From abf2035728dc65512428f703dcc4abf4ed00178f Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Thu, 16 May 2024 08:42:22 -0500
Subject: [PATCH 01/18] add cycle capability to rocoto yaml

---
 jobs/JLANDDA_ANALYSIS               |  8 ++---
 jobs/JLANDDA_FORECAST               |  8 ++---
 jobs/JLANDDA_PREP_BMAT              |  8 ++---
 jobs/JLANDDA_PREP_EXP               |  8 ++---
 jobs/JLANDDA_PREP_OBS               |  8 ++---
 parm/conda_environment.yml          |  2 +-
 parm/land_analysis_era5_hera.yaml   |  8 ++++-
 parm/land_analysis_era5_orion.yaml  |  8 ++++-
 parm/land_analysis_gswp3_hera.yaml  | 10 ++++--
 parm/land_analysis_gswp3_orion.yaml | 51 +++++++++++++++++++++--------
 parm/run_without_rocoto.sh          |  4 ++-
 scripts/exlandda_prep_obs.sh        | 14 +++++---
 12 files changed, 93 insertions(+), 44 deletions(-)

diff --git a/jobs/JLANDDA_ANALYSIS b/jobs/JLANDDA_ANALYSIS
index 9afa8043..910b6262 100755
--- a/jobs/JLANDDA_ANALYSIS
+++ b/jobs/JLANDDA_ANALYSIS
@@ -58,11 +58,11 @@ export RUN="${RUN:-landda}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/jobs/JLANDDA_FORECAST b/jobs/JLANDDA_FORECAST
index 13f42b5a..e04c5786 100755
--- a/jobs/JLANDDA_FORECAST
+++ b/jobs/JLANDDA_FORECAST
@@ -58,11 +58,11 @@ export RUN="${RUN:-landda}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/jobs/JLANDDA_PREP_BMAT b/jobs/JLANDDA_PREP_BMAT
index b8c35834..88c27555 100755
--- a/jobs/JLANDDA_PREP_BMAT
+++ b/jobs/JLANDDA_PREP_BMAT
@@ -58,11 +58,11 @@ export RUN="${RUN:-landda}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/jobs/JLANDDA_PREP_EXP b/jobs/JLANDDA_PREP_EXP
index 5748908f..cc03b593 100755
--- a/jobs/JLANDDA_PREP_EXP
+++ b/jobs/JLANDDA_PREP_EXP
@@ -58,11 +58,11 @@ export RUN="${RUN:-landda}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/jobs/JLANDDA_PREP_OBS b/jobs/JLANDDA_PREP_OBS
index e75c71a4..dd2422fc 100755
--- a/jobs/JLANDDA_PREP_OBS
+++ b/jobs/JLANDDA_PREP_OBS
@@ -58,11 +58,11 @@ export RUN="${RUN:-landda}"
 
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}${SLASH_ENSMEM_SUBDIR}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/parm/conda_environment.yml b/parm/conda_environment.yml
index b1ea918f..53cb4899 100644
--- a/parm/conda_environment.yml
+++ b/parm/conda_environment.yml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - pylint=2.17*
   - pytest=7.2*
-  - uwtools=2.1.1
+  - uwtools=2.2.0
diff --git a/parm/land_analysis_era5_hera.yaml b/parm/land_analysis_era5_hera.yaml
index d4eff5ac..fee5f3de 100644
--- a/parm/land_analysis_era5_hera.yaml
+++ b/parm/land_analysis_era5_hera.yaml
@@ -2,9 +2,11 @@ workflow:
   attrs:
     realtime: false
     scheduler: slurm
+    cyclethrottle: 24
+    taskthrottle: 24
   cycledef:
     - attrs:
-        group: epic
+        group: cycled
       spec: 201912210000 201912210000 24:00:00
   entities:
     MACHINE: "hera"
@@ -18,6 +20,8 @@ workflow:
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
     NPROCS_FORECAST: "6"
+    OBSDIR: ""
+    OBSDIR_SUBDIR: ""
     OBS_TYPES: "GHCN"
     DAtype: "letkfoi_snow"
     SNOWDEPTHVAR: "snwdph"
@@ -68,6 +72,8 @@ workflow:
       join: "&LOGDIR;/prep_exp.log"
     task_prep_obs:
       envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
diff --git a/parm/land_analysis_era5_orion.yaml b/parm/land_analysis_era5_orion.yaml
index 08859eba..ee12151d 100644
--- a/parm/land_analysis_era5_orion.yaml
+++ b/parm/land_analysis_era5_orion.yaml
@@ -2,9 +2,11 @@ workflow:
   attrs:
     realtime: false
     scheduler: slurm
+    cyclethrottle: 24
+    taskthrottle: 24
   cycledef:
     - attrs:
-        group: epic
+        group: cycled
       spec: 201912210000 201912210000 24:00:00
   entities:
     MACHINE: "orion"
@@ -18,6 +20,8 @@ workflow:
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
     NPROCS_FORECAST: "6"
+    OBSDIR: ""
+    OBSDIR_SUBDIR: ""
     OBS_TYPES: "GHCN"
     DAtype: "letkfoi_snow"
     SNOWDEPTHVAR: "snwdph"
@@ -68,6 +72,8 @@ workflow:
       join: "&LOGDIR;/prep_exp.log"
     task_prep_obs:
       envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_gswp3_hera.yaml
index 8f58c142..798af689 100644
--- a/parm/land_analysis_gswp3_hera.yaml
+++ b/parm/land_analysis_gswp3_hera.yaml
@@ -2,10 +2,12 @@ workflow:
   attrs:
     realtime: false
     scheduler: slurm
+    cyclethrottle: 24
+    taskthrottle: 24
   cycledef:
     - attrs:
-        group: epic
-      spec: 200001030000 200001030000 24:00:00
+        group: cycled
+      spec: 200001030000 200001040000 24:00:00
   entities:
     MACHINE: "hera"
     SCHED: "slurm"
@@ -18,6 +20,8 @@ workflow:
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
     NPROCS_FORECAST: "6"
+    OBSDIR: ""
+    OBSDIR_SUBDIR: ""
     OBS_TYPES: "GHCN"
     DAtype: "letkfoi_snow"
     SNOWDEPTHVAR: "snwdph"
@@ -68,6 +72,8 @@ workflow:
       join: "&LOGDIR;/prep_exp.log"
     task_prep_obs:
       envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index d6251707..a7c533da 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -2,10 +2,12 @@ workflow:
   attrs:
     realtime: false
     scheduler: slurm
+    cyclethrottle: 24
+    taskthrottle: 24
   cycledef:
     - attrs:
-        group: epic
-      spec: 200001030000 200001030000 24:00:00
+        group: cycled
+      spec: 200001030000 200001040000 24:00:00
   entities:
     MACHINE: "orion"
     SCHED: "slurm"
@@ -18,6 +20,8 @@ workflow:
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
     NPROCS_FORECAST: "6"
+    OBSDIR: ""
+    OBSDIR_SUBDIR: ""
     OBS_TYPES: "GHCN"
     DAtype: "letkfoi_snow"
     SNOWDEPTHVAR: "snwdph"
@@ -25,6 +29,7 @@ workflow:
     NET: "landda"
     envir: "test"
     model_ver: "v1.2.1"
+    RUN: "landda"
     HOMElandda: "&EXP_BASEDIR;/land-DA_workflow"
     PTMP: "&EXP_BASEDIR;/ptmp"
     COMROOT: "&PTMP;/&envir;/com"
@@ -32,15 +37,20 @@ workflow:
     KEEPDATA: "YES"
     WORKDIR: "&EXP_BASEDIR;/workdir/run_&FORCING;"
     LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
+    LOGFN_SUFFIX: "<cyclestr>_@Y@m@d.log</cyclestr>"
     PATHRT: "&EXP_BASEDIR;"
     PDY:  "<cyclestr>@Y@m@d</cyclestr>"
     cyc: "<cyclestr>@H</cyclestr>"
-    SLASH_ENSMEM_SUBDIR: ""
     PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
     NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
+    WARMSTART_DIR: ""
+    DATADEP_FILE1: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE2: "<cyclestr offset='-24:00:00'>&COMROOT;/&NET;/&model_ver;/&RUN;.@Y@m@d/@H/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
   tasks:
     task_prep_exp:
+      attrs:
+        cycledefs: cycled
       envars:
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
@@ -57,7 +67,6 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_exp" "&HOMElandda;" "&MACHINE;"'
@@ -65,9 +74,23 @@ workflow:
       cores: 1
       walltime: 00:02:00
       queue: batch
-      join: "&LOGDIR;/prep_exp.log"
+      join: "&LOGDIR;/prep_exp&LOGFN_SUFFIX;"
+      dependency:
+        or:
+          datadep_file1:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE1;"
+          datadep_file2:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE2;"
     task_prep_obs:
+      attrs:
+        cycledefs: cycled
       envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
@@ -82,7 +105,6 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
@@ -90,12 +112,14 @@ workflow:
       cores: 1
       walltime: 00:02:00
       queue: batch
-      join: "&LOGDIR;/prep_obs.log"
+      join: "&LOGDIR;/prep_obs&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
             task: prep_exp
     task_prep_bmat:
+      attrs:
+        cycledefs: cycled
       envars:
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
@@ -110,7 +134,6 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
         DAtype: "&DAtype;"
         SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
@@ -120,12 +143,14 @@ workflow:
       cores: 1
       walltime: 00:02:00
       queue: batch
-      join: "&LOGDIR;/prep_bmat.log"
+      join: "&LOGDIR;/prep_bmat&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
             task: prep_obs
     task_analysis:
+      attrs:
+        cycledefs: cycled
       envars:
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
@@ -143,7 +168,6 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
@@ -156,12 +180,14 @@ workflow:
       nodes: "1:ppn=&NPROCS_ANALYSIS;"
       walltime: 00:15:00
       queue: batch
-      join: "&LOGDIR;/analysis.log"
+      join: "&LOGDIR;/analysis&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
             task: prep_bmat
     task_forecast:
+      attrs:
+        cycledefs: cycled
       envars:
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
@@ -180,7 +206,6 @@ workflow:
         LOGDIR: "&LOGDIR;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
@@ -193,7 +218,7 @@ workflow:
       nodes: "1:ppn=&NPROCS_FORECAST;"
       walltime: 01:00:00
       queue: batch
-      join: "&LOGDIR;/forecast.log"
+      join: "&LOGDIR;/forecast&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
diff --git a/parm/run_without_rocoto.sh b/parm/run_without_rocoto.sh
index 87087e81..4514a6fb 100755
--- a/parm/run_without_rocoto.sh
+++ b/parm/run_without_rocoto.sh
@@ -19,7 +19,7 @@ if [ "${MACHINE}" = "hera" ]; then
   export EXP_BASEDIR="/scratch2/NAGAPE/epic/{USER}/landda_test"
   export JEDI_INSTALL="/scratch2/NAGAPE/epic/UFS_Land-DA/jedi_skylabv7.0"
 elif [ "${MACHINE}" = "orion" ]; then
-  export EXP_BASEDIR="/work/noaa/epic/chjeon/landda_test"
+  export EXP_BASEDIR="/work/noaa/epic/{USER}/landda_test"
   export JEDI_INSTALL="/work/noaa/epic/UFS_Land-DA/jedi_skylabv7.0"
 fi
 
@@ -27,6 +27,8 @@ export RES="96"
 export FCSTHR="24"
 export NPROCS_ANALYSIS="6"
 export NPROCS_FORECAST="6"
+export OBSDIR=""
+export OBSDIR_SUBDIR=""
 export OBS_TYPES="GHCN"
 export DAtype="letkfoi_snow"
 export SNOWDEPTHVAR="snwdph"
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index 2de0c8e0..cb865530 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -27,22 +27,26 @@ JEDIWORKDIR=${WORKDIR}/mem000/jedi
 
 cd $JEDIWORKDIR
 
-OBSDIR=${FIXlandda}/DA
 ################################################
 # 2. PREPARE OBS FILES
 ################################################
+OBSDIR="${OBSDIR:-${FIXlandda}/DA}"
 for obs in "${OBS_TYPES[@]}"; do
   # get the obs file name
   if [ ${obs} == "GTS" ]; then
-    obsfile=$OBSDIR/snow_depth/GTS/data_proc/${YYYY}${MM}/adpsfc_snow_${YYYY}${MM}${DD}${HH}.nc4
+    OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-snow_depth/GTS/data_proc}"
+    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}${MM}/adpsfc_snow_${YYYY}${MM}${DD}${HH}.nc4"
     # GHCN are time-stamped at 18. If assimilating at 00, need to use previous day's obs, so that
     # obs are within DA window.
   elif [ $ATMOS_FORC == "era5" ] && [ ${obs} == "GHCN" ]; then
-    obsfile=$OBSDIR/snow_depth/GHCN/data_proc/v3/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}_jediv7.nc
+    OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-snow_depth/GHCN/data_proc/v3}"
+    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc"
   elif [ $ATMOS_FORC == "gswp3" ] && [ ${obs} == "GHCN" ]; then
-    obsfile=$OBSDIR/snow_depth/GHCN/data_proc/v3/${YYYY}/fake_ghcn_snwd_ioda_${YYYP}${MP}${DP}_jediv7.nc
+    OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-snow_depth/GHCN/data_proc/v3}"
+    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc"
   elif [ ${obs} == "SYNTH" ]; then
-    obsfile=$OBSDIR/synthetic_noahmp/IODA.synthetic_gswp_obs.${YYYY}${MM}${DD}${HH}.nc
+    OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-synthetic_noahmp}"
+    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/IODA.synthetic_gswp_obs.${YYYY}${MM}${DD}${HH}.nc"
   else
     echo "do_landDA: Unknown obs type requested ${obs}, exiting"
     exit 1

From f86ad0620a4eb3fc4520139702bff07fd1b1b0c1 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Thu, 16 May 2024 10:29:26 -0500
Subject: [PATCH 02/18] remove task prep_bmat

---
 jobs/JLANDDA_PREP_BMAT                     | 104 ---------------------
 modulefiles/tasks/hera/task.prep_bmat.lua  |   8 --
 modulefiles/tasks/orion/task.prep_bmat.lua |   8 --
 parm/land_analysis_era5_orion.yaml         |  32 +------
 parm/land_analysis_gswp3_orion.yaml        |  41 +-------
 parm/run_without_rocoto.sh                 |  10 --
 scripts/exlandda_analysis.sh               | 100 ++++++++++++++------
 scripts/exlandda_forecast.sh               |  41 +++-----
 scripts/exlandda_prep_bmat.sh              |  78 ----------------
 scripts/exlandda_prep_exp.sh               |  54 +++--------
 scripts/exlandda_prep_obs.sh               |   8 +-
 11 files changed, 97 insertions(+), 387 deletions(-)
 delete mode 100755 jobs/JLANDDA_PREP_BMAT
 delete mode 100644 modulefiles/tasks/hera/task.prep_bmat.lua
 delete mode 100644 modulefiles/tasks/orion/task.prep_bmat.lua
 delete mode 100755 scripts/exlandda_prep_bmat.sh

diff --git a/jobs/JLANDDA_PREP_BMAT b/jobs/JLANDDA_PREP_BMAT
deleted file mode 100755
index 88c27555..00000000
--- a/jobs/JLANDDA_PREP_BMAT
+++ /dev/null
@@ -1,104 +0,0 @@
-#!/bin/bash
-
-date
-export PS4='+ $SECONDS + '
-set -xue
-#
-#-----------------------------------------------------------------------
-#
-# Set the NCO standard environment variables (Table 1, pp.4)
-#
-#-----------------------------------------------------------------------
-#
-export USHlandda="${HOMElandda}/ush"
-export EXEClandda="${HOMElandda}/exec"
-export PARMlandda="${HOMElandda}/parm"
-export FIXlandda="${HOMElandda}/fix"
-export SCRIPTSlandda="${HOMElandda}/scripts"
-#
-#-----------------------------------------------------------------------
-#
-# Define job and jobid by default for rocoto
-#
-#-----------------------------------------------------------------------
-#
-WORKFLOW_MANAGER="${WORKFLOW_MANAGER:-rocoto}"
-if [ "${WORKFLOW_MANAGER}" = "rocoto" ]; then
-  if [ "${SCHED}" = "slurm" ]; then
-    job=${SLURM_JOB_NAME}
-    pid=${SLURM_JOB_ID}
-  elif [ "${SCHED}" = "pbspro" ]; then
-    job=${PBS_JOBNAME}
-    pid=${PBS_JOBID}
-  else
-    job="task"
-    pid=$$
-  fi
-  jobid="${job}.${PDY}${cyc}.${pid}"
-fi
-#
-#-----------------------------------------------------------------------
-#
-# Create a temp working directory (DATA) and cd into it.
-#
-#-----------------------------------------------------------------------
-#
-export DATA="${DATA:-${DATAROOT}/${jobid}}"
-mkdir -p $DATA
-cd $DATA
-#
-#-----------------------------------------------------------------------
-#
-# Define NCO environment variables and set COM type definitions.
-#
-#-----------------------------------------------------------------------
-#
-export NET="${NET:-landda}"
-export RUN="${RUN:-landda}"
-
-[[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
-if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-fi
-
-mkdir -p ${COMOUT}
-
-# Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
-mkdir -p ${DATA_SHARE}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
-#
-#-----------------------------------------------------------------------
-#
-# Call the ex-script for this J-job.
-#
-#-----------------------------------------------------------------------
-#
-export pgmout="${DATA}/OUTPUT.$$"
-env
-
-${SCRIPTSlandda}/exlandda_prep_bmat.sh
-export err=$?; err_chk
-
-if [ -e "$pgmout" ]; then
-  cat $pgmout
-fi
-#
-#-----------------------------------------------------------------------
-#
-# Whether or not working directory DATA should be kept.
-#
-#-----------------------------------------------------------------------
-#
-if [ "${KEEPDATA}" = "NO" ]; then
-  rm -rf ${DATA}
-fi
-date
diff --git a/modulefiles/tasks/hera/task.prep_bmat.lua b/modulefiles/tasks/hera/task.prep_bmat.lua
deleted file mode 100644
index 8ad021a3..00000000
--- a/modulefiles/tasks/hera/task.prep_bmat.lua
+++ /dev/null
@@ -1,8 +0,0 @@
-prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
-prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
-
-load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-load(pathJoin("stack-python", stack_python_ver))
-
-load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.prep_bmat.lua b/modulefiles/tasks/orion/task.prep_bmat.lua
deleted file mode 100644
index 8ad021a3..00000000
--- a/modulefiles/tasks/orion/task.prep_bmat.lua
+++ /dev/null
@@ -1,8 +0,0 @@
-prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
-prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
-
-load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
-load(pathJoin("stack-python", stack_python_ver))
-
-load(pathJoin("prod_util", prod_util_ver))
diff --git a/parm/land_analysis_era5_orion.yaml b/parm/land_analysis_era5_orion.yaml
index ee12151d..846c883a 100644
--- a/parm/land_analysis_era5_orion.yaml
+++ b/parm/land_analysis_era5_orion.yaml
@@ -101,36 +101,6 @@ workflow:
         taskdep:
           attrs:
             task: prep_exp
-    task_prep_bmat:
-      envars:
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_bmat" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_bmat
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_bmat.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_obs
     task_analysis:
       envars:
         OBS_TYPES: "&OBS_TYPES;"
@@ -166,7 +136,7 @@ workflow:
       dependency:
         taskdep:
           attrs:
-            task: prep_bmat
+            task: prep_obs
     task_forecast:
       envars:
         OBS_TYPES: "&OBS_TYPES;"
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index a7c533da..51c958f6 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -15,6 +15,7 @@ workflow:
     EXP_NAME: "LETKF"
     EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
     JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA/jedi_skylabv7.0"
+    WARMSTART_DIR: ""
     FORCING: "gswp3"
     RES: "96"
     FCSTHR: "24"
@@ -35,7 +36,6 @@ workflow:
     COMROOT: "&PTMP;/&envir;/com"
     DATAROOT: "&PTMP;/&envir;/tmp"
     KEEPDATA: "YES"
-    WORKDIR: "&EXP_BASEDIR;/workdir/run_&FORCING;"
     LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
     LOGFN_SUFFIX: "<cyclestr>_@Y@m@d.log</cyclestr>"
     PATHRT: "&EXP_BASEDIR;"
@@ -43,7 +43,6 @@ workflow:
     cyc: "<cyclestr>@H</cyclestr>"
     PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
     NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
-    WARMSTART_DIR: ""
     DATADEP_FILE1: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
     DATADEP_FILE2: "<cyclestr offset='-24:00:00'>&COMROOT;/&NET;/&model_ver;/&RUN;.@Y@m@d/@H/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
@@ -59,8 +58,8 @@ workflow:
         ATMOS_FORC: "&FORCING;"
         RES: "&RES;"
         TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
+        RUN: "&RUN;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
         DATAROOT: "&DATAROOT;"
@@ -97,7 +96,6 @@ workflow:
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -117,37 +115,6 @@ workflow:
         taskdep:
           attrs:
             task: prep_exp
-    task_prep_bmat:
-      attrs:
-        cycledefs: cycled
-      envars:
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        PTIME: "&PTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_bmat" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_bmat
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_bmat&LOGFN_SUFFIX;"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_obs
     task_analysis:
       attrs:
         cycledefs: cycled
@@ -160,7 +127,6 @@ workflow:
         ATMOS_FORC: "&FORCING;"
         RES: "&RES;"
         TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -184,7 +150,7 @@ workflow:
       dependency:
         taskdep:
           attrs:
-            task: prep_bmat
+            task: prep_obs
     task_forecast:
       attrs:
         cycledefs: cycled
@@ -197,7 +163,6 @@ workflow:
         ATMOS_FORC: "&FORCING;"
         RES: "&RES;"
         TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
diff --git a/parm/run_without_rocoto.sh b/parm/run_without_rocoto.sh
index 4514a6fb..76ff4a37 100755
--- a/parm/run_without_rocoto.sh
+++ b/parm/run_without_rocoto.sh
@@ -82,16 +82,6 @@ else
   exit 2
 fi
 
-echo " ... PREP_BMAT running ... "
-${HOMElandda}/parm/task_load_modules_run_jjob.sh "prep_bmat" "${HOMElandda}" "${MACHINE}"
-export err=$?
-if [ $err = 0 ]; then
-  echo " === PREP_BMAT completed successfully === "
-else
-  echo " ERROR: PREP_BMAT failed !!! "
-  exit 3
-fi
-
 echo " ... ANALYSIS running ... "
 ${HOMElandda}/parm/task_load_modules_run_jjob.sh "analysis" "${HOMElandda}" "${MACHINE}"
 export err=$?
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index 1407e242..10fc483c 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -22,17 +22,12 @@ MP=${PTIME:4:2}
 DP=${PTIME:6:2}
 HP=${PTIME:8:2}
 
-mem_ens="mem000"
-
-MEM_WORKDIR=${WORKDIR}/${mem_ens}
-JEDIWORKDIR=${WORKDIR}/mem000/jedi
 FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+
 JEDI_STATICDIR=${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data
 JEDI_EXECDIR=${JEDI_INSTALL}/build/bin
-SAVE_INCR="YES"
-KEEPJEDIDIR="YES"
 
-cd $MEM_WORKDIR
+SAVE_INCR="YES"
 
 # load modulefiles
 BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
@@ -46,15 +41,64 @@ MPIEXEC=`which mpiexec`
 YAML_DA=construct
 GFSv17="NO"
 B=30 # back ground error std for LETKFOI
-   
-cd $JEDIWORKDIR
 
