From 4ad96952f0bccaedad3e9c558341fe5e28d813aa Mon Sep 17 00:00:00 2001
From: Rahul Mahajan <aerorahul@users.noreply.github.com>
Date: Fri, 13 Sep 2024 11:13:20 -0400
Subject: [PATCH 01/21] Disable native grid writes for non-JEDI experiments;
 update C384 compression options (#2914)

- enables writing native grid model output when doing JEDI-atm DA
- updates compression settings for C384 model output

Fixes #2891
---
 parm/config/gefs/config.ufs        | 39 ++++++++++++------------------
 parm/config/gfs/config.ufs         | 31 +++++++++---------------
 ush/forecast_postdet.sh            |  8 +++---
 ush/parsing_model_configure_FV3.sh |  6 ++++-
 4 files changed, 37 insertions(+), 47 deletions(-)

diff --git a/parm/config/gefs/config.ufs b/parm/config/gefs/config.ufs
index bfc11e3c5a..bc3950490e 100644
--- a/parm/config/gefs/config.ufs
+++ b/parm/config/gefs/config.ufs
@@ -80,8 +80,8 @@ case "${fv3_res}" in
         export nthreads_fv3_gfs=1
         export nthreads_ufs=1
         export nthreads_ufs_gfs=1
-	      export xr_cnvcld=.false. # Do not pass conv. clouds to Xu-Randall cloud fraction
-	      export cdmbgwd="0.071,2.1,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+        export xr_cnvcld=.false. # Do not pass conv. clouds to Xu-Randall cloud fraction
+        export cdmbgwd="0.071,2.1,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="40.0,1.77,1.0,1.0"   # settings for GSL drag suite
         export k_split=1
         export n_split=4
@@ -104,8 +104,8 @@ case "${fv3_res}" in
         export nthreads_fv3_gfs=1
         export nthreads_ufs=1
         export nthreads_ufs_gfs=1
-	      export xr_cnvcld=".false."  # Do not pass conv. clouds to Xu-Randall cloud fraction
-	      export cdmbgwd="0.14,1.8,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
+        export xr_cnvcld=".false."  # Do not pass conv. clouds to Xu-Randall cloud fraction
+        export cdmbgwd="0.14,1.8,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="20.0,2.5,1.0,1.0"   # settings for GSL drag suite
         export knob_ugwp_tauamp=3.0e-3      # setting for UGWPv1 non-stationary GWD
         export k_split=1
@@ -254,40 +254,33 @@ export ntasks_fv3_gfs
 export ntasks_quilt
 export ntasks_quilt_gfs
 
-# Determine whether to use compression in the write grid component based on resolution
+# Determine whether to use compression in the write grid component
+# and whether to use parallel NetCDF based on resolution
 case ${fv3_res} in
-  "C48" | "C96" | "C192" | "C384")
+  "C48" | "C96" | "C192")
     zstandard_level=0
     ideflate=0
     quantize_nsd=0
+    OUTPUT_FILETYPE_ATM="netcdf"
+    OUTPUT_FILETYPE_SFC="netcdf"
     ;;
-  "C768" | "C1152" | "C3072")
+  "C384" | "C768" | "C1152" | "C3072")
     zstandard_level=0
     ideflate=1
     quantize_nsd=5
-    ;;
-  *)
-    echo "FATAL ERROR: Unrecognized FV3 resolution ${fv3_res}"
-    exit 15
-    ;;
-esac
-export zstandard_level ideflate quantize_nsd
-
-# Determine whether to use parallel NetCDF based on resolution
-case ${fv3_res} in
-  "C48" | "C96" | "C192" | "C384")
-    OUTPUT_FILETYPE_ATM="netcdf"
-    OUTPUT_FILETYPE_SFC="netcdf"
-    ;;
-  "C768" | "C1152" | "C3072")
     OUTPUT_FILETYPE_ATM="netcdf_parallel"
-    OUTPUT_FILETYPE_SFC="netcdf_parallel"
+    if [[ "${fv3_res}" == "C384" ]]; then
+      OUTPUT_FILETYPE_SFC="netcdf"  # For C384, the write grid component is better off with serial netcdf
+    else
+      OUTPUT_FILETYPE_SFC="netcdf_parallel"
+    fi
     ;;
   *)
     echo "FATAL ERROR: Unrecognized FV3 resolution ${fv3_res}"
     exit 15
     ;;
 esac
+export zstandard_level ideflate quantize_nsd
 export OUTPUT_FILETYPE_ATM OUTPUT_FILETYPE_SFC
 
