67a2129e96acd6
+Subproject commit 485ccdfc4a7ed6deeb02d82c2cebe51b37e892f5
diff --git a/sorc/upp.fd b/sorc/upp.fd
deleted file mode 160000
index 83e83a938b..0000000000
--- a/sorc/upp.fd
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit 83e83a938b5794a628d30e66a54902dabe58737d
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 3f6ffcb8c2..aff4f5a394 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -217,12 +217,11 @@ FV3_out() {
   echo "SUB ${FUNCNAME[0]}: copying output data for FV3"
 
   # Copy configuration files
-  if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
-    ${NCP} "${DATA}/input.nml" "${COMOUT_CONF}/ufs.input.nml"
-    ${NCP} "${DATA}/model_configure" "${COMOUT_CONF}/ufs.model_configure"
-    ${NCP} "${DATA}/ufs.configure" "${COMOUT_CONF}/ufs.ufs.configure"
-    ${NCP} "${DATA}/diag_table" "${COMOUT_CONF}/ufs.diag_table"
-  fi
+  ${NCP} "${DATA}/input.nml" "${COMOUT_CONF}/ufs.input.nml"
+  ${NCP} "${DATA}/model_configure" "${COMOUT_CONF}/ufs.model_configure"
+  ${NCP} "${DATA}/ufs.configure" "${COMOUT_CONF}/ufs.ufs.configure"
+  ${NCP} "${DATA}/diag_table" "${COMOUT_CONF}/ufs.diag_table"
+ 
 
   # Create an array of fv3 restart files
   local fv3_restart_files tile_files fv3_restart_file restart_file