-mkdir -p output/DA/hofx
+if [[ $do_jedi == "YES" ]]; then
+  cres_file=${DATA}/${FILEDATE}.coupler.res
+  cp ${PARMlandda}/templates/template.coupler.res $cres_file
+
+  sed -i -e "s/XXYYYY/${YYYY}/g" $cres_file
+  sed -i -e "s/XXMM/${MM}/g" $cres_file
+  sed -i -e "s/XXDD/${DD}/g" $cres_file
+  sed -i -e "s/XXHH/${HH}/g" $cres_file
+  sed -i -e "s/XXYYYP/${YYYP}/g" $cres_file
+  sed -i -e "s/XXMP/${MP}/g" $cres_file
+  sed -i -e "s/XXDP/${DP}/g" $cres_file
+  sed -i -e "s/XXHP/${HP}/g" $cres_file
+fi
+
+################################################
+# CREATE BACKGROUND ENSEMBLE (LETKFOI)
+################################################
+
+if [[ ${DAtype} == "letkfoi_snow" ]]; then
+
+  if [ $GFSv17 == "YES" ]; then
+    SNOWDEPTHVAR="snodl"
+  else
+    SNOWDEPTHVAR="snwdph"
+    # replace field overwrite file
+    cp ${PARMlandda}/jedi/gfs-land.yaml ${DATA}/gfs-land.yaml
+  fi
+  # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
+  for ens in pos neg
+  do
+    if [ -e $DATA/mem_${ens} ]; then
+      rm -r $DATA/mem_${ens}
+    fi
+    mkdir -p $DATA/mem_${ens}
+    for tile in 1 2 3 4 5 6
+    do
+      cp ${COMIN}/${FILEDATE}.sfc_data.tile${tile}.nc ${DATA}/mem_${ens}/${FILEDATE}.sfc_data.tile${tile}.nc
+    done
+    cp ${DATA}/${FILEDATE}.coupler.res ${DATA}/mem_${ens}/${FILEDATE}.coupler.res
+  done
+
+  echo 'do_landDA: calling create ensemble'
+
+  # using ioda mods to get a python version with netCDF4
+  ${USHlandda}/letkf_create_ens.py $FILEDATE $SNOWDEPTHVAR $B
+  if [[ $? != 0 ]]; then
+    echo "letkf create failed"
+    exit 10
+  fi
+fi
 
 ################################################
-# 3. DETERMINE REQUESTED JEDI TYPE, CONSTRUCT YAMLS
+# DETERMINE REQUESTED JEDI TYPE, CONSTRUCT YAMLS
 ################################################
 
+mkdir -p output/DA/hofx
+
 do_DA="YES"
 do_HOFX="NO"
 
@@ -67,14 +111,14 @@ fi
 if [[ $do_DA == "YES" ]]; then 
 
   if [[ $YAML_DA == "construct" ]];then  # construct the yaml
-    cp ${PARMlandda}/jedi/${DAtype}.yaml ${JEDIWORKDIR}/letkf_land.yaml
+    cp ${PARMlandda}/jedi/${DAtype}.yaml ${DATA}/letkf_land.yaml
     for obs in "${OBS_TYPES[@]}";
     do 
       cat ${PARMlandda}/jedi/${obs}.yaml >> letkf_land.yaml
     done
   else # use specified yaml 
     echo "Using user specified YAML: ${YAML_DA}"
-    cp ${PARMlandda}/jedi/${YAML_DA} ${JEDIWORKDIR}/letkf_land.yaml
+    cp ${PARMlandda}/jedi/${YAML_DA} ${DATA}/letkf_land.yaml
   fi
 
   sed -i -e "s/XXYYYY/${YYYY}/g" letkf_land.yaml
@@ -96,14 +140,14 @@ fi
 if [[ $do_HOFX == "YES" ]]; then 
 
   if [[ $YAML_HOFX == "construct" ]];then  # construct the yaml
-    cp ${PARMlandda}/jedi/${DAtype}.yaml ${JEDIWORKDIR}/hofx_land.yaml
+    cp ${PARMlandda}/jedi/${DAtype}.yaml ${DATA}/hofx_land.yaml
     for obs in "${OBS_TYPES[@]}";
     do 
       cat ${PARMlandda}/jedi/${obs}.yaml >> hofx_land.yaml
     done
   else # use specified yaml 
     echo "Using user specified YAML: ${YAML_HOFX}"
-    cp ${PARMlandda}/jedi/${YAML_HOFX} ${JEDIWORKDIR}/hofx_land.yaml
+    cp ${PARMlandda}/jedi/${YAML_HOFX} ${DATA}/hofx_land.yaml
   fi
 
   sed -i -e "s/XXYYYY/${YYYY}/g" hofx_land.yaml
@@ -124,16 +168,13 @@ if [[ $do_HOFX == "YES" ]]; then
 fi
 
 if [[ "$GFSv17" == "NO" ]]; then
-  cp ${PARMlandda}/jedi/gfs-land.yaml ${JEDIWORKDIR}/gfs-land.yaml
+  cp ${PARMlandda}/jedi/gfs-land.yaml ${DATA}/gfs-land.yaml
 else
-  cp ${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data/fieldmetadata/gfs_v17-land.yaml ${JEDIWORKDIR}/gfs-land.yaml
+  cp ${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data/fieldmetadata/gfs_v17-land.yaml ${DATA}/gfs-land.yaml
 fi
 
 ################################################
-# 4. CREATE BACKGROUND ENSEMBLE (LETKFOI)
-################################################
-################################################
-# 5. RUN JEDI
+# RUN JEDI
 ################################################
 
 if [[ ! -e Data ]]; then
@@ -156,7 +197,7 @@ fi
 if [[ $do_HOFX == "YES" ]]; then
   export pgm="fv3jedi_letkf.x"
   . prep_step
-  ${MPIEXEC} -n $NPROC_JEDI ${JEDI_EXEC} hofx_land.yaml >>$pgmout 2>errfile
+  ${MPIEXEC} -n $NPROC_JEDI ${JEDI_EXECDIR}/$pgm hofx_land.yaml >>$pgmout 2>errfile
   export err=$?; err_chk
   cp errfile errfile_jedi_hofx
   if [[ $err != 0 ]]; then
@@ -166,7 +207,7 @@ if [[ $do_HOFX == "YES" ]]; then
 fi 
 
 ################################################
-# 6. APPLY INCREMENT TO UFS RESTARTS 
+# APPLY INCREMENT TO UFS RESTARTS 
 ################################################
 
 if [[ $do_DA == "YES" ]]; then 
@@ -201,20 +242,17 @@ EOF
 fi 
 
 ################################################
-# 7. CLEAN UP
+# CLEAN UP
 ################################################
 
 if [[ -d output/DA/hofx ]]; then
-  cp -r output/DA/hofx ${COMOUT}/${mem_ens}
+  mkdir -p ${COMOUT}/hofx
+  cp -r output/DA/hofx ${COMOUT}/hofx
 fi
 
 # keep increments
 if [ $SAVE_INCR == "YES" ] && [ $do_DA == "YES" ]; then
-  mkdir -p ${COMOUT}/${mem_ens}/jedi_incr
-  cp ${JEDIWORKDIR}/${FILEDATE}.xainc.sfc_data.tile*.nc  ${COMOUT}/${mem_ens}/jedi_incr
+  mkdir -p ${COMOUT}/jedi_incr
+  cp -p ${DATA}/${FILEDATE}.xainc.sfc_data.tile*.nc  ${COMOUT}/jedi_incr
 fi 
 
-# clean up 
-if [[ $KEEPJEDIDIR == "NO" ]]; then
-  rm -rf ${JEDIWORKDIR} 
-fi 
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index a635362e..d0be0709 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -26,15 +26,11 @@ nYYYY=${NTIME:0:4}
 nMM=${NTIME:4:2}
 nDD=${NTIME:6:2}
 nHH=${NTIME:8:2}
-mem_ens="mem000"
 
-MEM_WORKDIR=${WORKDIR}/${mem_ens}
 FREQ=$((${FCSTHR}*3600))
 RDD=$((${FCSTHR}/24))
 RHH=$((${FCSTHR}%24))
 
-cd $MEM_WORKDIR
-
 # load modulefiles
 BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
@@ -44,10 +40,6 @@ module use modulefiles; module load modules.landda
 MPIEXEC=`which mpiexec`
 MPIRUN=${MPIRUN:-`which mpiexec`}
 
-#SNOWDEPTHVAR=snwdph
-
-cd $MEM_WORKDIR
-
 #  convert back to vector, run model (all members) convert back to vector, run model (all members)
 if [[ ${do_jedi} == "YES" ]]; then
 
@@ -55,7 +47,7 @@ if [[ ${do_jedi} == "YES" ]]; then
     echo '************************************************'
     echo 'calling tile2vector' 
 
-    cp  ${PARMlandda}/templates/template.tile2vector tile2vector.namelist
+    cp ${PARMlandda}/templates/template.tile2vector tile2vector.namelist
 
     sed -i "s|FIXlandda|${FIXlandda}|g" tile2vector.namelist
     sed -i -e "s/XXYYYY/${YYYY}/g" tile2vector.namelist
@@ -78,14 +70,14 @@ if [[ ${do_jedi} == "YES" ]]; then
     fi
 
     # save analysis restart
-    mkdir -p ${COMOUT}/${mem_ens}/restarts/vector
-    cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/${mem_ens}/restarts/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+    mkdir -p ${COMOUT}/RESTART/vector
+    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
 
     echo '************************************************'
     echo 'running the forecast model' 
 	
     # update model namelist 
-    cp  ${PARMlandda}/templates/template.ufs-noahMP.namelist.${ATMOS_FORC}  ufs-land.namelist
+    cp ${PARMlandda}/templates/template.ufs-noahMP.namelist.${ATMOS_FORC} ufs-land.namelist
     
     sed -i "s|FIXlandda|${FIXlandda}|g" ufs-land.namelist
     sed -i -e "s/XXYYYY/${YYYY}/g" ufs-land.namelist
@@ -96,9 +88,6 @@ if [[ ${do_jedi} == "YES" ]]; then
     sed -i -e "s/XXRDD/${RDD}/g" ufs-land.namelist
     sed -i -e "s/XXRHH/${RHH}/g" ufs-land.namelist
 
-    # submit model
-    echo $MEM_WORKDIR
-
     nt=$SLURM_NTASKS
 
     export pgm="ufsLand.exe"
@@ -139,11 +128,11 @@ if [[ ${do_jedi} == "YES" ]]; then
     fi
 
     # save analysis restart
-    mkdir -p ${COMOUT}/${mem_ens}/restarts/tile
+    mkdir -p ${COMOUT}/RESTART/tile
     for tile in 1 2 3 4 5 6
     do
-      cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/${mem_ens}/restarts/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc    
-      cp ${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/${mem_ens}/restarts/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
+      cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc    
+      cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
     done  
 
     echo '************************************************'
@@ -173,14 +162,6 @@ if [[ ${do_jedi} == "YES" ]]; then
       exit 1
     fi
 
-    # create run folder
-    RUNDIR=${DATA}/noahmp/${TEST_NAME_RST}
-    [[ -d ${RUNDIR} ]] && echo "Warning: remove old run folder!" && rm -rf ${RUNDIR}
-    mkdir -p ${RUNDIR}
-    cd ${RUNDIR}
-
-    echo "NoahMP run dir= $RUNDIR"
-
     # modify some env variables - reduce core usage
     export ATM_compute_tasks=0
     export ATM_io_tasks=1
@@ -224,7 +205,7 @@ if [[ ${do_jedi} == "YES" ]]; then
     # restart
     if [ $WARM_START = .true. ]; then
       # NoahMP restart files
-      cp ${COMOUT}/${mem_ens}/restarts/tile/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
+      cp ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
 
       # CMEPS restart and pointer files
       RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
@@ -286,12 +267,12 @@ fi
 ############################
 # check model ouput (all members)
 if [[ ${ATMOS_FORC} == "era5" ]]; then
-  if [[ -e ${MEM_WORKDIR}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ]]; then
-    cp ${MEM_WORKDIR}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/${mem_ens}/restarts/vector/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
+  if [[ -e ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ]]; then
+    cp -p ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
   fi
 elif [[ ${ATMOS_FORC} == "gswp3" ]]; then
   for tile in 1 2 3 4 5 6
   do
-    cp ${RUNDIR}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${tile}.nc ${COMOUT}/${mem_ens}/restarts/tile/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${tile}.nc
+    cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${tile}.nc
   done
 fi
diff --git a/scripts/exlandda_prep_bmat.sh b/scripts/exlandda_prep_bmat.sh
deleted file mode 100755
index 83781500..00000000
--- a/scripts/exlandda_prep_bmat.sh
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/bin/sh
-
-set -ex
-
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members) 
-
-if [[ ${EXP_NAME} == "openloop" ]]; then
-  do_jedi="NO"
-else
-  do_jedi="YES"
-  SAVE_TILE="YES"
-fi
-
-TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
-YYYY=${PDY:0:4}
-MM=${PDY:4:2}
-DD=${PDY:6:2}
-HH=${cyc}
-
-mem_ens="mem000" 
-
-MEM_WORKDIR=${WORKDIR}/${mem_ens}
-JEDIWORKDIR=${WORKDIR}/mem000/jedi
-FILEDATE=${YYYY}${MM}${DD}.${HH}0000
-
-cd $MEM_WORKDIR
-
-# load modulefiles
-BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
-if [ -e ${BUILD_VERSION_FILE} ]; then
-  . ${BUILD_VERSION_FILE}
-fi
-module use modulefiles; module load modules.landda
-
-#SNOWDEPTHVAR=snwdph
-YAML_DA=construct
-GFSv17="NO"
-B=30 # back ground error std for LETKFOI
-cd $JEDIWORKDIR
-
-################################################
-# 4. CREATE BACKGROUND ENSEMBLE (LETKFOI)
-################################################
-
-if [[ ${DAtype} == "letkfoi_snow" ]]; then
-
-  if [ $GFSv17 == "YES" ]; then
-    SNOWDEPTHVAR="snodl"
-  else
-    SNOWDEPTHVAR="snwdph"
-    # replace field overwrite file
-    cp ${PARMlandda}/jedi/gfs-land.yaml ${JEDIWORKDIR}/gfs-land.yaml
-  fi
-  # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
-  for ens in pos neg
-  do
-    if [ -e $JEDIWORKDIR/mem_${ens} ]; then
-      rm -r $JEDIWORKDIR/mem_${ens}
-    fi
-    mkdir -p $JEDIWORKDIR/mem_${ens}
-    for tile in 1 2 3 4 5 6
-    do
-      cp ${JEDIWORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc  ${JEDIWORKDIR}/mem_${ens}/${FILEDATE}.sfc_data.tile${tile}.nc
-    done
-    cp ${JEDIWORKDIR}/${FILEDATE}.coupler.res ${JEDIWORKDIR}/mem_${ens}/${FILEDATE}.coupler.res
-  done
-
-  echo 'do_landDA: calling create ensemble'
-
-  # using ioda mods to get a python version with netCDF4
-  ${USHlandda}/letkf_create_ens.py $FILEDATE $SNOWDEPTHVAR $B
-  if [[ $? != 0 ]]; then
-    echo "letkf create failed"
-    exit 10
-  fi
-
-fi
diff --git a/scripts/exlandda_prep_exp.sh b/scripts/exlandda_prep_exp.sh
index 25787e74..77346763 100755
--- a/scripts/exlandda_prep_exp.sh
+++ b/scripts/exlandda_prep_exp.sh
@@ -6,13 +6,12 @@ set -ex
 # copy restarts to workdir, convert to UFS tile for DA (all members) 
 
 if [[ ${EXP_NAME} == "openloop" ]]; then
-    do_jedi="NO"
+  do_jedi="NO"
 else
-    do_jedi="YES"
-    SAVE_TILE="YES"
+  do_jedi="YES"
+  SAVE_TILE="YES"
 fi
 
-echo ${FIXlandda}, ${ATMOS_FORC}
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}
@@ -22,23 +21,17 @@ YYYP=${PTIME:0:4}
 MP=${PTIME:4:2}
 DP=${PTIME:6:2}
 HP=${PTIME:8:2}
-mem_ens="mem000" 
 
-MEM_WORKDIR=${WORKDIR}/${mem_ens}
-JEDIWORKDIR=${WORKDIR}/mem000/jedi
 FILEDATE=${YYYY}${MM}${DD}.${HH}0000
 
-mkdir -p ${MEM_WORKDIR}
-mkdir -p $MEM_WORKDIR/modulefiles
-cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $MEM_WORKDIR/modulefiles/modules.landda.lua
-cd $MEM_WORKDIR
+mkdir -p modulefiles
+cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
 
 # load modulefiles
 BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
   . ${BUILD_VERSION_FILE}
 fi
-
 module use modulefiles; module load modules.landda
 
 if [[ $do_jedi == "YES" ]]; then
@@ -46,18 +39,16 @@ if [[ $do_jedi == "YES" ]]; then
   if [[ $ATMOS_FORC == "era5" ]]; then
     # vector2tile for DA
     # copy restarts into work directory
-    rst_in=${COMOUT}/${mem_ens}/restarts/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+    rst_in=${COMIN}/RESTART/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
     if [[ ! -e ${rst_in} ]]; then
       rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
     fi
-    rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+    rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
     cp ${rst_in} ${rst_out}
 
     echo '************************************************'
     echo 'calling vector2tile' 
 
-    export MEM_WORKDIR
-
     # update vec2tile and tile2vec namelists
     cp  ${PARMlandda}/templates/template.vector2tile vector2tile.namelist
 
@@ -89,17 +80,15 @@ if [[ $do_jedi == "YES" ]]; then
     # tile2tile for DA
     echo '************************************************'
     echo 'calling tile2tile'    
-
-    export MEM_WORKDIR
    
     # copy restarts into work directory
     for tile in 1 2 3 4 5 6
     do
-      rst_in=${COMOUT}/${mem_ens}/restarts/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+      rst_in=${COMIN}/RESTART/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
       if [[ ! -e ${rst_in} ]]; then  
         rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
       fi
-      rst_out=${MEM_WORKDIR}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
+      rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
       cp ${rst_in} ${rst_out}
     done
 
@@ -129,39 +118,18 @@ if [[ $do_jedi == "YES" ]]; then
     fi
   fi
 
-  if [[ ! -e $JEDIWORKDIR ]]; then
-    mkdir -p $JEDIWORKDIR
-  fi    
-  cd $JEDIWORKDIR
-
   if  [[ $SAVE_TILE == "YES" ]]; then
     for tile in 1 2 3 4 5 6
     do
-      cp ${MEM_WORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc  ${MEM_WORKDIR}/${FILEDATE}.sfc_data_back.tile${tile}.nc
+      cp ${DATA}/${FILEDATE}.sfc_data.tile${tile}.nc ${COMOUT}/${FILEDATE}.sfc_data_back.tile${tile}.nc
     done
   fi
 
   #stage restarts for applying JEDI update (files will get directly updated)
   for tile in 1 2 3 4 5 6
   do
-    ln -fs ${MEM_WORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc ${JEDIWORKDIR}/${FILEDATE}.sfc_data.tile${tile}.nc
+    cp -p ${DATA}/${FILEDATE}.sfc_data.tile${tile}.nc ${COMOUT}/${FILEDATE}.sfc_data.tile${tile}.nc
   done
 
-  cres_file=${JEDIWORKDIR}/${FILEDATE}.coupler.res    
-
-  if [[ -e  ${MEM_WORKDIR}/${FILEDATE}.coupler.res ]]; then
-    ln -sf ${MEM_WORKDIR}/${FILEDATE}.coupler.res $cres_file
-  else #  if not present, need to create coupler.res for JEDI
-    cp ${PARMlandda}/templates/template.coupler.res $cres_file
-
-    sed -i -e "s/XXYYYY/${YYYY}/g" $cres_file
-    sed -i -e "s/XXMM/${MM}/g" $cres_file
-    sed -i -e "s/XXDD/${DD}/g" $cres_file
-    sed -i -e "s/XXHH/${HH}/g" $cres_file
-    sed -i -e "s/XXYYYP/${YYYP}/g" $cres_file
-    sed -i -e "s/XXMP/${MP}/g" $cres_file
-    sed -i -e "s/XXDP/${DP}/g" $cres_file
-    sed -i -e "s/XXHP/${HP}/g" $cres_file	
-  fi    
 fi # do_jedi setup
 
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index cb865530..6b8fff0a 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -21,11 +21,7 @@ MP=${PTIME:4:2}
 DP=${PTIME:6:2}
 HP=${PTIME:8:2}
 
-mem_ens="mem000" 
-
-JEDIWORKDIR=${WORKDIR}/mem000/jedi
-
-cd $JEDIWORKDIR
+mkdir -p "${COMOUT}/OBS"
 
 ################################################
 # 2. PREPARE OBS FILES
@@ -55,7 +51,7 @@ for obs in "${OBS_TYPES[@]}"; do
   # check obs are available
   if [[ -e $obsfile ]]; then
     echo "do_landDA: $i observations found: $obsfile"
-    ln -fs $obsfile  ${obs}_${YYYY}${MM}${DD}${HH}.nc
+    cp -p $obsfile ${COMOUT}/OBS/${obs}_${YYYY}${MM}${DD}${HH}.nc
   else
     echo "${obs} observations not found: $obsfile"
   fi

From df178dbc345e5f7c5b3ebff4d8346c8b01831f01 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 05:31:04 -0500
Subject: [PATCH 03/18] update ex-scripts

---
 parm/land_analysis_era5_orion.yaml  |  2 +-
 parm/land_analysis_gswp3_orion.yaml |  4 ++--
 scripts/exlandda_analysis.sh        | 13 +++++++++----
 scripts/exlandda_forecast.sh        |  2 +-
 scripts/exlandda_prep_exp.sh        |  2 +-
 scripts/exlandda_prep_obs.sh        |  4 ++--
 6 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/parm/land_analysis_era5_orion.yaml b/parm/land_analysis_era5_orion.yaml
index 846c883a..a3c1b45f 100644
--- a/parm/land_analysis_era5_orion.yaml
+++ b/parm/land_analysis_era5_orion.yaml
@@ -14,7 +14,7 @@ workflow:
     ACCOUNT: "epic"
     EXP_NAME: "LETKF"
     EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
-    JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA/jedi_skylabv7.0"
+    JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
     FORCING: "era5"
     RES: "96"
     FCSTHR: "24"
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 51c958f6..05cfc843 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -14,7 +14,7 @@ workflow:
     ACCOUNT: "epic"
     EXP_NAME: "LETKF"
     EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
-    JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA/jedi_skylabv7.0"
+    JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
     WARMSTART_DIR: ""
     FORCING: "gswp3"
     RES: "96"
@@ -37,7 +37,7 @@ workflow:
     DATAROOT: "&PTMP;/&envir;/tmp"
     KEEPDATA: "YES"
     LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
-    LOGFN_SUFFIX: "<cyclestr>_@Y@m@d.log</cyclestr>"
+    LOGFN_SUFFIX: "<cyclestr>_@Y@m@d@H.log</cyclestr>"
     PATHRT: "&EXP_BASEDIR;"
     PDY:  "<cyclestr>@Y@m@d</cyclestr>"
     cyc: "<cyclestr>@H</cyclestr>"
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index 10fc483c..59762cc8 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-set -ex
+set -xue
 
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members)
@@ -34,6 +34,8 @@ BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
   . ${BUILD_VERSION_FILE}
 fi
+mkdir -p modulefiles
+cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
 module use modulefiles; module load modules.landda
 MPIEXEC=`which mpiexec`
 