 # cpl defaults
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index b27845aec7..babbe1f2dd 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -356,40 +356,33 @@ export ntasks_fv3_gfs
 export ntasks_quilt_gdas
 export ntasks_quilt_gfs
 
-# Determine whether to use compression in the write grid component based on resolution
+# Determine whether to use compression in the write grid component
+# and whether to use parallel NetCDF based on resolution
 case ${fv3_res} in
-  "C48" | "C96" | "C192" | "C384")
+  "C48" | "C96" | "C192")
     zstandard_level=0
     ideflate=0
     quantize_nsd=0
+    OUTPUT_FILETYPE_ATM="netcdf"
+    OUTPUT_FILETYPE_SFC="netcdf"
     ;;
-  "C768" | "C1152" | "C3072")
+  "C384" | "C768" | "C1152" | "C3072")
     zstandard_level=0
     ideflate=1
     quantize_nsd=5
-    ;;
-  *)
-    echo "FATAL ERROR: Unrecognized FV3 resolution ${fv3_res}"
-    exit 15
-    ;;
-esac
-export zstandard_level ideflate quantize_nsd
-
-# Determine whether to use parallel NetCDF based on resolution
-case ${fv3_res} in
-  "C48" | "C96" | "C192" | "C384")
-    OUTPUT_FILETYPE_ATM="netcdf"
-    OUTPUT_FILETYPE_SFC="netcdf"
-    ;;
-  "C768" | "C1152" | "C3072")
     OUTPUT_FILETYPE_ATM="netcdf_parallel"
-    OUTPUT_FILETYPE_SFC="netcdf_parallel"
+    if [[ "${fv3_res}" == "C384" ]]; then
+      OUTPUT_FILETYPE_SFC="netcdf"  # For C384, the write grid component is better off with serial netcdf
+    else
+      OUTPUT_FILETYPE_SFC="netcdf_parallel"
+    fi
     ;;
   *)
     echo "FATAL ERROR: Unrecognized FV3 resolution ${fv3_res}"
     exit 15
     ;;
 esac
+export zstandard_level ideflate quantize_nsd
 export OUTPUT_FILETYPE_ATM OUTPUT_FILETYPE_SFC
 
 # cpl defaults
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index d13cb0df0c..58755d41d9 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -233,14 +233,14 @@ EOF
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${f_hhmmss}.nc"
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${f_hhmmss}.nc"
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${f_hhmmss}"
-        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${f_hhmmss}.nc"
-        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${f_hhmmss}.nc"
       else
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${FH3}.nc"
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${FH3}.nc"
         ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${FH3}"
-        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc"
-        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc"
+        if [[ "${DO_JEDIATMVAR:-}" == "YES" ]]; then
+          ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc"
+          ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc"
+        fi
       fi
       if [[ "${WRITE_DOPOST}" == ".true." ]]; then
         ${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
index 8f102fe298..7cf7bf8662 100755
--- a/ush/parsing_model_configure_FV3.sh
+++ b/ush/parsing_model_configure_FV3.sh
@@ -31,7 +31,11 @@ local WRITE_GROUP=${WRITE_GROUP:-1}
 local WRTTASK_PER_GROUP=${WRTTASK_PER_GROUP:-24}
 local ITASKS=1
 local OUTPUT_HISTORY=${OUTPUT_HISTORY:-".true."}
-local HISTORY_FILE_ON_NATIVE_GRID=".true."
+if [[ "${DO_JEDIATMVAR:-}" == "YES" ]]; then
+  local HISTORY_FILE_ON_NATIVE_GRID=".true."
+else
+  local HISTORY_FILE_ON_NATIVE_GRID=".false."
+fi
 local WRITE_DOPOST=${WRITE_DOPOST:-".false."}
 local WRITE_NSFLIP=${WRITE_NSFLIP:-".false."}
 local NUM_FILES=${NUM_FILES:-2}