@@ -43,6 +45,10 @@ GFSv17="NO"
 B=30 # back ground error std for LETKFOI
 
 if [[ $do_jedi == "YES" ]]; then
+
+  ln -nsf ${COMIN}/${FILEDATE}.sfc_data.tile*.nc .
+  ln -nsf ${COMIN}/OBS/*_${YYYY}${MM}${DD}${HH}.nc .
+
   cres_file=${DATA}/${FILEDATE}.coupler.res
   cp ${PARMlandda}/templates/template.coupler.res $cres_file
 
@@ -97,8 +103,6 @@ fi
 # DETERMINE REQUESTED JEDI TYPE, CONSTRUCT YAMLS
 ################################################
 
-mkdir -p output/DA/hofx
-
 do_DA="YES"
 do_HOFX="NO"
 
@@ -107,6 +111,7 @@ if [[ $do_DA == "NO" && $do_HOFX == "NO" ]]; then
   exit 0 
 fi
 
+mkdir -p output/DA/hofx
 # if yaml is specified by user, use that. Otherwise, build the yaml
 if [[ $do_DA == "YES" ]]; then 
 
@@ -247,7 +252,7 @@ fi
 
 if [[ -d output/DA/hofx ]]; then
   mkdir -p ${COMOUT}/hofx
-  cp -r output/DA/hofx ${COMOUT}/hofx
+  cp -rp output/DA/hofx ${COMOUT}
 fi
 
 # keep increments
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index d0be0709..7e7962f5 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-set -ex
+set -xue
 
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members)
diff --git a/scripts/exlandda_prep_exp.sh b/scripts/exlandda_prep_exp.sh
index 77346763..201aecfd 100755
--- a/scripts/exlandda_prep_exp.sh
+++ b/scripts/exlandda_prep_exp.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-set -ex
+set -xue
 
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members) 
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index 6b8fff0a..fd36c5e8 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-set -ex
+set -xue
 
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members) 
@@ -50,7 +50,7 @@ for obs in "${OBS_TYPES[@]}"; do
 
   # check obs are available
   if [[ -e $obsfile ]]; then
-    echo "do_landDA: $i observations found: $obsfile"
+    echo "do_landDA: $obs observations found: $obsfile"
     cp -p $obsfile ${COMOUT}/OBS/${obs}_${YYYY}${MM}${DD}${HH}.nc
   else
     echo "${obs} observations not found: $obsfile"

From 1f624fd7b8c1cf4d36da049c0dfa375255dac847 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 09:00:17 -0500
Subject: [PATCH 04/18] add pre_anal and post_anal

---
 jobs/JLANDDA_POST_ANAL                      | 104 +++++++
 jobs/{JLANDDA_PREP_EXP => JLANDDA_PRE_ANAL} |   2 +-
 parm/land_analysis_gswp3_orion.yaml         |  81 +++--
 parm/run_without_rocoto.sh                  |  26 +-
 scripts/exlandda_analysis.sh                |  52 +---
 scripts/exlandda_forecast.sh                | 328 +++++++-------------
 scripts/exlandda_post_anal.sh               | 130 ++++++++
 scripts/exlandda_pre_anal.sh                | 117 +++++++
 scripts/exlandda_prep_exp.sh                | 135 --------
 scripts/exlandda_prep_obs.sh                |   7 -
 10 files changed, 556 insertions(+), 426 deletions(-)
 create mode 100755 jobs/JLANDDA_POST_ANAL
 rename jobs/{JLANDDA_PREP_EXP => JLANDDA_PRE_ANAL} (98%)
 create mode 100755 scripts/exlandda_post_anal.sh
 create mode 100755 scripts/exlandda_pre_anal.sh
 delete mode 100755 scripts/exlandda_prep_exp.sh

diff --git a/jobs/JLANDDA_POST_ANAL b/jobs/JLANDDA_POST_ANAL
new file mode 100755
index 00000000..dbdb8861
--- /dev/null
+++ b/jobs/JLANDDA_POST_ANAL
@@ -0,0 +1,104 @@
+#!/bin/bash
+
+date
+export PS4='+ $SECONDS + '
+set -xue
+#
+#-----------------------------------------------------------------------
+#
+# Set the NCO standard environment variables (Table 1, pp.4)
+#
+#-----------------------------------------------------------------------
+#
+export USHlandda="${HOMElandda}/ush"
+export EXEClandda="${HOMElandda}/exec"
+export PARMlandda="${HOMElandda}/parm"
+export FIXlandda="${HOMElandda}/fix"
+export SCRIPTSlandda="${HOMElandda}/scripts"
+#
+#-----------------------------------------------------------------------
+#
+# Define job and jobid by default for rocoto
+#
+#-----------------------------------------------------------------------
+#
+WORKFLOW_MANAGER="${WORKFLOW_MANAGER:-rocoto}"
+if [ "${WORKFLOW_MANAGER}" = "rocoto" ]; then
+  if [ "${SCHED}" = "slurm" ]; then
+    job=${SLURM_JOB_NAME}
+    pid=${SLURM_JOB_ID}
+  elif [ "${SCHED}" = "pbspro" ]; then
+    job=${PBS_JOBNAME}
+    pid=${PBS_JOBID}
+  else
+    job="task"
+    pid=$$
+  fi
+  jobid="${job}.${PDY}${cyc}.${pid}"
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Create a temp working directory (DATA) and cd into it.
+#
+#-----------------------------------------------------------------------
+#
+export DATA="${DATA:-${DATAROOT}/${jobid}}"
+mkdir -p $DATA
+cd $DATA
+#
+#-----------------------------------------------------------------------
+#
+# Define NCO environment variables and set COM type definitions.
+#
+#-----------------------------------------------------------------------
+#
+export NET="${NET:-landda}"
+export RUN="${RUN:-landda}"
+
+[[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
+if [ "${MACHINE}" = "WCOSS2" ]; then
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+else
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+fi
+
+mkdir -p ${COMOUT}
+
+# Create a teomporary share directory
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+mkdir -p ${DATA_SHARE}
+
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+#
+#-----------------------------------------------------------------------
+#
+# Call the ex-script for this J-job.
+#
+#-----------------------------------------------------------------------
+#
+export pgmout="${DATA}/OUTPUT.$$"
+env
+
+${SCRIPTSlandda}/exlandda_post_anal.sh
+export err=$?; err_chk
+
+if [ -e "$pgmout" ]; then
+  cat $pgmout
+fi
+#
+#-----------------------------------------------------------------------
+#
+# Whether or not working directory DATA should be kept.
+#
+#-----------------------------------------------------------------------
+#
+if [ "${KEEPDATA}" = "NO" ]; then
+  rm -rf ${DATA}
+fi
+date
diff --git a/jobs/JLANDDA_PREP_EXP b/jobs/JLANDDA_PRE_ANAL
similarity index 98%
rename from jobs/JLANDDA_PREP_EXP
rename to jobs/JLANDDA_PRE_ANAL
index cc03b593..30750dd2 100755
--- a/jobs/JLANDDA_PREP_EXP
+++ b/jobs/JLANDDA_PRE_ANAL
@@ -85,7 +85,7 @@ setpdy.sh
 export pgmout="${DATA}/OUTPUT.$$"
 env
 
-${SCRIPTSlandda}/exlandda_prep_exp.sh
+${SCRIPTSlandda}/exlandda_pre_anal.sh
 export err=$?; err_chk
 
 if [ -e "$pgmout" ]; then
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 05cfc843..b121a0d8 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -47,7 +47,34 @@ workflow:
     DATADEP_FILE2: "<cyclestr offset='-24:00:00'>&COMROOT;/&NET;/&model_ver;/&RUN;.@Y@m@d/@H/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
   tasks:
-    task_prep_exp:
+    task_prep_obs:
+      attrs:
+        cycledefs: cycled
+      envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
+        OBS_TYPES: "&OBS_TYPES;"
+        MACHINE: "&MACHINE;"
+        SCHED: "&SCHED;"
+        ACCOUNT: "&ACCOUNT;"
+        EXP_NAME: "&EXP_NAME;"
+        ATMOS_FORC: "&FORCING;"
+        model_ver: "&model_ver;"
+        HOMElandda: "&HOMElandda;"
+        COMROOT: "&COMROOT;"
+        DATAROOT: "&DATAROOT;"
+        KEEPDATA: "&KEEPDATA;"
+        PDY: "&PDY;"
+        cyc: "&cyc;"
+        PTIME: "&PTIME;"
+      account: "&ACCOUNT;"
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
+      jobname: prep_obs
+      cores: 1
+      walltime: 00:02:00
+      queue: batch
+      join: "&LOGDIR;/prep_obs&LOGFN_SUFFIX;"
+    task_pre_anal:
       attrs:
         cycledefs: cycled
       envars:
@@ -68,12 +95,12 @@ workflow:
         cyc: "&cyc;"
         PTIME: "&PTIME;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_exp" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_exp
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "pre_anal" "&HOMElandda;" "&MACHINE;"'
+      jobname: pre_anal
       cores: 1
-      walltime: 00:02:00
+      walltime: 00:05:00
       queue: batch
-      join: "&LOGDIR;/prep_exp&LOGFN_SUFFIX;"
+      join: "&LOGDIR;/pre_anal&LOGFN_SUFFIX;"
       dependency:
         or:
           datadep_file1:
@@ -84,18 +111,18 @@ workflow:
             attrs:
               age: 5
             value: "&DATADEP_FILE2;"
-    task_prep_obs:
+    task_analysis:
       attrs:
         cycledefs: cycled
       envars:
-        OBSDIR: "&OBSDIR;"
-        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
+        RES: "&RES;"
+        TSTUB: "&TSTUB;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -104,22 +131,26 @@ workflow:
         PDY: "&PDY;"
         cyc: "&cyc;"
         PTIME: "&PTIME;"
+        NTIME: "&NTIME;"
+        DAtype: "&DAtype;"
+        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
+        NPROC_JEDI: "&NPROCS_ANALYSIS;"
+        JEDI_INSTALL: "&JEDI_INSTALL;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_obs
-      cores: 1
-      walltime: 00:02:00
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
+      jobname: analysis
+      nodes: "1:ppn=&NPROCS_ANALYSIS;"
+      walltime: 00:15:00
       queue: batch
-      join: "&LOGDIR;/prep_obs&LOGFN_SUFFIX;"
+      join: "&LOGDIR;/analysis&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
-            task: prep_exp
-    task_analysis:
+            task: pre_anal
+    task_post_anal:
       attrs:
         cycledefs: cycled
       envars:
-        OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
@@ -128,6 +159,7 @@ workflow:
         RES: "&RES;"
         TSTUB: "&TSTUB;"
         model_ver: "&model_ver;"
+        RUN: "&RUN;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
         DATAROOT: "&DATAROOT;"
@@ -135,22 +167,17 @@ workflow:
         PDY: "&PDY;"
         cyc: "&cyc;"
         PTIME: "&PTIME;"
-        NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        NPROC_JEDI: "&NPROCS_ANALYSIS;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
-      jobname: analysis
-      nodes: "1:ppn=&NPROCS_ANALYSIS;"
-      walltime: 00:15:00
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "post_anal" "&HOMElandda;" "&MACHINE;"'
+      jobname: post_anal
+      cores: 1
+      walltime: 00:05:00
       queue: batch
-      join: "&LOGDIR;/analysis&LOGFN_SUFFIX;"
+      join: "&LOGDIR;/post_anal&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
-            task: prep_obs
+            task: pre_anal
     task_forecast:
       attrs:
         cycledefs: cycled
diff --git a/parm/run_without_rocoto.sh b/parm/run_without_rocoto.sh
index 17c6d33d..971f7618 100755
--- a/parm/run_without_rocoto.sh
+++ b/parm/run_without_rocoto.sh
@@ -62,23 +62,23 @@ fi
 
 # Call J-job scripts
 #
-echo " ... PREP_EXP running ... "
-${HOMElandda}/parm/task_load_modules_run_jjob.sh "prep_exp" "${HOMElandda}" "${MACHINE}"
+echo " ... PREP_OBS running ... "
+${HOMElandda}/parm/task_load_modules_run_jjob.sh "prep_obs" "${HOMElandda}" "${MACHINE}"
 export err=$?
 if [ $err = 0 ]; then
-  echo " === PREP_EXP completed successfully === "
+  echo " === PREP_OBS completed successfully === "
 else
-  echo " ERROR: PREP_EXP failed !!! "
+  echo " ERROR: PREP_OBS failed !!! "
   exit 1
 fi
 
-echo " ... PREP_OBS running ... "
-${HOMElandda}/parm/task_load_modules_run_jjob.sh "prep_obs" "${HOMElandda}" "${MACHINE}"
+echo " ... PRE_ANAL running ... "
+${HOMElandda}/parm/task_load_modules_run_jjob.sh "pre_anal" "${HOMElandda}" "${MACHINE}"
 export err=$?
 if [ $err = 0 ]; then
-  echo " === PREP_OBS completed successfully === "
+  echo " === PRE_ANAL completed successfully === "
 else
-  echo " ERROR: PREP_OBS failed !!! "
+  echo " ERROR: PRE_ANAL failed !!! "
   exit 2
 fi
 
@@ -89,6 +89,16 @@ if [ $err = 0 ]; then
   echo " === Task ANALYSIS completed successfully === "
 else
   echo " ERROR: ANALYSIS failed !!! "
+  exit 3
+fi
+
+echo " ... POST_ANAL running ... "
+${HOMElandda}/parm/task_load_modules_run_jjob.sh "post_anal" "${HOMElandda}" "${MACHINE}"
+export err=$?
+if [ $err = 0 ]; then
+  echo " === POST_ANAL completed successfully === "
+else
+  echo " ERROR: POST_ANAL failed !!! "
   exit 4
 fi
 
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index 59762cc8..d30926c6 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -5,13 +5,6 @@ set -xue
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members)
 
-if [[ ${EXP_NAME} == "openloop" ]]; then
-  do_jedi="NO"
-else
-  do_jedi="YES"
-  SAVE_TILE="YES"
-fi
-
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}
@@ -27,8 +20,6 @@ FILEDATE=${YYYY}${MM}${DD}.${HH}0000
 JEDI_STATICDIR=${JEDI_INSTALL}/jedi-bundle/fv3-jedi/test/Data
 JEDI_EXECDIR=${JEDI_INSTALL}/build/bin
 
-SAVE_INCR="YES"
-
 # load modulefiles
 BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
@@ -44,23 +35,23 @@ YAML_DA=construct
 GFSv17="NO"
 B=30 # back ground error std for LETKFOI
 
-if [[ $do_jedi == "YES" ]]; then
-
-  ln -nsf ${COMIN}/${FILEDATE}.sfc_data.tile*.nc .
-  ln -nsf ${COMIN}/OBS/*_${YYYY}${MM}${DD}${HH}.nc .
+for itile in {1..6}
+do
+  cp ${COMIN}/${FILEDATE}.sfc_data.ini.tile${itile}.nc ${FILEDATE}.sfc_data.tile${itile}.nc
+done
+ln -nsf ${COMIN}/OBS/*_${YYYY}${MM}${DD}${HH}.nc .
 
-  cres_file=${DATA}/${FILEDATE}.coupler.res
-  cp ${PARMlandda}/templates/template.coupler.res $cres_file
+cres_file=${DATA}/${FILEDATE}.coupler.res
+cp ${PARMlandda}/templates/template.coupler.res $cres_file
 
-  sed -i -e "s/XXYYYY/${YYYY}/g" $cres_file
-  sed -i -e "s/XXMM/${MM}/g" $cres_file
-  sed -i -e "s/XXDD/${DD}/g" $cres_file
-  sed -i -e "s/XXHH/${HH}/g" $cres_file
-  sed -i -e "s/XXYYYP/${YYYP}/g" $cres_file
-  sed -i -e "s/XXMP/${MP}/g" $cres_file
-  sed -i -e "s/XXDP/${DP}/g" $cres_file
-  sed -i -e "s/XXHP/${HP}/g" $cres_file
-fi
+sed -i -e "s/XXYYYY/${YYYY}/g" $cres_file
+sed -i -e "s/XXMM/${MM}/g" $cres_file
+sed -i -e "s/XXDD/${DD}/g" $cres_file
+sed -i -e "s/XXHH/${HH}/g" $cres_file
+sed -i -e "s/XXYYYP/${YYYP}/g" $cres_file
+sed -i -e "s/XXMP/${MP}/g" $cres_file
+sed -i -e "s/XXDP/${DP}/g" $cres_file
+sed -i -e "s/XXHP/${HP}/g" $cres_file
 
 ################################################
 # CREATE BACKGROUND ENSEMBLE (LETKFOI)
@@ -82,10 +73,7 @@ if [[ ${DAtype} == "letkfoi_snow" ]]; then
       rm -r $DATA/mem_${ens}
     fi
     mkdir -p $DATA/mem_${ens}
-    for tile in 1 2 3 4 5 6
-    do
-      cp ${COMIN}/${FILEDATE}.sfc_data.tile${tile}.nc ${DATA}/mem_${ens}/${FILEDATE}.sfc_data.tile${tile}.nc
-    done
+    cp ${FILEDATE}.sfc_data.tile*.nc ${DATA}/mem_${ens}
     cp ${DATA}/${FILEDATE}.coupler.res ${DATA}/mem_${ens}/${FILEDATE}.coupler.res
   done
 
@@ -246,17 +234,11 @@ EOF
 
 fi 
 
-################################################
-# CLEAN UP
-################################################
-
 if [[ -d output/DA/hofx ]]; then
-  mkdir -p ${COMOUT}/hofx
   cp -rp output/DA/hofx ${COMOUT}
 fi
 
-# keep increments
-if [ $SAVE_INCR == "YES" ] && [ $do_DA == "YES" ]; then
+if [[ $do_DA == "YES" ]]; then
   mkdir -p ${COMOUT}/jedi_incr
   cp -p ${DATA}/${FILEDATE}.xainc.sfc_data.tile*.nc  ${COMOUT}/jedi_incr
 fi 
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 7e7962f5..ab9385eb 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -5,13 +5,6 @@ set -xue
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members)
 
-if [[ ${EXP_NAME} == "openloop" ]]; then
-  do_jedi="NO"
-else
-  do_jedi="YES"
-  SAVE_TILE="YES"
-fi
-
 MACHINE_ID=${MACHINE}
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
@@ -36,231 +29,140 @@ BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
   . ${BUILD_VERSION_FILE}
 fi
+mkdir -p modulefiles
+cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
 module use modulefiles; module load modules.landda
-MPIEXEC=`which mpiexec`
-MPIRUN=${MPIRUN:-`which mpiexec`}
-
-#  convert back to vector, run model (all members) convert back to vector, run model (all members)
-if [[ ${do_jedi} == "YES" ]]; then
-
-  if [[ ${ATMOS_FORC} == "era5" ]]; then
-    echo '************************************************'
-    echo 'calling tile2vector' 
-
-    cp ${PARMlandda}/templates/template.tile2vector tile2vector.namelist
-
-    sed -i "s|FIXlandda|${FIXlandda}|g" tile2vector.namelist
-    sed -i -e "s/XXYYYY/${YYYY}/g" tile2vector.namelist
-    sed -i -e "s/XXMM/${MM}/g" tile2vector.namelist
-    sed -i -e "s/XXDD/${DD}/g" tile2vector.namelist
-    sed -i -e "s/XXHH/${HH}/g" tile2vector.namelist
-    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
-    sed -i -e "s/XXRES/${RES}/g" tile2vector.namelist
-    sed -i -e "s/XXTSTUB/${TSTUB}/g" tile2vector.namelist
-    sed -i -e "s#XXTPATH#${TPATH}#g" tile2vector.namelist
-
-    export pgm="vector2tile_converter.exe"
-    . prep_step
-    ${EXEClandda}/$pgm tile2vector.namelist >>$pgmout 2>errfile
-    export err=$?; err_chk
-    cp errfile errfile_tile2vector
-    if [[ $err != 0 ]]; then
-      echo "tile2vector failed"
-      exit 10
-    fi
-
-    # save analysis restart
-    mkdir -p ${COMOUT}/RESTART/vector
-    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-
-    echo '************************************************'
-    echo 'running the forecast model' 
-	
-    # update model namelist 
-    cp ${PARMlandda}/templates/template.ufs-noahMP.namelist.${ATMOS_FORC} ufs-land.namelist
-    
-    sed -i "s|FIXlandda|${FIXlandda}|g" ufs-land.namelist
-    sed -i -e "s/XXYYYY/${YYYY}/g" ufs-land.namelist
-    sed -i -e "s/XXMM/${MM}/g" ufs-land.namelist
-    sed -i -e "s/XXDD/${DD}/g" ufs-land.namelist
-    sed -i -e "s/XXHH/${HH}/g" ufs-land.namelist
-    sed -i -e "s/XXFREQ/${FREQ}/g" ufs-land.namelist
-    sed -i -e "s/XXRDD/${RDD}/g" ufs-land.namelist
-    sed -i -e "s/XXRHH/${RHH}/g" ufs-land.namelist
-
-    nt=$SLURM_NTASKS
-
-    export pgm="ufsLand.exe"
-    . prep_step
-    ${MPIEXEC} -n 1 ${EXEClandda}/$pgm >>$pgmout 2>errfile
-    export err=$?; err_chk
-    cp errfile errfile_ufsLand
-    if [[ $err != 0 ]]; then
-      echo "ufsLand failed"
-      exit 10
-    fi
-
-  #  convert back to UFS tile, run model (all members)
-  elif [[ ${ATMOS_FORC} == "gswp3" ]]; then  
-    echo '************************************************'
-    echo 'calling tile2tile' 
-
-    cp ${PARMlandda}/templates/template.jedi2ufs jedi2ufs.namelist
-     
-    sed -i "s|FIXlandda|${FIXlandda}|g" jedi2ufs.namelist
-    sed -i -e "s/XXYYYY/${YYYY}/g" jedi2ufs.namelist
-    sed -i -e "s/XXMM/${MM}/g" jedi2ufs.namelist
-    sed -i -e "s/XXDD/${DD}/g" jedi2ufs.namelist
-    sed -i -e "s/XXHH/${HH}/g" jedi2ufs.namelist
-    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" jedi2ufs.namelist
-    sed -i -e "s/XXRES/${RES}/g" jedi2ufs.namelist
-    sed -i -e "s/XXTSTUB/${TSTUB}/g" jedi2ufs.namelist
-    sed -i -e "s#XXTPATH#${TPATH}#g" jedi2ufs.namelist
-
-    export pgm="tile2tile_converter.exe"
-    . prep_step
-    ${EXEClandda}/$pgm jedi2ufs.namelist >>$pgmout 2>errfile
-    export err=$?; err_chk
-    cp errfile errfile_tile2tile
-    if [[ $err != 0 ]]; then
-      echo "tile2tile failed"
-      exit 10
-    fi
-
-    # save analysis restart
-    mkdir -p ${COMOUT}/RESTART/tile
-    for tile in 1 2 3 4 5 6
-    do
-      cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc    
-      cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
-    done  
 
-    echo '************************************************'
-    echo 'running the forecast model' 
-
-    TEST_NAME=datm_cdeps_lnd_gswp3
-    TEST_NAME_RST=datm_cdeps_lnd_gswp3_rst
-    PATHRT=${HOMElandda}/sorc/ufs_model.fd/tests
-    RT_COMPILER=${RT_COMPILER:-intel}
-    ATOL="1e-7"
+MPIEXEC=`which mpiexec`
 
-    cp $PARMlandda/$TEST_NAME_RST ${PATHRT}/tests/$TEST_NAME_RST 
-    source ${PATHRT}/rt_utils.sh
-    source ${PATHRT}/default_vars.sh
-    source ${PATHRT}/tests/$TEST_NAME_RST
-    source ${PATHRT}/atparse.bash
+#  convert back to UFS tile, run model (all members)
+if [[ ${ATMOS_FORC} == "gswp3" ]]; then  
 
-    BL_DATE=20230816
-    RTPWD=${RTPWD:-${FIXlandda}/NEMSfv3gfs/develop-${BL_DATE}/INTEL/${TEST_NAME}}
-    INPUTDATA_ROOT=${INPUTDATA_ROOT:-${FIXlandda}/NEMSfv3gfs/input-data-20221101}
+  echo '************************************************'
+  echo 'running the forecast model' 
 
-    echo "RTPWD= $RTPWD"
-    echo "INPUTDATA_ROOT= $INPUTDATA_ROOT"
+  TEST_NAME=datm_cdeps_lnd_gswp3
+  TEST_NAME_RST=datm_cdeps_lnd_gswp3_rst
+  PATHRT=${HOMElandda}/sorc/ufs_model.fd/tests
+  RT_COMPILER=${RT_COMPILER:-intel}
+  ATOL="1e-7"
 
-    if [[ ! -d ${INPUTDATA_ROOT} ]] || [[ ! -d ${RTPWD} ]]; then
-      echo "Error: cannot find either folder for INPUTDATA_ROOT or RTPWD, please check!"
-      exit 1
-    fi
+  cp $PARMlandda/$TEST_NAME_RST ${PATHRT}/tests/$TEST_NAME_RST 
+  source ${PATHRT}/rt_utils.sh
+  source ${PATHRT}/default_vars.sh
+  source ${PATHRT}/tests/$TEST_NAME_RST
+  source ${PATHRT}/atparse.bash
 
-    # modify some env variables - reduce core usage
-    export ATM_compute_tasks=0
-    export ATM_io_tasks=1
-    export LND_tasks=6
-    export layout_x=1
-    export layout_y=1
-
-    # FV3 executable: 
-    if [[ $DATM_CDEPS = 'true' ]] || [[ $FV3 = 'true' ]] || [[ $S2S = 'true' ]]; then
-      if [[ $HAFS = 'false' ]] || [[ $FV3 = 'true' && $HAFS = 'true' ]]; then
-        atparse < ${PATHRT}/parm/${INPUT_NML:-input.nml.IN} > input.nml
-      fi
-    fi
+  BL_DATE=20230816
+  RTPWD=${RTPWD:-${FIXlandda}/NEMSfv3gfs/develop-${BL_DATE}/INTEL/${TEST_NAME}}
+  INPUTDATA_ROOT=${INPUTDATA_ROOT:-${FIXlandda}/NEMSfv3gfs/input-data-20221101}
 
-    atparse < ${PATHRT}/parm/${MODEL_CONFIGURE:-model_configure.IN} > model_configure
+  echo "RTPWD= $RTPWD"
+  echo "INPUTDATA_ROOT= $INPUTDATA_ROOT"
 
-    compute_petbounds_and_tasks
-
-    atparse < ${PATHRT}/parm/${UFS_CONFIGURE:-ufs.configure} > ufs.configure
-
-    # diag table
-    if [[ "Q${DIAG_TABLE:-}" != Q ]] ; then
-      atparse < ${PATHRT}/parm/diag_table/${DIAG_TABLE} > diag_table
-    fi
+  if [[ ! -d ${INPUTDATA_ROOT} ]] || [[ ! -d ${RTPWD} ]]; then
+    echo "Error: cannot find either folder for INPUTDATA_ROOT or RTPWD, please check!"
+    exit 1
+  fi
 
-    # Field table
-    if [[ "Q${FIELD_TABLE:-}" != Q ]] ; then
-      cp ${PATHRT}/parm/field_table/${FIELD_TABLE} field_table
+  # modify some env variables - reduce core usage
+  export ATM_compute_tasks=0
+  export ATM_io_tasks=1
+  export LND_tasks=6
+  export layout_x=1
+  export layout_y=1
+
+  # FV3 executable: 
+  if [[ $DATM_CDEPS = 'true' ]] || [[ $FV3 = 'true' ]] || [[ $S2S = 'true' ]]; then
+    if [[ $HAFS = 'false' ]] || [[ $FV3 = 'true' && $HAFS = 'true' ]]; then
+      atparse < ${PATHRT}/parm/${INPUT_NML:-input.nml.IN} > input.nml
     fi
+  fi
 
-    # Field Dictionary
-    cp ${PATHRT}/parm/fd_ufs.yaml fd_ufs.yaml 
-
-    # Set up the run directory
-    mkdir -p RESTART INPUT
-    cd INPUT
-    ln -nsf ${FIXlandda}/UFS_WM/DATM_GSWP3_input_data/* .
-    cd -
+  atparse < ${PATHRT}/parm/${MODEL_CONFIGURE:-model_configure.IN} > model_configure
 
-    SUFFIX=${RT_SUFFIX}
-    # restart
-    if [ $WARM_START = .true. ]; then
-      # NoahMP restart files
-      cp ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
+  compute_petbounds_and_tasks
 
-      # CMEPS restart and pointer files
-      RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
-      cp ${FIXlandda}/restarts/gswp3/${RFILE1} RESTART/.
-      ls -1 "RESTART/${RFILE1}">rpointer.cpl
+  atparse < ${PATHRT}/parm/${UFS_CONFIGURE:-ufs.configure} > ufs.configure
 
-      # CDEPS restart and pointer files
-      RFILE2=ufs.cpld.datm.r.${RESTART_FILE_SUFFIX_SECS}.nc
-      cp ${FIXlandda}/restarts/gswp3/${RFILE2} RESTART/.
-      ls -1 "RESTART/${RFILE2}">rpointer.atm
-    fi
+  # diag table
+  if [[ "Q${DIAG_TABLE:-}" != Q ]] ; then
+    atparse < ${PATHRT}/parm/diag_table/${DIAG_TABLE} > diag_table
+  fi
 
-    cd INPUT
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile1.nc C96.initial.tile1.nc
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile2.nc C96.initial.tile2.nc
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile3.nc C96.initial.tile3.nc
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile4.nc C96.initial.tile4.nc
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile5.nc C96.initial.tile5.nc
-    ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile6.nc C96.initial.tile6.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.maximum_snow_albedo.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.slope_type.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.soil_type.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.soil_color.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.substrate_temperature.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.vegetation_greenness.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.vegetation_type.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile1.nc oro_data.tile1.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile2.nc oro_data.tile2.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile3.nc oro_data.tile3.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile4.nc oro_data.tile4.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile5.nc oro_data.tile5.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile6.nc oro_data.tile6.nc
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_input_data/INPUT/C96_grid.tile*.nc .
-    ln -nsf ${FIXlandda}/UFS_WM/FV3_input_data/INPUT/grid_spec.nc C96_mosaic.nc
-    cd -
+  # Field table
+  if [[ "Q${FIELD_TABLE:-}" != Q ]] ; then
+    cp ${PATHRT}/parm/field_table/${FIELD_TABLE} field_table
+  fi
 
-    if [[ $DATM_CDEPS = 'true' ]]; then
-      atparse < ${PATHRT}/parm/${DATM_IN_CONFIGURE:-datm_in.IN} > datm_in
-      atparse < ${PATHRT}/parm/${DATM_STREAM_CONFIGURE:-datm.streams.IN} > datm.streams
-    fi
+  # Field Dictionary
+  cp ${PATHRT}/parm/fd_ufs.yaml fd_ufs.yaml 
+
+  # Set up the run directory
+  mkdir -p RESTART INPUT
+  cd INPUT
+  ln -nsf ${FIXlandda}/UFS_WM/DATM_GSWP3_input_data/* .
+  cd -
+
+  SUFFIX=${RT_SUFFIX}
+  # restart
+  if [ $WARM_START = .true. ]; then
+    # NoahMP restart files
+    cp ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
+
+    # CMEPS restart and pointer files
+    RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
+    cp ${FIXlandda}/restarts/gswp3/${RFILE1} RESTART/.
+    ls -1 "RESTART/${RFILE1}">rpointer.cpl
+
+    # CDEPS restart and pointer files
+    RFILE2=ufs.cpld.datm.r.${RESTART_FILE_SUFFIX_SECS}.nc
+    cp ${FIXlandda}/restarts/gswp3/${RFILE2} RESTART/.
+    ls -1 "RESTART/${RFILE2}">rpointer.atm
+  fi
 
-    # NoahMP table file
-    cp ${PATHRT}/parm/noahmptable.tbl noahmptable.tbl
+  cd INPUT
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile1.nc C96.initial.tile1.nc
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile2.nc C96.initial.tile2.nc
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile3.nc C96.initial.tile3.nc
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile4.nc C96.initial.tile4.nc
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile5.nc C96.initial.tile5.nc
+  ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile6.nc C96.initial.tile6.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.maximum_snow_albedo.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.slope_type.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.soil_type.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.soil_color.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.substrate_temperature.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.vegetation_greenness.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/C96.vegetation_type.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile1.nc oro_data.tile1.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile2.nc oro_data.tile2.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile3.nc oro_data.tile3.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile4.nc oro_data.tile4.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile5.nc oro_data.tile5.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_fix_tiled/C96/oro_C96.mx100.tile6.nc oro_data.tile6.nc
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_input_data/INPUT/C96_grid.tile*.nc .
+  ln -nsf ${FIXlandda}/UFS_WM/FV3_input_data/INPUT/grid_spec.nc C96_mosaic.nc
+  cd -
+
+  if [[ $DATM_CDEPS = 'true' ]]; then
+    atparse < ${PATHRT}/parm/${DATM_IN_CONFIGURE:-datm_in.IN} > datm_in
+    atparse < ${PATHRT}/parm/${DATM_STREAM_CONFIGURE:-datm.streams.IN} > datm.streams
+  fi
 
-    # start runs
-    echo "Start ufs-cdeps-land model run with TASKS: ${TASKS}"
-    export pgm="ufs_model"
-    . prep_step
-    ${MPIRUN} -n ${TASKS} ${EXEClandda}/$pgm >>$pgmout 2>errfile
-    export err=$?; err_chk
-    cp errfile errfile_ufs_model
-    if [[ $err != 0 ]]; then
-      echo "ufs_model failed"
-      exit 10
-    fi
+  # NoahMP table file
+  cp ${PATHRT}/parm/noahmptable.tbl noahmptable.tbl
+
+  # start runs
+  echo "Start ufs-cdeps-land model run with TASKS: ${TASKS}"
+  export pgm="ufs_model"
+  . prep_step
+  ${MPIEXEC} -n ${TASKS} ${EXEClandda}/$pgm >>$pgmout 2>errfile
+  export err=$?; err_chk
+  cp errfile errfile_ufs_model
+  if [[ $err != 0 ]]; then
+    echo "ufs_model failed"
+    exit 10
   fi
 fi
 
diff --git a/scripts/exlandda_post_anal.sh b/scripts/exlandda_post_anal.sh
new file mode 100755
index 00000000..074d6dce
--- /dev/null
+++ b/scripts/exlandda_post_anal.sh
@@ -0,0 +1,130 @@
+#!/bin/sh
+
+set -xue
+
+############################
+# copy restarts to workdir, convert to UFS tile for DA (all members)
+
+MACHINE_ID=${MACHINE}
+TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
+YYYY=${PDY:0:4}
+MM=${PDY:4:2}
+DD=${PDY:6:2}
+HH=${cyc}
+YYYP=${PTIME:0:4}
+MP=${PTIME:4:2}
+DP=${PTIME:6:2}
+HP=${PTIME:8:2}
+nYYYY=${NTIME:0:4}
+nMM=${NTIME:4:2}
+nDD=${NTIME:6:2}
+nHH=${NTIME:8:2}
+
+FREQ=$((${FCSTHR}*3600))
+RDD=$((${FCSTHR}/24))
+RHH=$((${FCSTHR}%24))
+
+# load modulefiles
+BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
+if [ -e ${BUILD_VERSION_FILE} ]; then
+  . ${BUILD_VERSION_FILE}
+fi
+mkdir -p modulefiles
+cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
+module use modulefiles; module load modules.landda
+
+MPIEXEC=`which mpiexec`
+
+#  convert back to vector, run model (all members) convert back to vector, run model (all members)
+if [[ ${ATMOS_FORC} == "era5" ]]; then
+  echo '************************************************'
+  echo 'calling tile2vector' 
+
+  cp ${PARMlandda}/templates/template.tile2vector tile2vector.namelist
+
+  sed -i "s|FIXlandda|${FIXlandda}|g" tile2vector.namelist
+  sed -i -e "s/XXYYYY/${YYYY}/g" tile2vector.namelist
+  sed -i -e "s/XXMM/${MM}/g" tile2vector.namelist
+  sed -i -e "s/XXDD/${DD}/g" tile2vector.namelist
+  sed -i -e "s/XXHH/${HH}/g" tile2vector.namelist
+  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
+  sed -i -e "s/XXRES/${RES}/g" tile2vector.namelist
+  sed -i -e "s/XXTSTUB/${TSTUB}/g" tile2vector.namelist
+  sed -i -e "s#XXTPATH#${TPATH}#g" tile2vector.namelist
+
+  export pgm="vector2tile_converter.exe"
+  . prep_step
+  ${EXEClandda}/$pgm tile2vector.namelist >>$pgmout 2>errfile
+  export err=$?; err_chk
+  cp errfile errfile_tile2vector
+  if [[ $err != 0 ]]; then
+    echo "tile2vector failed"
+    exit 10
+  fi
+
+  # save analysis restart
+  mkdir -p ${COMOUT}/RESTART/vector
+  cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+
+  echo '************************************************'
+  echo 'running the forecast model' 
+      
+  # update model namelist 
+  cp ${PARMlandda}/templates/template.ufs-noahMP.namelist.${ATMOS_FORC} ufs-land.namelist
+  
+  sed -i "s|FIXlandda|${FIXlandda}|g" ufs-land.namelist
+  sed -i -e "s/XXYYYY/${YYYY}/g" ufs-land.namelist
+  sed -i -e "s/XXMM/${MM}/g" ufs-land.namelist
+  sed -i -e "s/XXDD/${DD}/g" ufs-land.namelist
+  sed -i -e "s/XXHH/${HH}/g" ufs-land.namelist
+  sed -i -e "s/XXFREQ/${FREQ}/g" ufs-land.namelist
+  sed -i -e "s/XXRDD/${RDD}/g" ufs-land.namelist
+  sed -i -e "s/XXRHH/${RHH}/g" ufs-land.namelist
+
+  nt=$SLURM_NTASKS
+
+  export pgm="ufsLand.exe"
+  . prep_step
+  ${MPIEXEC} -n 1 ${EXEClandda}/$pgm >>$pgmout 2>errfile
+  export err=$?; err_chk
+  cp errfile errfile_ufsLand
+  if [[ $err != 0 ]]; then
+    echo "ufsLand failed"
+    exit 10
+  fi
+
+#  convert back to UFS tile, run model (all members)
+elif [[ ${ATMOS_FORC} == "gswp3" ]]; then  
+  echo '************************************************'
+  echo 'calling tile2tile' 
+
+  cp ${PARMlandda}/templates/template.jedi2ufs jedi2ufs.namelist
+   
+  sed -i "s|FIXlandda|${FIXlandda}|g" jedi2ufs.namelist
+  sed -i -e "s/XXYYYY/${YYYY}/g" jedi2ufs.namelist
+  sed -i -e "s/XXMM/${MM}/g" jedi2ufs.namelist
+  sed -i -e "s/XXDD/${DD}/g" jedi2ufs.namelist
+  sed -i -e "s/XXHH/${HH}/g" jedi2ufs.namelist
+  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" jedi2ufs.namelist
+  sed -i -e "s/XXRES/${RES}/g" jedi2ufs.namelist
+  sed -i -e "s/XXTSTUB/${TSTUB}/g" jedi2ufs.namelist
+  sed -i -e "s#XXTPATH#${TPATH}#g" jedi2ufs.namelist
+
+  export pgm="tile2tile_converter.exe"
+  . prep_step
+  ${EXEClandda}/$pgm jedi2ufs.namelist >>$pgmout 2>errfile
+  export err=$?; err_chk
+  cp errfile errfile_tile2tile
+  if [[ $err != 0 ]]; then
+    echo "tile2tile failed"
+    exit 10
+  fi
+
+  # save analysis restart
+  mkdir -p ${COMOUT}/RESTART/tile
+  for tile in 1 2 3 4 5 6
+  do
+    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc    
+    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
+  done  
+fi
diff --git a/scripts/exlandda_pre_anal.sh b/scripts/exlandda_pre_anal.sh
new file mode 100755
index 00000000..74b0394f
--- /dev/null
+++ b/scripts/exlandda_pre_anal.sh
@@ -0,0 +1,117 @@
+#!/bin/sh
+
+set -xue
+
+############################
+# copy restarts to workdir, convert to UFS tile for DA (all members) 
+
+TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
+YYYY=${PDY:0:4}
+MM=${PDY:4:2}
+DD=${PDY:6:2}
+HH=${cyc}
+YYYP=${PTIME:0:4}
+MP=${PTIME:4:2}
+DP=${PTIME:6:2}
+HP=${PTIME:8:2}
+
+FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+
+mkdir -p modulefiles
+cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
+
+# load modulefiles
+BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
+if [ -e ${BUILD_VERSION_FILE} ]; then
+  . ${BUILD_VERSION_FILE}
+fi
+module use modulefiles; module load modules.landda
+
+if [[ $ATMOS_FORC == "era5" ]]; then
+  # vector2tile for DA
+  # copy restarts into work directory
+  rst_in=${COMIN}/RESTART/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+  if [[ ! -e ${rst_in} ]]; then
+    rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+  fi
+  rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+  cp ${rst_in} ${rst_out}
+
+  echo '************************************************'
+  echo 'calling vector2tile' 
+
+  # update vec2tile and tile2vec namelists
+  cp  ${PARMlandda}/templates/template.vector2tile vector2tile.namelist
+
+  sed -i "s|FIXlandda|${FIXlandda}|g" vector2tile.namelist
+  sed -i -e "s/XXYYYY/${YYYY}/g" vector2tile.namelist
+  sed -i -e "s/XXMM/${MM}/g" vector2tile.namelist
+  sed -i -e "s/XXDD/${DD}/g" vector2tile.namelist
+  sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
+  sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
+  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
+  sed -i -e "s/XXRES/${RES}/g" vector2tile.namelist
+  sed -i -e "s/XXTSTUB/${TSTUB}/g" vector2tile.namelist
+  sed -i -e "s#XXTPATH#${TPATH}#g" vector2tile.namelist
+
+  # submit vec2tile 
+  echo '************************************************'
+  echo 'calling vector2tile' 
+
+  export pgm="vector2tile_converter.exe"
+  . prep_step
+  ${EXEClandda}/$pgm vector2tile.namelist >>$pgmout 2>errfile
+  cp errfile errfile_vector2tile
+  export err=$?; err_chk
+  if [[ $err != 0 ]]; then
+    echo "vec2tile failed"
+    exit
+  fi 
+elif [[ $ATMOS_FORC == "gswp3" ]]; then
+  # tile2tile for DA
+  echo '************************************************'
+  echo 'calling tile2tile'    
+ 
+  # copy restarts into work directory
+  for itile in {1..6}
+  do
+    rst_in=${COMIN}/RESTART/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+    if [[ ! -e ${rst_in} ]]; then  
+      rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
+    fi
+    rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc
+    cp ${rst_in} ${rst_out}
+  done
+
+  # update tile2tile namelist
+  cp  ${PARMlandda}/templates/template.ufs2jedi ufs2jedi.namelist
+
+  sed -i "s|FIXlandda|${FIXlandda}|g" ufs2jedi.namelist
+  sed -i -e "s/XXYYYY/${YYYY}/g" ufs2jedi.namelist
+  sed -i -e "s/XXMM/${MM}/g" ufs2jedi.namelist
+  sed -i -e "s/XXDD/${DD}/g" ufs2jedi.namelist
+  sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
+  sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
+  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" ufs2jedi.namelist
+  sed -i -e "s/XXRES/${RES}/g" ufs2jedi.namelist
+  sed -i -e "s/XXTSTUB/${TSTUB}/g" ufs2jedi.namelist
+  sed -i -e "s#XXTPATH#${TPATH}#g" ufs2jedi.namelist
+
+  # submit tile2tile
+  export pgm="tile2tile_converter.exe"
+  . prep_step
+  ${EXEClandda}/$pgm ufs2jedi.namelist >>$pgmout 2>errfile
+  cp errfile errfile_tile2tile
+  export err=$?; err_chk
+  if [[ $err != 0 ]]; then
+    echo "tile2tile failed"
+    exit 
+  fi
+fi
+
+#stage restarts for applying JEDI update to intermediate directory
+for itile in {1..6}
+do
+  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${COMOUT}/${FILEDATE}.sfc_data.tile${itile}.nc
+done
+
diff --git a/scripts/exlandda_prep_exp.sh b/scripts/exlandda_prep_exp.sh
deleted file mode 100755
index 201aecfd..00000000
--- a/scripts/exlandda_prep_exp.sh
+++ /dev/null
@@ -1,135 +0,0 @@
-#!/bin/sh
-
-set -xue
-
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members) 
-
-if [[ ${EXP_NAME} == "openloop" ]]; then
-  do_jedi="NO"
-else
-  do_jedi="YES"
-  SAVE_TILE="YES"
-fi
-
-TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
-YYYY=${PDY:0:4}
-MM=${PDY:4:2}
-DD=${PDY:6:2}
-HH=${cyc}
-YYYP=${PTIME:0:4}
-MP=${PTIME:4:2}
-DP=${PTIME:6:2}
-HP=${PTIME:8:2}
-
-FILEDATE=${YYYY}${MM}${DD}.${HH}0000
-
-mkdir -p modulefiles
-cp ${HOMElandda}/modulefiles/build_${MACHINE}_intel.lua $DATA/modulefiles/modules.landda.lua
-
-# load modulefiles
-BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
-if [ -e ${BUILD_VERSION_FILE} ]; then
-  . ${BUILD_VERSION_FILE}
-fi
-module use modulefiles; module load modules.landda
-
-if [[ $do_jedi == "YES" ]]; then
-
-  if [[ $ATMOS_FORC == "era5" ]]; then
-    # vector2tile for DA
-    # copy restarts into work directory
-    rst_in=${COMIN}/RESTART/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-    if [[ ! -e ${rst_in} ]]; then
-      rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-    fi
-    rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-    cp ${rst_in} ${rst_out}
-
-    echo '************************************************'
-    echo 'calling vector2tile' 
-
-    # update vec2tile and tile2vec namelists
-    cp  ${PARMlandda}/templates/template.vector2tile vector2tile.namelist
-
-    sed -i "s|FIXlandda|${FIXlandda}|g" vector2tile.namelist
-    sed -i -e "s/XXYYYY/${YYYY}/g" vector2tile.namelist
-    sed -i -e "s/XXMM/${MM}/g" vector2tile.namelist
-    sed -i -e "s/XXDD/${DD}/g" vector2tile.namelist
-    sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
-    sed -i -e "s/XXHH/${HH}/g" vector2tile.namelist
-    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
-    sed -i -e "s/XXRES/${RES}/g" vector2tile.namelist
-    sed -i -e "s/XXTSTUB/${TSTUB}/g" vector2tile.namelist
-    sed -i -e "s#XXTPATH#${TPATH}#g" vector2tile.namelist
-
-    # submit vec2tile 
-    echo '************************************************'
-    echo 'calling vector2tile' 
-
-    export pgm="vector2tile_converter.exe"
-    . prep_step
-    ${EXEClandda}/$pgm vector2tile.namelist >>$pgmout 2>errfile
-    cp errfile errfile_vector2tile
-    export err=$?; err_chk
-    if [[ $err != 0 ]]; then
-      echo "vec2tile failed"
-      exit
-    fi 
-  elif [[ $ATMOS_FORC == "gswp3" ]]; then
-    # tile2tile for DA
-    echo '************************************************'
-    echo 'calling tile2tile'    
-   
-    # copy restarts into work directory
-    for tile in 1 2 3 4 5 6
-    do
-      rst_in=${COMIN}/RESTART/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-      if [[ ! -e ${rst_in} ]]; then  
-        rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
-      fi
-      rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc
-      cp ${rst_in} ${rst_out}
-    done
-
-    # update tile2tile namelist
-    cp  ${PARMlandda}/templates/template.ufs2jedi ufs2jedi.namelist
-
-    sed -i "s|FIXlandda|${FIXlandda}|g" ufs2jedi.namelist
-    sed -i -e "s/XXYYYY/${YYYY}/g" ufs2jedi.namelist
-    sed -i -e "s/XXMM/${MM}/g" ufs2jedi.namelist
-    sed -i -e "s/XXDD/${DD}/g" ufs2jedi.namelist
-    sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
-    sed -i -e "s/XXHH/${HH}/g" ufs2jedi.namelist
-    sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" ufs2jedi.namelist
-    sed -i -e "s/XXRES/${RES}/g" ufs2jedi.namelist
-    sed -i -e "s/XXTSTUB/${TSTUB}/g" ufs2jedi.namelist
-    sed -i -e "s#XXTPATH#${TPATH}#g" ufs2jedi.namelist
-
-    # submit tile2tile
-    export pgm="tile2tile_converter.exe"
-    . prep_step
-    ${EXEClandda}/$pgm ufs2jedi.namelist >>$pgmout 2>errfile
-    cp errfile errfile_tile2tile
-    export err=$?; err_chk
-    if [[ $err != 0 ]]; then
-      echo "tile2tile failed"
-      exit 
-    fi
-  fi
-
-  if  [[ $SAVE_TILE == "YES" ]]; then
-    for tile in 1 2 3 4 5 6
-    do
-      cp ${DATA}/${FILEDATE}.sfc_data.tile${tile}.nc ${COMOUT}/${FILEDATE}.sfc_data_back.tile${tile}.nc
-    done
-  fi
-
-  #stage restarts for applying JEDI update (files will get directly updated)
-  for tile in 1 2 3 4 5 6
-  do
-    cp -p ${DATA}/${FILEDATE}.sfc_data.tile${tile}.nc ${COMOUT}/${FILEDATE}.sfc_data.tile${tile}.nc
-  done
-
-fi # do_jedi setup
-
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index fd36c5e8..cb2c269d 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -5,13 +5,6 @@ set -xue
 ############################
 # copy restarts to workdir, convert to UFS tile for DA (all members) 
 