From d8669822852a0922648606cf57509caa08fe40d2 Mon Sep 17 00:00:00 2001
From: Wei Huang <wei.huang@noaa.gov>
Date: Fri, 13 Sep 2024 13:39:27 -0600
Subject: [PATCH 02/21] Support gefs C48 on Azure (#2881)

Support global-worflow GEFS C48 on Azure

Make env. var. and yaml file changes, so global-workflow GEFS C48 case
can run properly on Google Cloud.

Resolves #2882
---
 env/AZUREPW.env                           | 48 +++++++++++++++++++++++
 parm/config/gefs/config.base              |  2 +-
 parm/config/gefs/config.resources         |  4 ++
 parm/config/gefs/config.resources.AZUREPW | 11 ++++++
 workflow/hosts/azurepw.yaml               |  2 +-
 5 files changed, 65 insertions(+), 2 deletions(-)
 create mode 100644 parm/config/gefs/config.resources.AZUREPW

diff --git a/env/AZUREPW.env b/env/AZUREPW.env
index 9e246a9cb4..c2faeb2bf6 100755
--- a/env/AZUREPW.env
+++ b/env/AZUREPW.env
@@ -43,6 +43,13 @@ if [[ "${step}" = "fcst" ]] || [[ "${step}" = "efcs" ]]; then
     export APRUN_UFS="${launcher} -n ${ufs_ntasks}"
     unset nnodes ufs_ntasks
 
+elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
+
+    export CFP_MP="YES"
+    if [[ "${step}" = "waveprep" ]]; then export MP_PULSE=0 ; fi
+    export wavempexec=${launcher}
+    export wave_mpmd=${mpmd_opt}
+
 elif [[ "${step}" = "post" ]]; then
 
     export NTHREADS_NP=${NTHREADS1}
@@ -52,4 +59,45 @@ elif [[ "${step}" = "post" ]]; then
     [[ ${NTHREADS_DWN} -gt ${max_threads_per_task} ]] && export NTHREADS_DWN=${max_threads_per_task}
     export APRUN_DWN="${launcher} -n ${ntasks_dwn}"
 
+elif [[ "${step}" = "atmos_products" ]]; then
+
+    export USE_CFP="YES"  # Use MPMD for downstream product generation on Hera
+
+elif [[ "${step}" = "oceanice_products" ]]; then
+
+    export NTHREADS_OCNICEPOST=${NTHREADS1}
+    export APRUN_OCNICEPOST="${launcher} -n 1 --cpus-per-task=${NTHREADS_OCNICEPOST}"
+
+elif [[ "${step}" = "ecen" ]]; then
+
+    export NTHREADS_ECEN=${NTHREADSmax}
+    export APRUN_ECEN="${APRUN}"
+
+    export NTHREADS_CHGRES=${threads_per_task_chgres:-12}
+    [[ ${NTHREADS_CHGRES} -gt ${max_tasks_per_node} ]] && export NTHREADS_CHGRES=${max_tasks_per_node}
+    export APRUN_CHGRES="time"
+
+    export NTHREADS_CALCINC=${threads_per_task_calcinc:-1}
+    [[ ${NTHREADS_CALCINC} -gt ${max_threads_per_task} ]] && export NTHREADS_CALCINC=${max_threads_per_task}
+    export APRUN_CALCINC="${APRUN}"
+
+elif [[ "${step}" = "esfc" ]]; then
+
+    export NTHREADS_ESFC=${NTHREADSmax}
+    export APRUN_ESFC="${APRUN}"
+
+    export NTHREADS_CYCLE=${threads_per_task_cycle:-14}
+    [[ ${NTHREADS_CYCLE} -gt ${max_tasks_per_node} ]] && export NTHREADS_CYCLE=${max_tasks_per_node}
+    export APRUN_CYCLE="${APRUN}"
+
+elif [[ "${step}" = "epos" ]]; then
+
+    export NTHREADS_EPOS=${NTHREADSmax}
+    export APRUN_EPOS="${APRUN}"
+
+elif [[ "${step}" = "fit2obs" ]]; then
+
+    export NTHREADS_FIT2OBS=${NTHREADS1}
+    export MPIRUN="${APRUN}"
+
 fi
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index 47474fb108..883957ed0c 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -342,7 +342,7 @@ export DELETE_COM_IN_ARCHIVE_JOB="YES"   # NO=retain ROTDIR.  YES default in arc
 export NUM_SND_COLLECTIVES=${NUM_SND_COLLECTIVES:-9}
 