-if [[ ${EXP_NAME} == "openloop" ]]; then
-  do_jedi="NO"
-else
-  do_jedi="YES"
-  SAVE_TILE="YES"
-fi
-
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}
 DD=${PDY:6:2}

From 71942ca6e4acfb33b99b0c04a23cf906e5b3266b Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 09:18:16 -0500
Subject: [PATCH 05/18] update task modules

---
 modulefiles/tasks/hera/task.analysis.lua                  | 2 +-
 modulefiles/tasks/hera/task.forecast.lua                  | 2 +-
 .../tasks/hera/{task.prep_exp.lua => task.post_anal.lua}  | 2 +-
 .../{orion/task.prep_exp.lua => hera/task.pre_anal.lua}   | 2 +-
 modulefiles/tasks/hera/task.prep_obs.lua                  | 2 +-
 modulefiles/tasks/orion/task.analysis.lua                 | 2 +-
 modulefiles/tasks/orion/task.forecast.lua                 | 2 +-
 modulefiles/tasks/orion/task.post_anal.lua                | 8 ++++++++
 modulefiles/tasks/orion/task.pre_anal.lua                 | 8 ++++++++
 modulefiles/tasks/orion/task.prep_obs.lua                 | 2 +-
 10 files changed, 24 insertions(+), 8 deletions(-)
 rename modulefiles/tasks/hera/{task.prep_exp.lua => task.post_anal.lua} (79%)
 rename modulefiles/tasks/{orion/task.prep_exp.lua => hera/task.pre_anal.lua} (79%)
 create mode 100644 modulefiles/tasks/orion/task.post_anal.lua
 create mode 100644 modulefiles/tasks/orion/task.pre_anal.lua

diff --git a/modulefiles/tasks/hera/task.analysis.lua b/modulefiles/tasks/hera/task.analysis.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/hera/task.analysis.lua
+++ b/modulefiles/tasks/hera/task.analysis.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/hera/task.forecast.lua b/modulefiles/tasks/hera/task.forecast.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/hera/task.forecast.lua
+++ b/modulefiles/tasks/hera/task.forecast.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/hera/task.prep_exp.lua b/modulefiles/tasks/hera/task.post_anal.lua
similarity index 79%
rename from modulefiles/tasks/hera/task.prep_exp.lua
rename to modulefiles/tasks/hera/task.post_anal.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/hera/task.prep_exp.lua
+++ b/modulefiles/tasks/hera/task.post_anal.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.prep_exp.lua b/modulefiles/tasks/hera/task.pre_anal.lua
similarity index 79%
rename from modulefiles/tasks/orion/task.prep_exp.lua
rename to modulefiles/tasks/hera/task.pre_anal.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/orion/task.prep_exp.lua
+++ b/modulefiles/tasks/hera/task.pre_anal.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/hera/task.prep_obs.lua b/modulefiles/tasks/hera/task.prep_obs.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/hera/task.prep_obs.lua
+++ b/modulefiles/tasks/hera/task.prep_obs.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.analysis.lua b/modulefiles/tasks/orion/task.analysis.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/orion/task.analysis.lua
+++ b/modulefiles/tasks/orion/task.analysis.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.forecast.lua b/modulefiles/tasks/orion/task.forecast.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/orion/task.forecast.lua
+++ b/modulefiles/tasks/orion/task.forecast.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.post_anal.lua b/modulefiles/tasks/orion/task.post_anal.lua
new file mode 100644
index 00000000..d7439d6d
--- /dev/null
+++ b/modulefiles/tasks/orion/task.post_anal.lua
@@ -0,0 +1,8 @@
+prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
+prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
+
+load(pathJoin("stack-intel", stack_intel_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
+load(pathJoin("stack-python", stack_python_ver))
+
+load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.pre_anal.lua b/modulefiles/tasks/orion/task.pre_anal.lua
new file mode 100644
index 00000000..d7439d6d
--- /dev/null
+++ b/modulefiles/tasks/orion/task.pre_anal.lua
@@ -0,0 +1,8 @@
+prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
+prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
+
+load(pathJoin("stack-intel", stack_intel_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
+load(pathJoin("stack-python", stack_python_ver))
+
+load(pathJoin("prod_util", prod_util_ver))
diff --git a/modulefiles/tasks/orion/task.prep_obs.lua b/modulefiles/tasks/orion/task.prep_obs.lua
index 8ad021a3..d7439d6d 100644
--- a/modulefiles/tasks/orion/task.prep_obs.lua
+++ b/modulefiles/tasks/orion/task.prep_obs.lua
@@ -2,7 +2,7 @@ prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack"))
 prepend_path("MODULEPATH", os.getenv("modulepath_spack_stack_jedi"))
 
 load(pathJoin("stack-intel", stack_intel_ver))
-load(pathJoin("stack-intel-oneapi-mpi", stack_impi_ver))
+load(pathJoin("stack-intel-oneapi-mpi", stack_intel_oneapi_mpi_ver))
 load(pathJoin("stack-python", stack_python_ver))
 
 load(pathJoin("prod_util", prod_util_ver))

From 676c021de9a5b8bca0763a2e4d1e95edc931ec4c Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 12:06:40 -0500
Subject: [PATCH 06/18] to meet nco standards

---
 parm/land_analysis_gswp3_orion.yaml | 11 +++--------
 scripts/exlandda_analysis.sh        | 21 +++++++++++++--------
 scripts/exlandda_forecast.sh        | 13 +++++--------
 scripts/exlandda_post_anal.sh       | 20 +++++++++-----------
 scripts/exlandda_pre_anal.sh        |  5 ++++-
 scripts/exlandda_prep_obs.sh        |  4 ++--
 6 files changed, 36 insertions(+), 38 deletions(-)

diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index b121a0d8..90f8cf1f 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -167,6 +167,7 @@ workflow:
         PDY: "&PDY;"
         cyc: "&cyc;"
         PTIME: "&PTIME;"
+        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "post_anal" "&HOMElandda;" "&MACHINE;"'
       jobname: post_anal
@@ -177,7 +178,7 @@ workflow:
       dependency:
         taskdep:
           attrs:
-            task: pre_anal
+            task: analysis
     task_forecast:
       attrs:
         cycledefs: cycled
@@ -188,8 +189,6 @@ workflow:
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -198,12 +197,8 @@ workflow:
         LOGDIR: "&LOGDIR;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        PTIME: "&PTIME;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
       jobname: forecast
@@ -214,4 +209,4 @@ workflow:
       dependency:
         taskdep:
           attrs:
-            task: analysis
+            task: post_anal
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index d30926c6..4cf3b803 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -37,9 +37,9 @@ B=30 # back ground error std for LETKFOI
 
 for itile in {1..6}
 do
-  cp ${COMIN}/${FILEDATE}.sfc_data.ini.tile${itile}.nc ${FILEDATE}.sfc_data.tile${itile}.nc
+  cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
 done
-ln -nsf ${COMIN}/OBS/*_${YYYY}${MM}${DD}${HH}.nc .
+ln -nsf ${COMIN}/obs/*_${YYYY}${MM}${DD}${HH}.nc .
 
 cres_file=${DATA}/${FILEDATE}.coupler.res
 cp ${PARMlandda}/templates/template.coupler.res $cres_file
@@ -200,7 +200,7 @@ if [[ $do_HOFX == "YES" ]]; then
 fi 
 
 ################################################
-# APPLY INCREMENT TO UFS RESTARTS 
+# Create increment files
 ################################################
 
 if [[ $do_DA == "YES" ]]; then 
@@ -232,14 +232,19 @@ EOF
     fi
   fi
 
+  for itile in {1..6}
+  do
+    cp -p ${DATA}/${FILEDATE}.xainc.sfc_data.tile${itile}.nc ${COMOUT}
+  done
+
 fi 
 
+for itile in {1..6}
+do
+  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${COMOUT}
+done
+
 if [[ -d output/DA/hofx ]]; then
   cp -rp output/DA/hofx ${COMOUT}
 fi
 
-if [[ $do_DA == "YES" ]]; then
-  mkdir -p ${COMOUT}/jedi_incr
-  cp -p ${DATA}/${FILEDATE}.xainc.sfc_data.tile*.nc  ${COMOUT}/jedi_incr
-fi 
-
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index ab9385eb..e921bc74 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -11,19 +11,11 @@ YYYY=${PDY:0:4}
 MM=${PDY:4:2}
 DD=${PDY:6:2}
 HH=${cyc}
-YYYP=${PTIME:0:4}
-MP=${PTIME:4:2}
-DP=${PTIME:6:2}
-HP=${PTIME:8:2}
 nYYYY=${NTIME:0:4}
 nMM=${NTIME:4:2}
 nDD=${NTIME:6:2}
 nHH=${NTIME:8:2}
 
-FREQ=$((${FCSTHR}*3600))
-RDD=$((${FCSTHR}/24))
-RHH=$((${FCSTHR}%24))
-
 # load modulefiles
 BUILD_VERSION_FILE="${HOMElandda}/versions/build.ver_${MACHINE}"
 if [ -e ${BUILD_VERSION_FILE} ]; then
@@ -35,6 +27,11 @@ module use modulefiles; module load modules.landda
 
 MPIEXEC=`which mpiexec`
 
+for itile in {1..6}
+do
+  cp ${COMIN}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc .
+done
+
 #  convert back to UFS tile, run model (all members)
 if [[ ${ATMOS_FORC} == "gswp3" ]]; then  
 
diff --git a/scripts/exlandda_post_anal.sh b/scripts/exlandda_post_anal.sh
index 074d6dce..22b73488 100755
--- a/scripts/exlandda_post_anal.sh
+++ b/scripts/exlandda_post_anal.sh
@@ -11,14 +11,6 @@ YYYY=${PDY:0:4}
 MM=${PDY:4:2}
 DD=${PDY:6:2}
 HH=${cyc}
-YYYP=${PTIME:0:4}
-MP=${PTIME:4:2}
-DP=${PTIME:6:2}
-HP=${PTIME:8:2}
-nYYYY=${NTIME:0:4}
-nMM=${NTIME:4:2}
-nDD=${NTIME:6:2}
-nHH=${NTIME:8:2}
 
 FREQ=$((${FCSTHR}*3600))
 RDD=$((${FCSTHR}/24))
@@ -35,6 +27,13 @@ module use modulefiles; module load modules.landda
 
 MPIEXEC=`which mpiexec`
 
+FILEDATE=${YYYY}${MM}${DD}.${HH}0000
+for itile in {1..6}
+do
+  cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
+  cp ${DATA_SHARE}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc .
+done
+
 #  convert back to vector, run model (all members) convert back to vector, run model (all members)
 if [[ ${ATMOS_FORC} == "era5" ]]; then
   echo '************************************************'
@@ -122,9 +121,8 @@ elif [[ ${ATMOS_FORC} == "gswp3" ]]; then
 
   # save analysis restart
   mkdir -p ${COMOUT}/RESTART/tile
-  for tile in 1 2 3 4 5 6
+  for itile in {1..6}
   do
-    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc    
-    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${tile}.nc
+    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
   done  
 fi
diff --git a/scripts/exlandda_pre_anal.sh b/scripts/exlandda_pre_anal.sh
index 74b0394f..9ed911aa 100755
--- a/scripts/exlandda_pre_anal.sh
+++ b/scripts/exlandda_pre_anal.sh
@@ -36,6 +36,7 @@ if [[ $ATMOS_FORC == "era5" ]]; then
   fi
   rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
   cp ${rst_in} ${rst_out}
+  cp -p ${rst_out} ${DATA_SHARE}
 
   echo '************************************************'
   echo 'calling vector2tile' 
@@ -81,6 +82,8 @@ elif [[ $ATMOS_FORC == "gswp3" ]]; then
     fi
     rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc
     cp ${rst_in} ${rst_out}
+    # copy restart to data share dir for post_anal
+    cp -p ${rst_out} ${DATA_SHARE}
   done
 
   # update tile2tile namelist
@@ -112,6 +115,6 @@ fi
 #stage restarts for applying JEDI update to intermediate directory
 for itile in {1..6}
 do
-  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${COMOUT}/${FILEDATE}.sfc_data.tile${itile}.nc
+  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
 done
 
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index cb2c269d..c3799e94 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -14,7 +14,7 @@ MP=${PTIME:4:2}
 DP=${PTIME:6:2}
 HP=${PTIME:8:2}
 
-mkdir -p "${COMOUT}/OBS"
+mkdir -p "${COMOUT}/obs"
 
 ################################################
 # 2. PREPARE OBS FILES
@@ -44,7 +44,7 @@ for obs in "${OBS_TYPES[@]}"; do
   # check obs are available
   if [[ -e $obsfile ]]; then
     echo "do_landDA: $obs observations found: $obsfile"
-    cp -p $obsfile ${COMOUT}/OBS/${obs}_${YYYY}${MM}${DD}${HH}.nc
+    cp -p $obsfile ${COMOUT}/obs/${obs}_${YYYY}${MM}${DD}${HH}.nc
   else
     echo "${obs} observations not found: $obsfile"
   fi

From 18ce7a46738be59cc044248c1aa8febed3cc278d Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 15:10:15 -0500
Subject: [PATCH 07/18] introduce data_restart

---
 jobs/JLANDDA_FORECAST               |   2 +
 jobs/JLANDDA_POST_ANAL              |   2 +
 jobs/JLANDDA_PRE_ANAL               |   2 +
 parm/land_analysis_era5_hera.yaml   | 206 ----------------------------
 parm/land_analysis_era5_orion.yaml  | 176 ------------------------
 parm/land_analysis_gswp3_hera.yaml  |   1 +
 parm/land_analysis_gswp3_orion.yaml |  13 +-
 scripts/exlandda_analysis.sh        |   5 +-
 scripts/exlandda_forecast.sh        |  33 ++---
 scripts/exlandda_post_anal.sh       |  13 +-
 scripts/exlandda_pre_anal.sh        |  51 +++----
 11 files changed, 72 insertions(+), 432 deletions(-)
 delete mode 100644 parm/land_analysis_era5_hera.yaml
 delete mode 100644 parm/land_analysis_era5_orion.yaml

diff --git a/jobs/JLANDDA_FORECAST b/jobs/JLANDDA_FORECAST
index e04c5786..337cd273 100755
--- a/jobs/JLANDDA_FORECAST
+++ b/jobs/JLANDDA_FORECAST
@@ -70,6 +70,8 @@ mkdir -p ${COMOUT}
 # Create a teomporary share directory
 export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
 mkdir -p ${DATA_SHARE}
+export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
+mkdir -p ${DATA_RESTART}
 
 # Run setpdy to initialize PDYm and PDYp variables
 export cycle="${cycle:-t${cyc}z}"
diff --git a/jobs/JLANDDA_POST_ANAL b/jobs/JLANDDA_POST_ANAL
index dbdb8861..1a896664 100755
--- a/jobs/JLANDDA_POST_ANAL
+++ b/jobs/JLANDDA_POST_ANAL
@@ -70,6 +70,8 @@ mkdir -p ${COMOUT}
 # Create a teomporary share directory
 export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
 mkdir -p ${DATA_SHARE}
+export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
+mkdir -p ${DATA_RESTART}
 
 # Run setpdy to initialize PDYm and PDYp variables
 export cycle="${cycle:-t${cyc}z}"
diff --git a/jobs/JLANDDA_PRE_ANAL b/jobs/JLANDDA_PRE_ANAL
index 30750dd2..f15e2323 100755
--- a/jobs/JLANDDA_PRE_ANAL
+++ b/jobs/JLANDDA_PRE_ANAL
@@ -70,6 +70,8 @@ mkdir -p ${COMOUT}
 # Create a teomporary share directory
 export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
 mkdir -p ${DATA_SHARE}
+export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
+mkdir -p ${DATA_RESTART}
 
 # Run setpdy to initialize PDYm and PDYp variables
 export cycle="${cycle:-t${cyc}z}"
diff --git a/parm/land_analysis_era5_hera.yaml b/parm/land_analysis_era5_hera.yaml
deleted file mode 100644
index fee5f3de..00000000
--- a/parm/land_analysis_era5_hera.yaml
+++ /dev/null
@@ -1,206 +0,0 @@
-workflow:
-  attrs:
-    realtime: false
-    scheduler: slurm
-    cyclethrottle: 24
-    taskthrottle: 24
-  cycledef:
-    - attrs:
-        group: cycled
-      spec: 201912210000 201912210000 24:00:00
-  entities:
-    MACHINE: "hera"
-    SCHED: "slurm"
-    ACCOUNT: "nems"
-    EXP_NAME: "LETKF"
-    EXP_BASEDIR: "/scratch2/NAGAPE/epic/{USER}/landda_test"
-    JEDI_INSTALL: "/scratch2/NAGAPE/epic/UFS_Land-DA/jedi_skylabv7.0"
-    FORCING: "era5"
-    RES: "96"
-    FCSTHR: "24"
-    NPROCS_ANALYSIS: "6"
-    NPROCS_FORECAST: "6"
-    OBSDIR: ""
-    OBSDIR_SUBDIR: ""
-    OBS_TYPES: "GHCN"
-    DAtype: "letkfoi_snow"
-    SNOWDEPTHVAR: "snwdph"
-    TSTUB: "oro_C96.mx100"
-    NET: "landda"
-    envir: "test"
-    model_ver: "v1.2.1"
-    HOMElandda: "&EXP_BASEDIR;/land-DA_workflow"
-    PTMP: "&EXP_BASEDIR;/ptmp"
-    COMROOT: "&PTMP;/&envir;/com"
-    DATAROOT: "&PTMP;/&envir;/tmp"
-    KEEPDATA: "YES"
-    WORKDIR: "&EXP_BASEDIR;/workdir/run_&FORCING;"
-    LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
-    PATHRT: "&EXP_BASEDIR;"
-    PDY:  "<cyclestr>@Y@m@d</cyclestr>"
-    cyc: "<cyclestr>@H</cyclestr>"
-    SLASH_ENSMEM_SUBDIR: ""
-    PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
-    NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
-  log: "&LOGDIR;/workflow.log"
-  tasks:
-    task_prep_exp:
-      envars:
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_exp" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_exp
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_exp.log"
-    task_prep_obs:
-      envars:
-        OBSDIR: "&OBSDIR;"
-        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_obs
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_obs.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_exp
-    task_prep_bmat:
-      envars:
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_bmat" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_bmat
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_bmat.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_obs
-    task_analysis:
-      envars:
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        NPROC_JEDI: "&NPROCS_ANALYSIS;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
-      jobname: analysis
-      nodes: "1:ppn=&NPROCS_ANALYSIS;"
-      walltime: 00:15:00
-      queue: batch
-      join: "&LOGDIR;/analysis.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_bmat
-    task_forecast:
-      envars:
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        LOGDIR: "&LOGDIR;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-        FCSTHR: "&FCSTHR;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
-      jobname: forecast
-      nodes: "1:ppn=&NPROCS_FORECAST;"
-      walltime: 00:30:00
-      queue: batch
-      join: "&LOGDIR;/forecast.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: analysis
diff --git a/parm/land_analysis_era5_orion.yaml b/parm/land_analysis_era5_orion.yaml
deleted file mode 100644
index a3c1b45f..00000000
--- a/parm/land_analysis_era5_orion.yaml
+++ /dev/null
@@ -1,176 +0,0 @@
-workflow:
-  attrs:
-    realtime: false
-    scheduler: slurm
-    cyclethrottle: 24
-    taskthrottle: 24
-  cycledef:
-    - attrs:
-        group: cycled
-      spec: 201912210000 201912210000 24:00:00
-  entities:
-    MACHINE: "orion"
-    SCHED: "slurm"
-    ACCOUNT: "epic"
-    EXP_NAME: "LETKF"
-    EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
-    JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
-    FORCING: "era5"
-    RES: "96"
-    FCSTHR: "24"
-    NPROCS_ANALYSIS: "6"
-    NPROCS_FORECAST: "6"
-    OBSDIR: ""
-    OBSDIR_SUBDIR: ""
-    OBS_TYPES: "GHCN"
-    DAtype: "letkfoi_snow"
-    SNOWDEPTHVAR: "snwdph"
-    TSTUB: "oro_C96.mx100"
-    NET: "landda"
-    envir: "test"
-    model_ver: "v1.2.1"
-    HOMElandda: "&EXP_BASEDIR;/land-DA_workflow"
-    PTMP: "&EXP_BASEDIR;/ptmp"
-    COMROOT: "&PTMP;/&envir;/com"
-    DATAROOT: "&PTMP;/&envir;/tmp"
-    KEEPDATA: "YES"
-    WORKDIR: "&EXP_BASEDIR;/workdir/run_&FORCING;"
-    LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
-    PATHRT: "&EXP_BASEDIR;"
-    PDY:  "<cyclestr>@Y@m@d</cyclestr>"
-    cyc: "<cyclestr>@H</cyclestr>"
-    SLASH_ENSMEM_SUBDIR: ""
-    PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
-    NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
-  log: "&LOGDIR;/workflow.log"
-  tasks:
-    task_prep_exp:
-      envars:
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_exp" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_exp
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_exp.log"
-    task_prep_obs:
-      envars:
-        OBSDIR: "&OBSDIR;"
-        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_obs
-      cores: 1
-      walltime: 00:02:00
-      queue: batch
-      join: "&LOGDIR;/prep_obs.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_exp
-    task_analysis:
-      envars:
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        NPROC_JEDI: "&NPROCS_ANALYSIS;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
-      jobname: analysis
-      nodes: "1:ppn=&NPROCS_ANALYSIS;"
-      walltime: 00:15:00
-      queue: batch
-      join: "&LOGDIR;/analysis.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: prep_obs
-    task_forecast:
-      envars:
-        OBS_TYPES: "&OBS_TYPES;"
-        MACHINE: "&MACHINE;"
-        SCHED: "&SCHED;"
-        ACCOUNT: "&ACCOUNT;"
-        EXP_NAME: "&EXP_NAME;"
-        ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
-        model_ver: "&model_ver;"
-        HOMElandda: "&HOMElandda;"
-        COMROOT: "&COMROOT;"
-        DATAROOT: "&DATAROOT;"
-        KEEPDATA: "&KEEPDATA;"
-        LOGDIR: "&LOGDIR;"
-        PDY: "&PDY;"
-        cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
-        NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-        FCSTHR: "&FCSTHR;"
-      account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
-      jobname: forecast
-      nodes: "1:ppn=&NPROCS_FORECAST;"
-      walltime: 00:30:00
-      queue: batch
-      join: "&LOGDIR;/forecast.log"
-      dependency:
-        taskdep:
-          attrs:
-            task: analysis
diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_gswp3_hera.yaml
index 798af689..1cba9dad 100644
--- a/parm/land_analysis_gswp3_hera.yaml
+++ b/parm/land_analysis_gswp3_hera.yaml
@@ -8,6 +8,7 @@ workflow:
     - attrs:
         group: cycled
       spec: 200001030000 200001040000 24:00:00
+# for era5: spec:  201912210000 201912210000 24:00:00
   entities:
     MACHINE: "hera"
     SCHED: "slurm"
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 90f8cf1f..84b904f5 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -8,6 +8,7 @@ workflow:
     - attrs:
         group: cycled
       spec: 200001030000 200001040000 24:00:00
+# for era5: spec:  201912210000 201912210000 24:00:00
   entities:
     MACHINE: "orion"
     SCHED: "slurm"
@@ -44,7 +45,9 @@ workflow:
     PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
     NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
     DATADEP_FILE1: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
-    DATADEP_FILE2: "<cyclestr offset='-24:00:00'>&COMROOT;/&NET;/&model_ver;/&RUN;.@Y@m@d/@H/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE2: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
+    DATADEP_FILE3: "<cyclestr>&DATAROOT/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE3: "<cyclestr>&DATAROOT/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
   tasks:
     task_prep_obs:
@@ -111,6 +114,14 @@ workflow:
             attrs:
               age: 5
             value: "&DATADEP_FILE2;"
+          datadep_file3:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE3;"
+          datadep_file4:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE4;"
     task_analysis:
       attrs:
         cycledefs: cycled
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index 4cf3b803..03cbfc83 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -2,9 +2,6 @@
 
 set -xue
 
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members)
-
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}
@@ -200,7 +197,7 @@ if [[ $do_HOFX == "YES" ]]; then
 fi 
 
 ################################################
-# Create increment files
+# Apply Increment to UFS sfc_data files
 ################################################
 
 if [[ $do_DA == "YES" ]]; then 
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index e921bc74..3fd651ac 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -2,9 +2,6 @@
 
 set -xue
 
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members)
-
 MACHINE_ID=${MACHINE}
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
@@ -27,10 +24,6 @@ module use modulefiles; module load modules.landda
 
 MPIEXEC=`which mpiexec`
 
-for itile in {1..6}
-do
-  cp ${COMIN}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc .
-done
 
 #  convert back to UFS tile, run model (all members)
 if [[ ${ATMOS_FORC} == "gswp3" ]]; then  
@@ -38,6 +31,11 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   echo '************************************************'
   echo 'running the forecast model' 
 
+  for itile in {1..6}
+  do
+    cp ${COMIN}/RESTART/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
+  done
+
   TEST_NAME=datm_cdeps_lnd_gswp3
   TEST_NAME_RST=datm_cdeps_lnd_gswp3_rst
   PATHRT=${HOMElandda}/sorc/ufs_model.fd/tests
@@ -105,7 +103,7 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   # restart
   if [ $WARM_START = .true. ]; then
     # NoahMP restart files
-    cp ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
+    cp ${COMOUT}/RESTART/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
 
     # CMEPS restart and pointer files
     RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
@@ -161,17 +159,16 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
     echo "ufs_model failed"
     exit 10
   fi
-fi
 
-############################
-# check model ouput (all members)
-if [[ ${ATMOS_FORC} == "era5" ]]; then
-  if [[ -e ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ]]; then
-    cp -p ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
-  fi
-elif [[ ${ATMOS_FORC} == "gswp3" ]]; then
-  for tile in 1 2 3 4 5 6
+  # copy model ouput to COM
+  for itile in {1..6}
+  do
+    cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${itile}.nc ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc
+  done
+
+  # link restart for next cycle
+  for itile in {1..6}
   do
-    cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${tile}.nc ${COMOUT}/RESTART/tile/ufs_land_restart_back.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${tile}.nc
+    ln -nsf ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc ${DATA_RESTART}
   done
 fi
diff --git a/scripts/exlandda_post_anal.sh b/scripts/exlandda_post_anal.sh
index 22b73488..b2fe1690 100755
--- a/scripts/exlandda_post_anal.sh
+++ b/scripts/exlandda_post_anal.sh
@@ -62,8 +62,7 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
   fi
 
   # save analysis restart
-  mkdir -p ${COMOUT}/RESTART/vector
-  cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/RESTART/vector/ufs_land_restart_anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+  cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc ${COMOUT}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
 
   echo '************************************************'
   echo 'running the forecast model' 
@@ -92,6 +91,12 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
     exit 10
   fi
 
+  mkdir -p ${COMOUT}/RESTART
+  cp -p ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
+
+  # link restart for next cycle
+  ln -nsf ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${DATA_RESTART}
+
 #  convert back to UFS tile, run model (all members)
 elif [[ ${ATMOS_FORC} == "gswp3" ]]; then  
   echo '************************************************'
@@ -120,9 +125,9 @@ elif [[ ${ATMOS_FORC} == "gswp3" ]]; then
   fi
 
   # save analysis restart
-  mkdir -p ${COMOUT}/RESTART/tile
+  mkdir -p ${COMOUT}/RESTART
   for itile in {1..6}
   do
-    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ${COMOUT}/RESTART/tile/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
+    cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ${COMOUT}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc
   done  
 fi
diff --git a/scripts/exlandda_pre_anal.sh b/scripts/exlandda_pre_anal.sh
index 9ed911aa..790808fd 100755
--- a/scripts/exlandda_pre_anal.sh
+++ b/scripts/exlandda_pre_anal.sh
@@ -2,9 +2,6 @@
 
 set -xue
 
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members) 
-
 TPATH=${FIXlandda}/forcing/${ATMOS_FORC}/orog_files/
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}
@@ -30,13 +27,16 @@ module use modulefiles; module load modules.landda
 if [[ $ATMOS_FORC == "era5" ]]; then
   # vector2tile for DA
   # copy restarts into work directory
-  rst_in=${COMIN}/RESTART/vector/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-  if [[ ! -e ${rst_in} ]]; then
-    rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
+  rst_fn="ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc"
+  if [[ -e ${DATA_RESTART}/${rst_fn} ]]; then
+    cp ${DATA_RESTART}/${rst_fn} .      
+  elif [[ -e ${WARMSTART_DIR}/${rst_fn} ]]; then
+    cp ${WARMSTART_DIR}/${rst_fn} .
+  else
+    echo "Initial restart file does not exist"
+    exit 11
   fi
-  rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-  cp ${rst_in} ${rst_out}
-  cp -p ${rst_out} ${DATA_SHARE}
+  cp -p ${rst_fn} ${DATA_SHARE}
 
   echo '************************************************'
   echo 'calling vector2tile' 
@@ -66,8 +66,10 @@ if [[ $ATMOS_FORC == "era5" ]]; then
   export err=$?; err_chk
   if [[ $err != 0 ]]; then
     echo "vec2tile failed"
-    exit
+    exit 12
   fi 
+
+
 elif [[ $ATMOS_FORC == "gswp3" ]]; then
   # tile2tile for DA
   echo '************************************************'
@@ -76,14 +78,17 @@ elif [[ $ATMOS_FORC == "gswp3" ]]; then
   # copy restarts into work directory
   for itile in {1..6}
   do
-    rst_in=${COMIN}/RESTART/tile/ufs_land_restart_back.${YYYY}-${MM}-${DD}_${HH}-00-00.nc
-    if [[ ! -e ${rst_in} ]]; then  
-      rst_in=${FIXlandda}/restarts/${ATMOS_FORC}/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
+    rst_fn="ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc"
+    if [[ -e ${DATA_RESTART}/${rst_fn} ]]; then
+      cp ${DATA_RESTART}/${rst_fn} .
+    elif [[ -e ${WARMSTART_DIR}/${rst_fn} ]]; then
+      cp ${WARMSTART_DIR}/${rst_fn} .
+    else
+      echo "Initial restart files do not exist"
+      exit 21
     fi
-    rst_out=${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc
-    cp ${rst_in} ${rst_out}
     # copy restart to data share dir for post_anal
-    cp -p ${rst_out} ${DATA_SHARE}
+    cp -p ${rst_fn} ${DATA_SHARE}
   done
 
   # update tile2tile namelist
@@ -108,13 +113,13 @@ elif [[ $ATMOS_FORC == "gswp3" ]]; then
   export err=$?; err_chk
   if [[ $err != 0 ]]; then
     echo "tile2tile failed"
-    exit 
+    exit 22 
   fi
-fi
 
-#stage restarts for applying JEDI update to intermediate directory
-for itile in {1..6}
-do
-  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
-done
+  #stage restarts for applying JEDI update to intermediate directory
+  for itile in {1..6}
+  do
+    cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
+  done
+fi
 

From 822decdc238c2bb1434bfab5a832309182046b9f Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 16:24:07 -0500
Subject: [PATCH 08/18] fix typo in xml yaml

---
 parm/land_analysis_gswp3_orion.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 84b904f5..5c29abf1 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -16,7 +16,7 @@ workflow:
     EXP_NAME: "LETKF"
     EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
     JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
-    WARMSTART_DIR: ""
+    WARMSTART_DIR: "/work/noaa/epic/UFS_Land-DA_Dev/DATA_RESTART"
     FORCING: "gswp3"
     RES: "96"
     FCSTHR: "24"
@@ -46,8 +46,8 @@ workflow:
     NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
     DATADEP_FILE1: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
     DATADEP_FILE2: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
-    DATADEP_FILE3: "<cyclestr>&DATAROOT/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
-    DATADEP_FILE3: "<cyclestr>&DATAROOT/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
+    DATADEP_FILE3: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE4: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
   tasks:
     task_prep_obs:
@@ -88,6 +88,7 @@ workflow:
         ATMOS_FORC: "&FORCING;"
         RES: "&RES;"
         TSTUB: "&TSTUB;"
+        WARMSTART_DIR: "&WARMSTART_DIR;"
         model_ver: "&model_ver;"
         RUN: "&RUN;"
         HOMElandda: "&HOMElandda;"

From 07de1b0a85645bd4f7244fe8706d2c8c67ed6549 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Fri, 17 May 2024 17:01:11 -0500
Subject: [PATCH 09/18] fix typo in forecast script

---
 scripts/exlandda_forecast.sh  | 11 +++++++----
 scripts/exlandda_post_anal.sh |  6 ++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 3fd651ac..3cbf1f51 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -33,7 +33,7 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
 
   for itile in {1..6}
   do
-    cp ${COMIN}/RESTART/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
+    cp ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
   done
 
   TEST_NAME=datm_cdeps_lnd_gswp3
@@ -103,7 +103,10 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   # restart
   if [ $WARM_START = .true. ]; then
     # NoahMP restart files
-    cp ${COMOUT}/RESTART/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
+    for itile in {1..6}
+    do
+      ln -nsf ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc RESTART/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile${itile}.nc
+    done
 
     # CMEPS restart and pointer files
     RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
@@ -163,12 +166,12 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   # copy model ouput to COM
   for itile in {1..6}
   do
-    cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${itile}.nc ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc
+    cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${itile}.nc ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc
   done
 
   # link restart for next cycle
   for itile in {1..6}
   do
-    ln -nsf ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc ${DATA_RESTART}
+    ln -nsf ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc ${DATA_RESTART}
   done
 fi
diff --git a/scripts/exlandda_post_anal.sh b/scripts/exlandda_post_anal.sh
index b2fe1690..40ba2c46 100755
--- a/scripts/exlandda_post_anal.sh
+++ b/scripts/exlandda_post_anal.sh
@@ -91,11 +91,10 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
     exit 10
   fi
 
-  mkdir -p ${COMOUT}/RESTART
-  cp -p ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
+  cp -p ${DATA}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc
 
   # link restart for next cycle
-  ln -nsf ${COMOUT}/RESTART/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${DATA_RESTART}
+  ln -nsf ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${DATA_RESTART}
 
 #  convert back to UFS tile, run model (all members)
 elif [[ ${ATMOS_FORC} == "gswp3" ]]; then  
@@ -125,7 +124,6 @@ elif [[ ${ATMOS_FORC} == "gswp3" ]]; then
   fi
 
   # save analysis restart
-  mkdir -p ${COMOUT}/RESTART
   for itile in {1..6}
   do
     cp -p ${DATA}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ${COMOUT}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc

From 4fb2a3b745eb7c6447a47c627e3daa338572d203 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sat, 18 May 2024 18:56:26 -0500
Subject: [PATCH 10/18] clean up scripts

---
 parm/run_without_rocoto.sh   | 2 ++
 scripts/exlandda_prep_obs.sh | 2 --
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/run_without_rocoto.sh b/parm/run_without_rocoto.sh
index 971f7618..7b9f8e5c 100755
--- a/parm/run_without_rocoto.sh
+++ b/parm/run_without_rocoto.sh
@@ -18,9 +18,11 @@ export FORCING="era5"
 if [ "${MACHINE}" = "hera" ]; then
   export EXP_BASEDIR="/scratch2/NAGAPE/epic/{USER}/landda_test"
   export JEDI_INSTALL="/scratch2/NAGAPE/epic/UFS_Land-DA/jedi_skylabv7.0"
+  export WARMSTART_DIR=""
 elif [ "${MACHINE}" = "orion" ]; then
   export EXP_BASEDIR="/work/noaa/epic/{USER}/landda_test"
   export JEDI_INSTALL="/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
+  export WARMSTART_DIR="/work/noaa/epic/UFS_Land-DA_Dev/DATA_RESTART"
 fi
 
 export RES="96"
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index c3799e94..1ec3b88a 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -2,8 +2,6 @@
 
 set -xue
 
-############################
-# copy restarts to workdir, convert to UFS tile for DA (all members) 
 
 YYYY=${PDY:0:4}
 MM=${PDY:4:2}

From b7d8e54517c8ac12f8bbe8eebe3cf4a8777d7875 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 09:41:07 -0500
Subject: [PATCH 11/18] update scripts for era5

---
 parm/land_analysis_gswp3_hera.yaml  | 144 ++++++++++++++++------------
 parm/land_analysis_gswp3_orion.yaml |   7 +-
 scripts/exlandda_analysis.sh        |   3 +-
 scripts/exlandda_post_anal.sh       |  16 +++-
 scripts/exlandda_pre_anal.sh        |  12 +--
 scripts/exlandda_prep_obs.sh        |   2 +-
 6 files changed, 107 insertions(+), 77 deletions(-)

diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_gswp3_hera.yaml
index 1cba9dad..63930aea 100644
--- a/parm/land_analysis_gswp3_hera.yaml
+++ b/parm/land_analysis_gswp3_hera.yaml
@@ -7,16 +7,17 @@ workflow:
   cycledef:
     - attrs:
         group: cycled
-      spec: 200001030000 200001040000 24:00:00
-# for era5: spec:  201912210000 201912210000 24:00:00
+      spec: 200001030000 200001040000 24:00:00   # for gswp3
+#      spec: 201912210000 201912220000 24:00:00   # for era5
   entities:
-    MACHINE: "hera"
+    MACHINE: "orion"
     SCHED: "slurm"
-    ACCOUNT: "nems"
+    ACCOUNT: "epic"
     EXP_NAME: "LETKF"
     EXP_BASEDIR: "/scratch2/NAGAPE/epic/{USER}/landda_test"
-    JEDI_INSTALL: "/scratch2/NAGAPE/epic/UFS_Land-DA/jedi_skylabv7.0"
-    FORCING: "gswp3"
+    JEDI_INSTALL: "/scratch2/NAGAPE/epic/UFS_Land-DA_Dev/jedi_v7"
+    WARMSTART_DIR: "/scratch2/NAGAPE/epic/UFS_Land-DA_Dev/DATA_RESTART"
+    FORCING: "gswp3"   # "gswp3" or "era5"
     RES: "96"
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
@@ -30,31 +31,37 @@ workflow:
     NET: "landda"
     envir: "test"
     model_ver: "v1.2.1"
+    RUN: "landda"
     HOMElandda: "&EXP_BASEDIR;/land-DA_workflow"
     PTMP: "&EXP_BASEDIR;/ptmp"
     COMROOT: "&PTMP;/&envir;/com"
     DATAROOT: "&PTMP;/&envir;/tmp"
     KEEPDATA: "YES"
-    WORKDIR: "&EXP_BASEDIR;/workdir/run_&FORCING;"
     LOGDIR: "&COMROOT;/output/logs/run_&FORCING;"
+    LOGFN_SUFFIX: "<cyclestr>_@Y@m@d@H.log</cyclestr>"
     PATHRT: "&EXP_BASEDIR;"
     PDY:  "<cyclestr>@Y@m@d</cyclestr>"
     cyc: "<cyclestr>@H</cyclestr>"
-    SLASH_ENSMEM_SUBDIR: ""
     PTIME:  "<cyclestr offset='-24:00:00'>@Y@m@d@H</cyclestr>"
     NTIME:  "<cyclestr offset='24:00:00'>@Y@m@d@H</cyclestr>"
+    DATADEP_FILE1: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE2: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
+    DATADEP_FILE3: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.tile1.nc</cyclestr>"
+    DATADEP_FILE4: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@d_@H-00-00.nc</cyclestr>"
   log: "&LOGDIR;/workflow.log"
   tasks:
-    task_prep_exp:
+    task_prep_obs:
+      attrs:
+        cycledefs: cycled
       envars:
+        OBSDIR: "&OBSDIR;"
+        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
+        OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -62,54 +69,72 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_exp" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_exp
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
+      jobname: prep_obs
       cores: 1
       walltime: 00:02:00
       queue: batch
-      join: "&LOGDIR;/prep_exp.log"
-    task_prep_obs:
+      join: "&LOGDIR;/prep_obs&LOGFN_SUFFIX;"
+    task_pre_anal:
+      attrs:
+        cycledefs: cycled
       envars:
-        OBSDIR: "&OBSDIR;"
-        OBSDIR_SUBDIR: "&OBSDIR_SUBDIR;"
-        OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
+        RES: "&RES;"
+        TSTUB: "&TSTUB;"
+        WARMSTART_DIR: "&WARMSTART_DIR;"
         model_ver: "&model_ver;"
+        RUN: "&RUN;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
         DATAROOT: "&DATAROOT;"
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_obs" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_obs
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "pre_anal" "&HOMElandda;" "&MACHINE;"'
+      jobname: pre_anal
       cores: 1
-      walltime: 00:02:00
+      walltime: 00:05:00
       queue: batch
-      join: "&LOGDIR;/prep_obs.log"
+      join: "&LOGDIR;/pre_anal&LOGFN_SUFFIX;"
       dependency:
-        taskdep:
-          attrs:
-            task: prep_exp
-    task_prep_bmat:
+        or:
+          datadep_file1:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE1;"
+          datadep_file2:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE2;"
+          datadep_file3:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE3;"
+          datadep_file4:
+            attrs:
+              age: 5
+            value: "&DATADEP_FILE4;"
+    task_analysis:
+      attrs:
+        cycledefs: cycled
       envars:
+        OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        WORKDIR: "&WORKDIR;"
+        RES: "&RES;"
+        TSTUB: "&TSTUB;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -117,24 +142,27 @@ workflow:
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
+        NTIME: "&NTIME;"
         DAtype: "&DAtype;"
         SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
+        NPROC_JEDI: "&NPROCS_ANALYSIS;"
+        JEDI_INSTALL: "&JEDI_INSTALL;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "prep_bmat" "&HOMElandda;" "&MACHINE;"'
-      jobname: prep_bmat
-      cores: 1
-      walltime: 00:02:00
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
+      jobname: analysis
+      nodes: "1:ppn=&NPROCS_ANALYSIS;"
+      walltime: 00:15:00
       queue: batch
-      join: "&LOGDIR;/prep_bmat.log"
+      join: "&LOGDIR;/analysis&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
-            task: prep_obs
-    task_analysis:
+            task: pre_anal
+    task_post_anal:
+      attrs:
+        cycledefs: cycled
       envars:
-        OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
         SCHED: "&SCHED;"
         ACCOUNT: "&ACCOUNT;"
@@ -142,33 +170,31 @@ workflow:
         ATMOS_FORC: "&FORCING;"
         RES: "&RES;"
         TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
+        RUN: "&RUN;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
         DATAROOT: "&DATAROOT;"
         KEEPDATA: "&KEEPDATA;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
         PTIME: "&PTIME;"
         NTIME: "&NTIME;"
-        DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        NPROC_JEDI: "&NPROCS_ANALYSIS;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
+        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
-      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "analysis" "&HOMElandda;" "&MACHINE;"'
-      jobname: analysis
-      nodes: "1:ppn=&NPROCS_ANALYSIS;"
-      walltime: 00:15:00
+      command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "post_anal" "&HOMElandda;" "&MACHINE;"'
+      jobname: post_anal
+      cores: 1
+      walltime: 00:05:00
       queue: batch
-      join: "&LOGDIR;/analysis.log"
+      join: "&LOGDIR;/post_anal&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
-            task: prep_bmat
+            task: analysis
     task_forecast:
+      attrs:
+        cycledefs: cycled
       envars:
         OBS_TYPES: "&OBS_TYPES;"
         MACHINE: "&MACHINE;"
@@ -176,9 +202,6 @@ workflow:
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
-        RES: "&RES;"
-        TSTUB: "&TSTUB;"
-        WORKDIR: "&WORKDIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
@@ -187,21 +210,16 @@ workflow:
         LOGDIR: "&LOGDIR;"
         PDY: "&PDY;"
         cyc: "&cyc;"
-        SLASH_ENSMEM_SUBDIR: "&SLASH_ENSMEM_SUBDIR;"
-        PTIME: "&PTIME;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
-        SNOWDEPTHVAR: "&SNOWDEPTHVAR;"
-        JEDI_INSTALL: "&JEDI_INSTALL;"
-        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
       jobname: forecast
       nodes: "1:ppn=&NPROCS_FORECAST;"
-      walltime: 00:45:00
+      walltime: 01:00:00
       queue: batch
-      join: "&LOGDIR;/forecast.log"
+      join: "&LOGDIR;/forecast&LOGFN_SUFFIX;"
       dependency:
         taskdep:
           attrs:
-            task: analysis
+            task: post_anal
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 5c29abf1..76941b00 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -7,8 +7,8 @@ workflow:
   cycledef:
     - attrs:
         group: cycled
-      spec: 200001030000 200001040000 24:00:00
-# for era5: spec:  201912210000 201912210000 24:00:00
+      spec: 200001030000 200001040000 24:00:00   # for gswp3
+#      spec: 201912210000 201912220000 24:00:00   # for era5
   entities:
     MACHINE: "orion"
     SCHED: "slurm"
@@ -17,7 +17,7 @@ workflow:
     EXP_BASEDIR: "/work/noaa/epic/{USER}/landda_test"
     JEDI_INSTALL: "/work/noaa/epic/UFS_Land-DA_Dev/jedi_v7"
     WARMSTART_DIR: "/work/noaa/epic/UFS_Land-DA_Dev/DATA_RESTART"
-    FORCING: "gswp3"
+    FORCING: "gswp3"   # "gswp3" or "era5"
     RES: "96"
     FCSTHR: "24"
     NPROCS_ANALYSIS: "6"
@@ -179,6 +179,7 @@ workflow:
         PDY: "&PDY;"
         cyc: "&cyc;"
         PTIME: "&PTIME;"
+        NTIME: "&NTIME;"
         FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "post_anal" "&HOMElandda;" "&MACHINE;"'
diff --git a/scripts/exlandda_analysis.sh b/scripts/exlandda_analysis.sh
index 03cbfc83..fdf82312 100755
--- a/scripts/exlandda_analysis.sh
+++ b/scripts/exlandda_analysis.sh
@@ -32,6 +32,7 @@ YAML_DA=construct
 GFSv17="NO"
 B=30 # back ground error std for LETKFOI
 