 # The tracker, genesis, and METplus jobs are not supported on CSPs yet
-# TODO: we should place these in workflow/hosts/[csp]pw.yaml as part of AWS/AZURE/GOOGLE setup, not for general.
+# TODO: we should place these in workflow/hosts/[aws|azure|google]pw.yaml as part of CSP's setup, not for general.
 if [[ "${machine}" =~ "PW" ]]; then
    export DO_WAVE="NO"
 fi
diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
index 79f3426f56..a96bb02bd9 100644
--- a/parm/config/gefs/config.resources
+++ b/parm/config/gefs/config.resources
@@ -43,6 +43,10 @@ case ${machine} in
     export PARTITION_BATCH="compute"
     max_tasks_per_node=36
     ;;
+  "AZUREPW")
+    export PARTITION_BATCH="compute"
+    max_tasks_per_node=24
+    ;;
   "GOOGLEPW")
     export PARTITION_BATCH="compute"
     max_tasks_per_node=32
diff --git a/parm/config/gefs/config.resources.AZUREPW b/parm/config/gefs/config.resources.AZUREPW
new file mode 100644
index 0000000000..96303139d8
--- /dev/null
+++ b/parm/config/gefs/config.resources.AZUREPW
@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+# AZURE-specific job resources
+
+export is_exclusive="True"
+unset memory
+
+# shellcheck disable=SC2312
+for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
+  unset "${mem_var}"
+done
diff --git a/workflow/hosts/azurepw.yaml b/workflow/hosts/azurepw.yaml
index 2155c67dea..d59736e653 100644
--- a/workflow/hosts/azurepw.yaml
+++ b/workflow/hosts/azurepw.yaml
@@ -18,7 +18,7 @@ CHGRP_RSTPROD: 'YES'
 CHGRP_CMD: 'chgrp rstprod' # TODO: This is not yet supported.
 HPSSARCH: 'NO'
 HPSS_PROJECT: emc-global #TODO: See `ATARDIR` below.
-BASE_CPLIC: '/bucket/global-workflow-shared-data/ICSDIR/prototype_ICs'
+BASE_IC: '/bucket/global-workflow-shared-data/ICSDIR'
 LOCALARCH: 'NO'
 ATARDIR: '' # TODO: This will not yet work from AZURE.
 MAKE_NSSTBUFR: 'NO'

From 19455ba32cffd47f409ca711bec80adb3fe7c3d4 Mon Sep 17 00:00:00 2001
From: Jeffrey Whitaker <jeffrey.s.whitaker@noaa.gov>
Date: Fri, 13 Sep 2024 18:22:20 -0600
Subject: [PATCH 03/21] add 1 deg ocean/ice info to
 parm/config/gfs/config.resources (#2922)