+# Import input files
 for itile in {1..6}
 do
   cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
@@ -168,7 +169,7 @@ fi
 ################################################
 
 if [[ ! -e Data ]]; then
-  ln -s $JEDI_STATICDIR Data 
+  ln -nsf $JEDI_STATICDIR Data 
 fi
 
 echo 'do_landDA: calling fv3-jedi'
diff --git a/scripts/exlandda_post_anal.sh b/scripts/exlandda_post_anal.sh
index 40ba2c46..92891d46 100755
--- a/scripts/exlandda_post_anal.sh
+++ b/scripts/exlandda_post_anal.sh
@@ -11,6 +11,10 @@ YYYY=${PDY:0:4}
 MM=${PDY:4:2}
 DD=${PDY:6:2}
 HH=${cyc}
+nYYYY=${NTIME:0:4}
+nMM=${NTIME:4:2}
+nDD=${NTIME:6:2}
+nHH=${NTIME:8:2}
 
 FREQ=$((${FCSTHR}*3600))
 RDD=$((${FCSTHR}/24))
@@ -31,7 +35,6 @@ FILEDATE=${YYYY}${MM}${DD}.${HH}0000
 for itile in {1..6}
 do
   cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
-  cp ${DATA_SHARE}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc .
 done
 
 #  convert back to vector, run model (all members) convert back to vector, run model (all members)
@@ -39,6 +42,8 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
   echo '************************************************'
   echo 'calling tile2vector' 
 
+  cp ${DATA_SHARE}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.nc .
+
   cp ${PARMlandda}/templates/template.tile2vector tile2vector.namelist
 
   sed -i "s|FIXlandda|${FIXlandda}|g" tile2vector.namelist
@@ -46,7 +51,7 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
   sed -i -e "s/XXMM/${MM}/g" tile2vector.namelist
   sed -i -e "s/XXDD/${DD}/g" tile2vector.namelist
   sed -i -e "s/XXHH/${HH}/g" tile2vector.namelist
-  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" vector2tile.namelist
+  sed -i -e "s/MODEL_FORCING/${ATMOS_FORC}/g" tile2vector.namelist
   sed -i -e "s/XXRES/${RES}/g" tile2vector.namelist
   sed -i -e "s/XXTSTUB/${TSTUB}/g" tile2vector.namelist
   sed -i -e "s#XXTPATH#${TPATH}#g" tile2vector.namelist
@@ -96,11 +101,16 @@ if [[ ${ATMOS_FORC} == "era5" ]]; then
   # link restart for next cycle
   ln -nsf ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.nc ${DATA_RESTART}
 
-#  convert back to UFS tile, run model (all members)
+#  convert back to UFS tile
 elif [[ ${ATMOS_FORC} == "gswp3" ]]; then  
   echo '************************************************'
   echo 'calling tile2tile' 
 
+  for itile in {1..6}
+  do
+    cp ${DATA_SHARE}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc .
+  done
+
   cp ${PARMlandda}/templates/template.jedi2ufs jedi2ufs.namelist
    
   sed -i "s|FIXlandda|${FIXlandda}|g" jedi2ufs.namelist
diff --git a/scripts/exlandda_pre_anal.sh b/scripts/exlandda_pre_anal.sh
index 790808fd..c54472ca 100755
--- a/scripts/exlandda_pre_anal.sh
+++ b/scripts/exlandda_pre_anal.sh
@@ -69,7 +69,6 @@ if [[ $ATMOS_FORC == "era5" ]]; then
     exit 12
   fi 
 
-
 elif [[ $ATMOS_FORC == "gswp3" ]]; then
   # tile2tile for DA
   echo '************************************************'
@@ -116,10 +115,11 @@ elif [[ $ATMOS_FORC == "gswp3" ]]; then
     exit 22 
   fi
 
-  #stage restarts for applying JEDI update to intermediate directory
-  for itile in {1..6}
-  do
-    cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
-  done
 fi
 
+#stage restarts for applying JEDI update to intermediate directory
+for itile in {1..6}
+do
+  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
+done
+
diff --git a/scripts/exlandda_prep_obs.sh b/scripts/exlandda_prep_obs.sh
index 1ec3b88a..83e19ff2 100755
--- a/scripts/exlandda_prep_obs.sh
+++ b/scripts/exlandda_prep_obs.sh
@@ -27,7 +27,7 @@ for obs in "${OBS_TYPES[@]}"; do
     # obs are within DA window.
   elif [ $ATMOS_FORC == "era5" ] && [ ${obs} == "GHCN" ]; then
     OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-snow_depth/GHCN/data_proc/v3}"
-    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc"
+    obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}_jediv7.nc"
   elif [ $ATMOS_FORC == "gswp3" ] && [ ${obs} == "GHCN" ]; then
     OBSDIR_SUBDIR="${OBSDIR_SUBDIR:-snow_depth/GHCN/data_proc/v3}"
     obsfile="${OBSDIR}/${OBSDIR_SUBDIR}/${YYYY}/ghcn_snwd_ioda_${YYYP}${MP}${DP}.nc"

From 8907a991a4e473ddf3e82ee867525b85329e537b Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 12:15:30 -0500
Subject: [PATCH 12/18] remove cyc from comin/comout

---
 jobs/JLANDDA_ANALYSIS        | 20 +++++++-------
 jobs/JLANDDA_FORECAST        | 22 ++++++++-------
 jobs/JLANDDA_POST_ANAL       | 20 +++++++-------
 jobs/JLANDDA_PREP_OBS        | 20 +++++++-------
 jobs/JLANDDA_PRE_ANAL        | 20 +++++++-------
 scripts/exlandda_forecast.sh | 52 +++++++++++++++++++++---------------
 6 files changed, 82 insertions(+), 72 deletions(-)

diff --git a/jobs/JLANDDA_ANALYSIS b/jobs/JLANDDA_ANALYSIS
index 910b6262..30ddb154 100755
--- a/jobs/JLANDDA_ANALYSIS
+++ b/jobs/JLANDDA_ANALYSIS
@@ -56,25 +56,25 @@ cd $DATA
 export NET="${NET:-landda}"
 export RUN="${RUN:-landda}"
 
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
 fi
 
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
 mkdir -p ${DATA_SHARE}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
 #
 #-----------------------------------------------------------------------
 #
diff --git a/jobs/JLANDDA_FORECAST b/jobs/JLANDDA_FORECAST
index 337cd273..1c7c328f 100755
--- a/jobs/JLANDDA_FORECAST
+++ b/jobs/JLANDDA_FORECAST
@@ -56,27 +56,29 @@ cd $DATA
 export NET="${NET:-landda}"
 export RUN="${RUN:-landda}"
 
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMINm1="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDYm1})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMINm1="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDYm1}}"
 fi
 
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
 mkdir -p ${DATA_SHARE}
 export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
 mkdir -p ${DATA_RESTART}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
 #
 #-----------------------------------------------------------------------
 #
diff --git a/jobs/JLANDDA_POST_ANAL b/jobs/JLANDDA_POST_ANAL
index 1a896664..38e25d72 100755
--- a/jobs/JLANDDA_POST_ANAL
+++ b/jobs/JLANDDA_POST_ANAL
@@ -56,27 +56,27 @@ cd $DATA
 export NET="${NET:-landda}"
 export RUN="${RUN:-landda}"
 
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
 fi
 
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
 mkdir -p ${DATA_SHARE}
 export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
 mkdir -p ${DATA_RESTART}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
 #
 #-----------------------------------------------------------------------
 #
diff --git a/jobs/JLANDDA_PREP_OBS b/jobs/JLANDDA_PREP_OBS
index dd2422fc..d3e0a720 100755
--- a/jobs/JLANDDA_PREP_OBS
+++ b/jobs/JLANDDA_PREP_OBS
@@ -56,25 +56,25 @@ cd $DATA
 export NET="${NET:-landda}"
 export RUN="${RUN:-landda}"
 
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
 fi
 
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
 mkdir -p ${DATA_SHARE}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
 #
 #-----------------------------------------------------------------------
 #
diff --git a/jobs/JLANDDA_PRE_ANAL b/jobs/JLANDDA_PRE_ANAL
index f15e2323..16858ba6 100755
--- a/jobs/JLANDDA_PRE_ANAL
+++ b/jobs/JLANDDA_PRE_ANAL
@@ -56,27 +56,27 @@ cd $DATA
 export NET="${NET:-landda}"
 export RUN="${RUN:-landda}"
 
+# Run setpdy to initialize PDYm and PDYp variables
+export cycle="${cycle:-t${cyc}z}"
+setpdy.sh
+. ./PDY
+
 [[ "$WORKFLOW_MANAGER" = "rocoto" ]] && export COMROOT=$COMROOT
 if [ "${MACHINE}" = "WCOSS2" ]; then
-  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
-  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY}/${cyc})}"
+  export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
+  export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
 else
-  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
-  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}/${cyc}}"
+  export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
+  export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
 fi
 
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}${cyc}}"
+export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
 mkdir -p ${DATA_SHARE}
 export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
 mkdir -p ${DATA_RESTART}
-
-# Run setpdy to initialize PDYm and PDYp variables
-export cycle="${cycle:-t${cyc}z}"
-setpdy.sh
-. ./PDY
 #
 #-----------------------------------------------------------------------
 #
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 3cbf1f51..9ebc6c6c 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -31,11 +31,6 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   echo '************************************************'
   echo 'running the forecast model' 
 
-  for itile in {1..6}
-  do
-    cp ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
-  done
-
   TEST_NAME=datm_cdeps_lnd_gswp3
   TEST_NAME_RST=datm_cdeps_lnd_gswp3_rst
   PATHRT=${HOMElandda}/sorc/ufs_model.fd/tests
@@ -100,24 +95,35 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   cd -
 
   SUFFIX=${RT_SUFFIX}
-  # restart
-  if [ $WARM_START = .true. ]; then
-    # NoahMP restart files
-    for itile in {1..6}
-    do
-      ln -nsf ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc RESTART/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile${itile}.nc
-    done
-
-    # CMEPS restart and pointer files
-    RFILE1=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
-    cp ${FIXlandda}/restarts/gswp3/${RFILE1} RESTART/.
-    ls -1 "RESTART/${RFILE1}">rpointer.cpl
-
-    # CDEPS restart and pointer files
-    RFILE2=ufs.cpld.datm.r.${RESTART_FILE_SUFFIX_SECS}.nc
-    cp ${FIXlandda}/restarts/gswp3/${RFILE2} RESTART/.
-    ls -1 "RESTART/${RFILE2}">rpointer.atm
+
+  # Retrieve input files for restart
+  # NoahMP restart files
+  for itile in {1..6}
+  do
+    ln -nsf ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc RESTART/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}_${HH}-0000.tile${itile}.nc
+  done
+
+  # CMEPS restart and pointer files
+  rfile1=ufs.cpld.cpl.r.${YYYY}-${MM}-${DD}_${HH}-0000.nc
+  if [[ -e "${COMINm1}/${rfile1}" ]]; then
+    cp "${COMINm1}/${rfile1}" RESTART/.
+  elif [[ -e "${WARMSTART_DIR}/${rfile1}" ]]; then
+    cp "${WARMSTART_DIR}/${rfile1}" RESTART/.
+  else
+    cp ${FIXlandda}/restarts/gswp3/${rfile1} RESTART/.
+  fi
+  ls -1 "RESTART/${rfile11}">rpointer.cpl
+
+  # CDEPS restart and pointer files
+  rfile2=ufs.cpld.datm.r.${YYYY}-${MM}-${DD}_${HH}-0000.nc
+  if [[ -e "${COMINm1}/${rfile2}" ]]; then
+    cp "${COMINm1}/${rfile2}" RESTART/.
+  elif [[ -e "${WARMSTART_DIR}/${rfile2}" ]]; then
+    cp "${WARMSTART_DIR}/${rfile2}" RESTART/.
+  else
+    cp ${FIXlandda}/restarts/gswp3/${rfile2} RESTART/.
   fi
+  ls -1 "RESTART/${rfile2}">rpointer.atm
 
   cd INPUT
   ln -nsf ${FIXlandda}/UFS_WM/NOAHMP_IC/ufs-land_C96_init_fields.tile1.nc C96.initial.tile1.nc
@@ -168,6 +174,8 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   do
     cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${itile}.nc ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc
   done
+  cp -p ${DATA}/ufs.cpld.datm.r.${nYYYY}-${nMM}-${nHH}-0000.nc ${COMOUT}
+  cp -p ${DATA}/RESTART/ufs.cpld.cpl.r.${nYYYY}-${nMM}-${nHH}-0000.nc ${COMOUT}
 
   # link restart for next cycle
   for itile in {1..6}

From 3b1f1e1af0c355bc845a0a0f314886ff77a872c4 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 12:42:24 -0500
Subject: [PATCH 13/18] fix typo in forecast script

---
 parm/land_analysis_gswp3_hera.yaml  |  1 +
 parm/land_analysis_gswp3_orion.yaml |  1 +
 scripts/exlandda_forecast.sh        | 10 +++++-----
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_gswp3_hera.yaml
index 63930aea..1ebcba8d 100644
--- a/parm/land_analysis_gswp3_hera.yaml
+++ b/parm/land_analysis_gswp3_hera.yaml
@@ -202,6 +202,7 @@ workflow:
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
+        WARMSTART_DIR: "&WARMSTART_DIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index 76941b00..db219e42 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -202,6 +202,7 @@ workflow:
         ACCOUNT: "&ACCOUNT;"
         EXP_NAME: "&EXP_NAME;"
         ATMOS_FORC: "&FORCING;"
+        WARMSTART_DIR: "&WARMSTART_DIR;"
         model_ver: "&model_ver;"
         HOMElandda: "&HOMElandda;"
         COMROOT: "&COMROOT;"
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 9ebc6c6c..4e2560c0 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -104,7 +104,7 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   done
 
   # CMEPS restart and pointer files
-  rfile1=ufs.cpld.cpl.r.${YYYY}-${MM}-${DD}_${HH}-0000.nc
+  rfile1="ufs.cpld.cpl.r.${YYYY}-${MM}-${DD}-00000.nc"
   if [[ -e "${COMINm1}/${rfile1}" ]]; then
     cp "${COMINm1}/${rfile1}" RESTART/.
   elif [[ -e "${WARMSTART_DIR}/${rfile1}" ]]; then
@@ -112,10 +112,10 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   else
     cp ${FIXlandda}/restarts/gswp3/${rfile1} RESTART/.
   fi
-  ls -1 "RESTART/${rfile11}">rpointer.cpl
+  ls -1 "RESTART/${rfile1}">rpointer.cpl
 
   # CDEPS restart and pointer files
-  rfile2=ufs.cpld.datm.r.${YYYY}-${MM}-${DD}_${HH}-0000.nc
+  rfile2="ufs.cpld.datm.r.${YYYY}-${MM}-${DD}-00000.nc"
   if [[ -e "${COMINm1}/${rfile2}" ]]; then
     cp "${COMINm1}/${rfile2}" RESTART/.
   elif [[ -e "${WARMSTART_DIR}/${rfile2}" ]]; then
@@ -174,8 +174,8 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   do
     cp -p ${DATA}/ufs.cpld.lnd.out.${nYYYY}-${nMM}-${nDD}-00000.tile${itile}.nc ${COMOUT}/ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile${itile}.nc
   done
-  cp -p ${DATA}/ufs.cpld.datm.r.${nYYYY}-${nMM}-${nHH}-0000.nc ${COMOUT}
-  cp -p ${DATA}/RESTART/ufs.cpld.cpl.r.${nYYYY}-${nMM}-${nHH}-0000.nc ${COMOUT}
+  cp -p ${DATA}/ufs.cpld.datm.r.${nYYYY}-${nMM}-${nDD}-00000.nc ${COMOUT}
+  cp -p ${DATA}/RESTART/ufs.cpld.cpl.r.${nYYYY}-${nMM}-${nDD}-00000.nc ${COMOUT}
 
   # link restart for next cycle
   for itile in {1..6}

From f80a878e2205871e16584f05e5a46a70aaacc6cd Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 12:55:08 -0500
Subject: [PATCH 14/18] fix typo

---
 scripts/exlandda_forecast.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 4e2560c0..947e070c 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -100,7 +100,7 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   # NoahMP restart files
   for itile in {1..6}
   do
-    ln -nsf ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc RESTART/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}_${HH}-0000.tile${itile}.nc
+    ln -nsf ${COMIN}/ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc RESTART/ufs.cpld.lnd.out.${YYYY}-${MM}-${DD}-00000.tile${itile}.nc
   done
 
   # CMEPS restart and pointer files

From 589e3d01d53f44123f0d48d0f455b2eb5578211d Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 13:58:30 -0500
Subject: [PATCH 15/18] add templates for diag_table and model_configure

---
 jobs/JLANDDA_FORECAST                   |   4 +-
 parm/land_analysis_gswp3_hera.yaml      |   1 +
 parm/land_analysis_gswp3_orion.yaml     |   1 +
 parm/templates/template.diag_table      | 283 ++++++++++++++++++++++++
 parm/templates/template.model_configure |   9 +
 scripts/exlandda_forecast.sh            |  18 +-
 6 files changed, 311 insertions(+), 5 deletions(-)
 create mode 100644 parm/templates/template.diag_table
 create mode 100644 parm/templates/template.model_configure

diff --git a/jobs/JLANDDA_FORECAST b/jobs/JLANDDA_FORECAST
index 1c7c328f..007d0568 100755
--- a/jobs/JLANDDA_FORECAST
+++ b/jobs/JLANDDA_FORECAST
@@ -65,11 +65,11 @@ setpdy.sh
 if [ "${MACHINE}" = "WCOSS2" ]; then
   export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
   export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
-  export COMINm1="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDYm1})}"
+  export COMINm1="${COMINm1:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDYm1})}"
 else
   export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
   export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
-  export COMINm1="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDYm1}}"
+  export COMINm1="${COMINm1:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDYm1}}"
 fi
 