Adds 1 deg ocean, ice information to config.resources so 1 deg ocean
jobs can run
---
 parm/config/gfs/config.resources | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index b50e1c5fbb..a89c72e951 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -527,6 +527,7 @@ case ${step} in
     case ${OCNRES} in
       "025") ntasks=480;;
       "050")  ntasks=16;;
+      "100")  ntasks=16;;
       "500")  ntasks=16;;
       *)
         echo "FATAL ERROR: Resources not defined for job ${step} at resolution ${OCNRES}"
@@ -550,6 +551,10 @@ case ${step} in
         ntasks=16
         memory="96GB"
         ;;
+      "100")
+        ntasks=16
+        memory="96GB"
+        ;;
       "500")
         ntasks=16
         memory="24GB"
@@ -576,6 +581,10 @@ case ${step} in
         ntasks=16
         memory="96GB"
         ;;
+      "100")
+        ntasks=16
+        memory="96GB"
+        ;;
       "500")
         ntasks=16
         memory="24GB"
@@ -602,6 +611,10 @@ case ${step} in
         ntasks=16
         memory="96GB"
         ;;
+      "100")
+        ntasks=16
+        memory="96GB"
+        ;;
       "500")
         ntasks=16
         memory="24GB"
@@ -630,6 +643,9 @@ case ${step} in
       "050")
         memory="32GB"
         ntasks=16;;
+      "100")
+        memory="32GB"
+        ntasks=16;;
       "500")
         memory="32GB"
         ntasks=8;;

From a13bbef6a9341f09349d145642a068f438edd736 Mon Sep 17 00:00:00 2001
From: DavidBurrows-NCO <82525974+DavidBurrows-NCO@users.noreply.github.com>
Date: Sat, 14 Sep 2024 10:35:39 -0400
Subject: [PATCH 04/21] Build GDASApp and unset memory in Gaea-C5 xml files
 (#2912)

In preparation for GDASApp CI tests, add GDASApp build capability to
global-workflow and remove memory specifications for Gaea-C5 xml setup
(in Ref to #2727)
  Resolves #2535
  Resolves #2910
  Resolves #2911
---
 parm/config/gfs/config.resources.GAEA | 1 +
 sorc/build_all.sh                     | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/parm/config/gfs/config.resources.GAEA b/parm/config/gfs/config.resources.GAEA
index 51007b5b4f..a4d4ddfece 100644
--- a/parm/config/gfs/config.resources.GAEA
+++ b/parm/config/gfs/config.resources.GAEA
@@ -21,6 +21,7 @@ case ${step} in
 
 esac
 
+unset memory
 # shellcheck disable=SC2312
 for mem_var in $(env | grep '^memory_' | cut -d= -f1); do
   unset "${mem_var}"
diff --git a/sorc/build_all.sh b/sorc/build_all.sh
index 79ae3c937f..b2f4e6ce0e 100755
--- a/sorc/build_all.sh
+++ b/sorc/build_all.sh
@@ -145,7 +145,7 @@ build_opts["ww3prepost"]="${_wave_opt} ${_verbose_opt} ${_build_ufs_opt} ${_buil
 
 # Optional DA builds
 if [[ "${_build_ufsda}" == "YES" ]]; then
-   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" && "${MACHINE_ID}" != "hercules" && "${MACHINE_ID}" != "wcoss2" && "${MACHINE_ID}" != "noaacloud" ]]; then
+   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" && "${MACHINE_ID}" != "hercules" && "${MACHINE_ID}" != "wcoss2" && "${MACHINE_ID}" != "noaacloud" && "${MACHINE_ID}" != "gaea" ]]; then
       echo "NOTE: The GDAS App is not supported on ${MACHINE_ID}.  Disabling build."
    else
       build_jobs["gdas"]=8

From b7f71e015671ae993df59f8da4f860627e834a02 Mon Sep 17 00:00:00 2001
From: AntonMFernando-NOAA
 <167725623+AntonMFernando-NOAA@users.noreply.github.com>
Date: Sat, 14 Sep 2024 11:46:50 -0400
Subject: [PATCH 05/21] Cleanup job for GEFS (#2919)