 mkdir -p ${COMOUT}
diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_gswp3_hera.yaml
index 1ebcba8d..c62e9f9a 100644
--- a/parm/land_analysis_gswp3_hera.yaml
+++ b/parm/land_analysis_gswp3_hera.yaml
@@ -213,6 +213,7 @@ workflow:
         cyc: "&cyc;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
+        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
       jobname: forecast
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_gswp3_orion.yaml
index db219e42..4642e7f8 100644
--- a/parm/land_analysis_gswp3_orion.yaml
+++ b/parm/land_analysis_gswp3_orion.yaml
@@ -213,6 +213,7 @@ workflow:
         cyc: "&cyc;"
         NTIME: "&NTIME;"
         DAtype: "&DAtype;"
+        FCSTHR: "&FCSTHR;"
       account: "&ACCOUNT;"
       command: '&HOMElandda;/parm/task_load_modules_run_jjob.sh "forecast" "&HOMElandda;" "&MACHINE;"'
       jobname: forecast
diff --git a/parm/templates/template.diag_table b/parm/templates/template.diag_table
new file mode 100644
index 00000000..68a515fd
--- /dev/null
+++ b/parm/templates/template.diag_table
@@ -0,0 +1,283 @@
+XXYYYYMMDD.00Z.1760x880.64bit.non-mono
+XXYYYY XXMM XXDD XXHH 0 0
+
+"fv3_history",    0,  "hours",  1,  "hours",  "time"
+"fv3_history2d",  0,  "hours",  1,  "hours",  "time"
+######################
+"ocn%4yr%2mo%2dy%2hr",      6,  "hours", 1, "hours", "time", 6, "hours", "1901 1 1 0 0 0"
+"SST%4yr%2mo%2dy",      1,  "days",  1, "days",  "time", 1, "days",  "1901 1 1 0 0 0"
+##############################################
+# static fields
+ "ocean_model", "geolon",      "geolon",      "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolat",      "geolat",      "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolon_c",    "geolon_c",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolat_c",    "geolat_c",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolon_u",    "geolon_u",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolat_u",    "geolat_u",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolon_v",    "geolon_v",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "geolat_v",    "geolat_v",    "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+# "ocean_model", "depth_ocean", "depth_ocean", "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+# "ocean_model", "wet",         "wet",         "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "wet_c",       "wet_c",       "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "wet_u",       "wet_u",       "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "wet_v",       "wet_v",       "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "sin_rot",     "sin_rot",     "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+ "ocean_model", "cos_rot",     "cos_rot",     "ocn%4yr%2mo%2dy%2hr", "all", .false., "none", 2
+
+# ocean output TSUV and others
+ "ocean_model", "SSH",       "SSH",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "SST",       "SST",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "SSS",       "SSS",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "speed",     "speed",    "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "SSU",       "SSU",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "SSV",       "SSV",      "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "frazil",    "frazil",   "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "ePBL_h_ML", "ePBL",     "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "MLD_003",   "MLD_003",  "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "MLD_0125",  "MLD_0125", "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+
+# save daily SST
+ "ocean_model", "geolon",      "geolon",      "SST%4yr%2mo%2dy", "all", .false., "none", 2
+ "ocean_model", "geolat",      "geolat",      "SST%4yr%2mo%2dy", "all", .false., "none", 2
+ "ocean_model", "SST",         "sst",         "SST%4yr%2mo%2dy", "all", .true.,  "none", 2
+
+# Z-Space Fields Provided for CMIP6 (CMOR Names):
+#===============================================
+ "ocean_model_z","uo","uo"      ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model_z","vo","vo"      ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model_z","so","so"      ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model_z","temp","temp"  ,"ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+
+# forcing
+ "ocean_model", "taux",      "taux",                     "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "tauy",      "tauy",                     "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "latent",    "latent",                   "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "sensible",  "sensible",                 "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "SW",        "SW",                       "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "LW",        "LW",                       "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "evap",      "evap",                     "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "lprec",     "lprec",                    "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "lrunoff",   "lrunoff",                  "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+# "ocean_model", "frunoff",   "frunoff",                  "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "fprec",     "fprec",                    "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "LwLatSens", "LwLatSens",                "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+ "ocean_model", "Heat_PmE",  "Heat_PmE",                 "ocn%4yr%2mo%2dy%2hr","all",.true.,"none",2
+#
+###
+# FV3 variabls needed for NGGPS evaluation
+###
+"gfs_dyn",     "ucomp",       "ugrd",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "vcomp",       "vgrd",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "sphum",       "spfh",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "temp",        "tmp",       "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "liq_wat",     "clwmr",     "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "o3mr",        "o3mr",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "delp",        "dpres",     "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "delz",        "delz",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "w",           "dzdt",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "ice_wat",     "icmr",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "rainwat",     "rwmr",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "snowwat",     "snmr",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "graupel",     "grle",      "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "ps",          "pressfc",   "fv3_history",    "all",  .false.,  "none",  2
+"gfs_dyn",     "hs",          "hgtsfc",    "fv3_history",    "all",  .false.,  "none",  2
+#"gfs_dyn",     "ice_nc",      "nicp",      "fv3_history",  "all",  .false.,  "none",  2
+#"gfs_dyn",     "rain_nc",     "ntrnc",     "fv3_history",  "all",  .false.,  "none",  2
+
+"gfs_phys",  "frzr",          "frzr",        "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "frzrb",         "frzrb",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "frozr",         "frozr",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "frozrb",        "frozrb",      "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "tsnowp",        "tsnowp",      "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "tsnowpb",       "tsnowpb",     "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "rhonewsn",      "rhonewsn",    "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "ALBDO_ave",     "albdo_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "cnvprcp_ave",   "cprat_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "cnvprcpb_ave",  "cpratb_ave",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "totprcp_ave",   "prate_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "totprcpb_ave",  "prateb_ave",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "DLWRF",         "dlwrf_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "DLWRFI",        "dlwrf",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "ULWRF",         "ulwrf_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "ULWRFI",        "ulwrf",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "DSWRF",         "dswrf_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "DSWRFI",        "dswrf",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "USWRF",         "uswrf_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "USWRFI",        "uswrf",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "DSWRFtoa",      "dswrf_avetoa","fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "USWRFtoa",      "uswrf_avetoa","fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "ULWRFtoa",      "ulwrf_avetoa","fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "gflux_ave",     "gflux_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "hpbl",          "hpbl",        "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "lhtfl_ave",     "lhtfl_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "shtfl_ave",     "shtfl_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "pwat",          "pwat",        "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "soilm",         "soilm",       "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDC_aveclm",   "tcdc_aveclm", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDC_avebndcl", "tcdc_avebndcl",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDC_avehcl",   "tcdc_avehcl", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDC_avelcl",   "tcdc_avelcl", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDC_avemcl",   "tcdc_avemcl", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TCDCcnvcl",     "tcdccnvcl",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PREScnvclt",    "prescnvclt",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PREScnvclb",    "prescnvclb",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avehct",   "pres_avehct", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avehcb",   "pres_avehcb", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TEMP_avehct",   "tmp_avehct",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avemct",   "pres_avemct", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avemcb",   "pres_avemcb", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TEMP_avemct",   "tmp_avemct",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avelct",   "pres_avelct", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "PRES_avelcb",   "pres_avelcb", "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "TEMP_avelct",   "tmp_avelct",  "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "u-gwd_ave",     "u-gwd_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "v-gwd_ave",     "v-gwd_ave",   "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "dusfc",         "uflx_ave",    "fv3_history2d",         "all",  .false.,  "none",  2
+"gfs_phys",  "dvsfc",         "vflx_ave",    "fv3_history2d",         "all",  .false.,  "none",  2
+#"gfs_phys",  "cnvw",          "cnvcldwat",   "fv3_history2d",         "all",  .false.,  "none",  2
+
+"gfs_phys",    "psurf",       "pressfc",   "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "u10m",        "ugrd10m",   "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "v10m",        "vgrd10m",   "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "crain",       "crain",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "tprcp",       "tprcp",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "hgtsfc",      "orog",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "weasd",       "weasd",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "f10m",        "f10m",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "q2m",         "spfh2m",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "t2m",         "tmp2m",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "tsfc",        "tmpsfc",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "vtype",       "vtype",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "stype",       "sotyp",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slmsksfc",    "land",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "vfracsfc",    "veg",       "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "zorlsfc",     "sfcr",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "uustar",      "fricv",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilt1",      "soilt1"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilt2",      "soilt2"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilt3",      "soilt3"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilt4",      "soilt4"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilw1",      "soilw1"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilw2",      "soilw2"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilw3",      "soilw3"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "soilw4",      "soilw4"     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slc_1",       "soill1",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slc_2",       "soill2",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slc_3",       "soill3",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slc_4",       "soill4",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "slope",       "sltyp",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "alnsf",       "alnsf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "alnwf",       "alnwf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "alvsf",       "alvsf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "alvwf",       "alvwf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "canopy",      "cnwat",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "facsf",       "facsf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "facwf",       "facwf",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "ffhh",        "ffhh",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "ffmm",        "ffmm",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "fice",        "icec",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "hice",        "icetk",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "snoalb",      "snoalb",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "shdmax",      "shdmax",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "shdmin",      "shdmin",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "snowd",       "snod",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "tg3",         "tg3",       "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "tisfc",       "tisfc",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "tref",        "tref",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "z_c",         "zc",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "c_0",         "c0",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "c_d",         "cd",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "w_0",         "w0",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "w_d",         "wd",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xt",          "xt",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xz",          "xz",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "dt_cool",     "dtcool",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xs",          "xs",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xu",          "xu",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xv",          "xv",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xtts",        "xtts",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "xzts",        "xzts",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "d_conv",      "dconv",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_sfc",     "qrain",       "qrain",     "fv3_history2d",  "all",  .false.,  "none",  2
+
+"gfs_phys",    "acond",        "acond",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "cduvb_ave",    "cduvb_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "cpofp",        "cpofp",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "duvb_ave",     "duvb_ave",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csdlf_ave",    "csdlf",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csusf_ave",    "csusf",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csusf_avetoa", "csusftoa",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csdsf_ave",    "csdsf",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csulf_ave",    "csulf",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "csulf_avetoa", "csulftoa",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "cwork_ave",    "cwork_aveclm",  "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "evbs_ave",     "evbs_ave",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "evcw_ave",     "evcw_ave",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "fldcp",        "fldcp",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "hgt_hyblev1",  "hgt_hyblev1",   "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "spfh_hyblev1", "spfh_hyblev1",  "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "ugrd_hyblev1", "ugrd_hyblev1",  "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "vgrd_hyblev1", "vgrd_hyblev1",  "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "tmp_hyblev1",  "tmp_hyblev1",   "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "gfluxi",       "gflux",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "lhtfl",        "lhtfl",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "shtfl",        "shtfl",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "pevpr",        "pevpr",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "pevpr_ave",    "pevpr_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "sbsno_ave",    "sbsno_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "sfexc",        "sfexc",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "snohf",        "snohf",         "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "snowc_ave",    "snowc_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "spfhmax2m",    "spfhmax_max2m", "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "spfhmin2m",    "spfhmin_min2m", "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "tmpmax2m",     "tmax_max2m",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "tmpmin2m",     "tmin_min2m",    "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "ssrun_acc",    "ssrun_acc",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "sunsd_acc",    "sunsd_acc",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "watr_acc",     "watr_acc",      "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "wilt",         "wilt",          "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "vbdsf_ave",    "vbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "vddsf_ave",    "vddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "nbdsf_ave",    "nbdsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "nddsf_ave",    "nddsf_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "trans_ave",    "trans_ave",     "fv3_history2d",  "all",  .false.,  "none",  2
+
+"gfs_phys",    "AOD_550",      "aod550",        "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "DU_AOD_550",   "du_aod550",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "SU_AOD_550",   "su_aod550",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "BC_AOD_550",   "bc_aod550",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "OC_AOD_550",   "oc_aod550",     "fv3_history2d",  "all",  .false.,  "none",  2
+"gfs_phys",    "SS_AOD_550",   "ss_aod550",     "fv3_history2d",  "all",  .false.,  "none",  2
+#=============================================================================================
+#
+#====> This file can be used with diag_manager/v2.0a (or higher) <====
+#
+#
+#  FORMATS FOR FILE ENTRIES (not all input values are used)
+#  ------------------------
+#
+#"file_name", output_freq, "output_units", format, "time_units", "long_name",
+#
+#
+#output_freq:  > 0  output frequency in "output_units"
+#              = 0  output frequency every time step
+#              =-1  output frequency at end of run
+#
+#output_units = units used for output frequency
+#               (years, months, days, minutes, hours, seconds)
+#
+#time_units   = units used to label the time axis
+#               (days, minutes, hours, seconds)
+#
+#
+#  FORMAT FOR FIELD ENTRIES (not all input values are used)
+#  ------------------------
+#
+#"module_name", "field_name", "output_name", "file_name" "time_sampling", time_avg, "other_opts", packing
+#
+#time_avg = .true. or .false.
+#
+#packing  = 1  double precision
+#         = 2  float
+#         = 4  packed 16-bit integers
+#         = 8  packed 1-byte (not tested?)
diff --git a/parm/templates/template.model_configure b/parm/templates/template.model_configure
new file mode 100644
index 00000000..568b2f86
--- /dev/null
+++ b/parm/templates/template.model_configure
@@ -0,0 +1,9 @@
+start_year:              XXYYYY
+start_month:             XXMM
+start_day:               XXDD
+start_hour:              XXHH
+start_minute:            0
+start_second:            0
+nhours_fcst:             XXFCSTHR
+dt_atmos:                900
+fhrot:                   0
diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index 947e070c..df31292c 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -8,6 +8,7 @@ YYYY=${PDY:0:4}
 MM=${PDY:4:2}
 DD=${PDY:6:2}
 HH=${cyc}
+YYYYMMDD=${PDY}
 nYYYY=${NTIME:0:4}
 nMM=${NTIME:4:2}
 nDD=${NTIME:6:2}
@@ -69,15 +70,26 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
     fi
   fi
 
-  atparse < ${PATHRT}/parm/${MODEL_CONFIGURE:-model_configure.IN} > model_configure
+  # Set model_configure
+  cp ${PARMlandda}/templates/template.model_configure model_configure
+  sed -i -e "s/XXYYYY/${YYYY}/g" model_configure
+  sed -i -e "s/XXMM/${MM}/g" model_configure
+  sed -i -e "s/XXDD/${DD}/g" model_configure
+  sed -i -e "s/XXHH/${HH}/g" model_configure
+  sed -i -e "s/XXFCSTHR/${FCSTHR}/g" model_configure
 
   compute_petbounds_and_tasks
 
   atparse < ${PATHRT}/parm/${UFS_CONFIGURE:-ufs.configure} > ufs.configure
 
-  # diag table
+  # set diag table
   if [[ "Q${DIAG_TABLE:-}" != Q ]] ; then
-    atparse < ${PATHRT}/parm/diag_table/${DIAG_TABLE} > diag_table
+    cp ${PARMlandda}/templates/template.diag_table diag_table
+    sed -i -e "s/XXYYYYMMDD/${YYYYMMDD}/g" diag_table
+    sed -i -e "s/XXYYYY/${YYYY}/g" diag_table
+    sed -i -e "s/XXMM/${MM}/g" diag_table
+    sed -i -e "s/XXDD/${DD}/g" diag_table
+    sed -i -e "s/XXHH/${HH}/g" diag_table
   fi
 
   # Field table

From 3b4fac0da34c708cc5f68c13ba840cb91f31e558 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Sun, 19 May 2024 14:41:01 -0500
Subject: [PATCH 16/18] change cp to ln

---
 scripts/exlandda_forecast.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/exlandda_forecast.sh b/scripts/exlandda_forecast.sh
index df31292c..38be885b 100755
--- a/scripts/exlandda_forecast.sh
+++ b/scripts/exlandda_forecast.sh
@@ -118,22 +118,22 @@ if [[ ${ATMOS_FORC} == "gswp3" ]]; then
   # CMEPS restart and pointer files
   rfile1="ufs.cpld.cpl.r.${YYYY}-${MM}-${DD}-00000.nc"
   if [[ -e "${COMINm1}/${rfile1}" ]]; then
-    cp "${COMINm1}/${rfile1}" RESTART/.
+    ln -nsf "${COMINm1}/${rfile1}" RESTART/.
   elif [[ -e "${WARMSTART_DIR}/${rfile1}" ]]; then
-    cp "${WARMSTART_DIR}/${rfile1}" RESTART/.
+    ln -nsf "${WARMSTART_DIR}/${rfile1}" RESTART/.
   else
-    cp ${FIXlandda}/restarts/gswp3/${rfile1} RESTART/.
+    ln -nsf ${FIXlandda}/restarts/gswp3/${rfile1} RESTART/.
   fi
   ls -1 "RESTART/${rfile1}">rpointer.cpl
 
   # CDEPS restart and pointer files
   rfile2="ufs.cpld.datm.r.${YYYY}-${MM}-${DD}-00000.nc"
   if [[ -e "${COMINm1}/${rfile2}" ]]; then
-    cp "${COMINm1}/${rfile2}" RESTART/.
+    ln -nsf "${COMINm1}/${rfile2}" RESTART/.
   elif [[ -e "${WARMSTART_DIR}/${rfile2}" ]]; then
-    cp "${WARMSTART_DIR}/${rfile2}" RESTART/.
+    ln -nsf "${WARMSTART_DIR}/${rfile2}" RESTART/.
   else
-    cp ${FIXlandda}/restarts/gswp3/${rfile2} RESTART/.
+    ln -nsf ${FIXlandda}/restarts/gswp3/${rfile2} RESTART/.
   fi
   ls -1 "RESTART/${rfile2}">rpointer.atm
 

From 8914d21185b06e9e845907d76ffc887113abc315 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Mon, 20 May 2024 07:48:15 -0500
Subject: [PATCH 17/18] change name of sample yaml files

---
 parm/{land_analysis_gswp3_hera.yaml => land_analysis_hera.yaml}   | 0
 parm/{land_analysis_gswp3_orion.yaml => land_analysis_orion.yaml} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename parm/{land_analysis_gswp3_hera.yaml => land_analysis_hera.yaml} (100%)
 rename parm/{land_analysis_gswp3_orion.yaml => land_analysis_orion.yaml} (100%)

diff --git a/parm/land_analysis_gswp3_hera.yaml b/parm/land_analysis_hera.yaml
similarity index 100%
rename from parm/land_analysis_gswp3_hera.yaml
rename to parm/land_analysis_hera.yaml
diff --git a/parm/land_analysis_gswp3_orion.yaml b/parm/land_analysis_orion.yaml
similarity index 100%
rename from parm/land_analysis_gswp3_orion.yaml
rename to parm/land_analysis_orion.yaml

From 898af4becbed1942c2fb942ec7f71d59ea9ffe89 Mon Sep 17 00:00:00 2001
From: Chan-Hoo Jeon <chan-hoo.jeon@noaa.gov>
Date: Mon, 20 May 2024 10:09:52 -0500
Subject: [PATCH 18/18] update users guide

---
 .../BuildingRunningTesting/BuildRunLandDA.rst | 64 ++++++++-----------
 .../BuildingRunningTesting/TestingLandDA.rst  |  7 +-
 2 files changed, 32 insertions(+), 39 deletions(-)

diff --git a/doc/source/BuildingRunningTesting/BuildRunLandDA.rst b/doc/source/BuildingRunningTesting/BuildRunLandDA.rst
index 70dae2cf..9e85c4f6 100644
--- a/doc/source/BuildingRunningTesting/BuildRunLandDA.rst
+++ b/doc/source/BuildingRunningTesting/BuildRunLandDA.rst
@@ -111,12 +111,9 @@ Copy the experiment settings into ``land_analysis.yaml``:
 .. code-block:: console
 
    cd $LANDDAROOT/land-DA_workflow/parm
-   cp land_analysis_<forcing>_<platform>.yaml land_analysis.yaml
+   cp land_analysis_<platform>.yaml land_analysis.yaml
 
-where: 
-
-   * ``<forcing>`` is either ``gswp3`` or ``era5`` forcing data.
-   * ``<platform>`` is ``hera`` or ``orion``.
+where ``<platform>`` is ``hera`` or ``orion``.
    
 Users will need to configure certain elements of their experiment in ``land_analysis.yaml``: 
 
@@ -124,7 +121,8 @@ Users will need to configure certain elements of their experiment in ``land_anal
    * ``ACCOUNT:`` A valid account name. Hera, Orion, and most NOAA RDHPCS systems require a valid account name; other systems may not
    * ``EXP_BASEDIR:`` The full path to the directory where land-DA_workflow was cloned (i.e., ``$LANDDAROOT``)
    * ``JEDI_INSTALL:`` The full path to the system's ``jedi-bundle`` installation
-   * ``LANDDA_INPUTS:`` The full path to the experiment data. See :ref:`Data <GetData>` below for information on prestaged data on Level 1 platforms. 
+   * ``FORCING:`` Forcing options; ``gswp3`` or ``era5``
+   * ``cycledef/spec:`` Cycle specification
 
 .. note::
 
@@ -151,7 +149,7 @@ Data
    | Orion     | /work/noaa/epic/UFS_Land-DA/inputs               |
    +-----------+--------------------------------------------------+
 
-Users who have difficulty accessing the data on Hera or Orion may download it according to the instructions in :numref:`Section %s <GetDataC>` and set ``LANDDA_INPUTS`` to point to the location of the downloaded data. Similarly, users with access to data for additional experiments may set the path to that data in ``LANDDA_INPUTS``. 
+Users who have difficulty accessing the data on Hera or Orion may download it according to the instructions in :numref:`Section %s <GetDataC>`. Its sub-directories are soft-linked to the ``fix`` directory of the land-DA workflow by the build script ``sorc/app_build.sh``.
 
 .. _generate-wflow:
 
@@ -186,16 +184,16 @@ Each Land DA experiment includes multiple tasks that must be run in order to sat
 
    * - J-job Task
      - Description
-   * - JLANDDA_PREP_EXP
-     - Sets up the experiment
    * - JLANDDA_PREP_OBS
-     - Sets up the observation files
-   * - JLANDDA_PREP_BMAT
-     - Sets up the :term:`JEDI` run
+     - Sets up the observation data files
+   * - JLANDDA_PRE_ANAL
+     - Transfers the snow data from the restart files to the surface data files
    * - JLANDDA_ANALYSIS
-     - Runs JEDI
+     - Runs :term:`JEDI` and adds the increment to the surface data files
+   * - JLANDDA_POST_ANAL
+     - Transfers the JEDI result from the surface data files to the restart files
    * - JLANDDA_FORECAST
-     - Runs forecast
+     - Runs the forecast model
 
 Users may run these tasks :ref:`using the Rocoto workflow manager <run-w-rocoto>` or :ref:`using a batch script <run-batch-script>`. 
 
@@ -246,7 +244,7 @@ The experiment has successfully completed when all tasks say SUCCEEDED under STA
 Run Without Rocoto
 --------------------
 
-Users may choose not to run the workflow with uwtools and Rocoto. To run the :term:`J-jobs` scripts in the ``jobs`` directory, navigate to the ``parm`` directory and edit ``run_without_rocoto.sh`` (e.g., using vim or preferred command line editor). Users will likely need to change the ``MACHINE``, ``ACCOUNT``, and ``EXP_BASEDIR`` variables to match their system. Then, run ``run_without_rocoto.sh``:
+Users may choose not to run the workflow with uwtools and Rocoto for a non-cycled run. To run the :term:`J-jobs` scripts in the ``jobs`` directory, navigate to the ``parm`` directory and edit ``run_without_rocoto.sh`` (e.g., using vim or preferred command line editor). Users will likely need to change the ``MACHINE``, ``ACCOUNT``, and ``EXP_BASEDIR`` variables to match their system. Then, run ``run_without_rocoto.sh``:
 
 .. code-block:: console
 
@@ -265,32 +263,24 @@ As the experiment progresses, it will generate a number of directories to hold i
     ├── ptmp (<PTMP>)
     │     └── test (<envir>)
     │           └── com
-    │                 ├── landda (<NET>)
-    │                 │     └── vX.Y.Z (<model_ver>)
-    │                 │           └── landda.YYYYMMDD (<RUN>.<PDY>)
-    │                 │                 └── HH (<cyc>)
-    │                 │                       ├── DA: Directory containing the output files of JEDI run
-    │                 │                       │     ├── hofx
-    │                 │                       │     └── jedi_incr
-    │                 │                       └── mem000: Directory containing the output files
-    │                 └── output
-    │                       └── logs
-    │                             └── run_<forcing> (<LOGDIR>): Directory containing the log file of the Rocoto workflow
-    └── workdir(<WORKDIR>)
-          └── run_<forcing>
-                └── mem000: Working directory
+    │                ├── landda (<NET>)
+    │                │     └── vX.Y.Z (<model_ver>)
+    │                │           └── landda.YYYYMMDD (<RUN>.<PDY>): Directory containing the output files
+    │                └── output
+    │                      └── logs
+    │                            └── run_<forcing> (<LOGDIR>): Directory containing the log file of the Rocoto workflow
+    └── tmp (<DATAROOT>)
+         ├── <jobid> (<DATA>): Working directory
+         └── DATA_SHARE
+               ├── YYYYMMDD (<PDY>): Directory containing the intermediate or temporary files
+               └── DATA_RESTART: Directory containing the soft-links to the restart files for the next cycles
 
 ``<forcing>`` refers to the type of forcing data used (``gswp3`` or ``era5``). Each variable in parentheses and angle brackets (e.g., ``(<VAR>)``) is the name for the directory defined in the file ``land_analysis.yaml``. In the future, this directory structure will be further modified to meet the :nco:`NCO Implementation Standards<>`.
 
-Check for the background and analysis files in the experiment directory:
+Check for the output files for each cycle in the experiment directory:
 
 .. code-block:: console
 
-   ls -l $LANDDAROOT/ptmp/test/com/landda/v1.2.1/landda.<PDY>/<cyc>/run_<forcing>/mem000/restarts/<vector_or_tile>
-
-where: 
-
-   * ``<forcing>`` is either ``era5`` or ``gswp3``, and
-   * ``<vector_or_tile>`` is either ``vector`` or ``tile`` depending on whether ERA5 or GSWP3 forcing data was used, respectively. 
+   ls -l $LANDDAROOT/ptmp/test/com/landda/v1.2.1/landda.YYYYMMDD
 
-The experiment should generate several restart files. 
+where ``YYYYMMDD`` is the cycle date. The experiment should generate several restart files. 
diff --git a/doc/source/BuildingRunningTesting/TestingLandDA.rst b/doc/source/BuildingRunningTesting/TestingLandDA.rst
index 986a2245..ba7d3cd6 100644
--- a/doc/source/BuildingRunningTesting/TestingLandDA.rst
+++ b/doc/source/BuildingRunningTesting/TestingLandDA.rst
@@ -18,12 +18,15 @@ From the working directory (``$LANDDAROOT``), navigate to ``build``. Then run:
 .. code-block:: console
    
    salloc --ntasks 8 --exclusive --qos=debug --partition=debug --time=00:30:00 --account=<account_name>
-   module use modulefiles && module load landda_<platform>.intel 
+   cd land-DA_workflow/sorc/build
+   source ../../versions/build.ver_<platform>
+   module use ../../modulefiles
+   module load build_<platform>_intel 
    ctest
 
 where ``<account_name>`` corresponds to the user's actual account name and ``<platform>`` is ``hera`` or ``orion``.
 
-This will allocate a compute node, load the appropriate modulefiles, and run the CTests. 
+This will submit an interactive job, load the appropriate modulefiles, and run the CTests. 
 
 Tests
 *******