As forecast ensemble jobs are added to the global workflow, this PR
ensures the output is being cleaned up properly once it is no longer
needed.
  Resolves #833
---
 parm/config/gefs/config.cleanup   |  1 +
 parm/config/gefs/config.resources |  8 ++++++++
 workflow/applications/gefs.py     |  4 ++--
 workflow/rocoto/gefs_tasks.py     | 27 +++++++++++++++++++++++++++
 4 files changed, 38 insertions(+), 2 deletions(-)
 create mode 120000 parm/config/gefs/config.cleanup

diff --git a/parm/config/gefs/config.cleanup b/parm/config/gefs/config.cleanup
new file mode 120000
index 0000000000..839ed6c194
--- /dev/null
+++ b/parm/config/gefs/config.cleanup
@@ -0,0 +1 @@
+../gfs/config.cleanup
\ No newline at end of file
diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
index a96bb02bd9..690fdf919a 100644
--- a/parm/config/gefs/config.resources
+++ b/parm/config/gefs/config.resources
@@ -295,6 +295,14 @@ case ${step} in
     export threads_per_task=1
     export memory="4096M"
     ;;
+
+  "cleanup")
+    export walltime="00:15:00"
+    export ntasks=1
+    export tasks_per_node=1
+    export threads_per_task=1
+    export memory="4096M"
+    ;;
   *)
     echo "FATAL ERROR: Invalid job ${step} passed to ${BASH_SOURCE[0]}"
     exit 1
diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py
index 1db3c51287..afb4072596 100644
--- a/workflow/applications/gefs.py
+++ b/workflow/applications/gefs.py
@@ -17,7 +17,7 @@ def _get_app_configs(self):
         """
         Returns the config_files that are involved in gefs
         """
-        configs = ['stage_ic', 'fcst', 'atmos_products', 'arch']
+        configs = ['stage_ic', 'fcst', 'atmos_products', 'arch', 'cleanup']
 
         if self.nens > 0:
             configs += ['efcs', 'atmos_ensstat']
@@ -82,6 +82,6 @@ def get_task_names(self):
         if self.do_extractvars:
             tasks += ['extractvars']
 
-        tasks += ['arch']
+        tasks += ['arch', 'cleanup']
 
         return {f"{self.run}": tasks}
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index 70a39cea5a..8a4f148f24 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -546,6 +546,9 @@ def arch(self):
                 deps.append(rocoto.add_dependency(dep_dict))
                 dep_dict = {'type': 'metatask', 'name': 'wave_post_bndpnt_bull'}
                 deps.append(rocoto.add_dependency(dep_dict))
+        if self.app_config.do_extractvars:
+            dep_dict = {'type': 'metatask', 'name': 'extractvars'}
+            deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps, dep_condition='and')
 
         resources = self.get_resource('arch')
@@ -564,3 +567,27 @@ def arch(self):
         task = rocoto.create_task(task_dict)
 
         return task
+
+    def cleanup(self):
+        deps = []
+        dep_dict = {'type': 'task', 'name': 'arch'}
+        deps.append(rocoto.add_dependency(dep_dict))
+
+        dependencies = rocoto.create_dependency(dep=deps)
+
+        resources = self.get_resource('cleanup')
+        task_name = 'cleanup'
+        task_dict = {'task_name': task_name,
+                     'resources': resources,
+                     'envars': self.envars,
+                     'cycledef': 'gefs',
+                     'dependency': dependencies,
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/cleanup.sh',
+                     'job_name': f'{self.pslot}_{task_name}_@H',
+                     'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
+                     'maxtries': '&MAXTRIES;'
+                     }
+
+        task = rocoto.create_task(task_dict)
+
+        return task

From 03ee9f8faf301860f5ef6ae87163df76736f53d7 Mon Sep 17 00:00:00 2001
From: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com>
Date: Sun, 15 Sep 2024 22:51:28 -0400
Subject: [PATCH 06/21] Update config.resources for bufr sounding job postsnd
 (#2917)

This PR updates the parm/config/gfs/config.resources and env/WCOSS2.env
files for the BUFR sounding job "postsnd." It includes adjustments to
resource settings such as tasks per node and memory allocations for
various GFS resolutions, including C768, C1152, and others.

Here are the proposed changes:

C768: 7 nodes, 21 tasks per node
C1152: 16 nodes, 9 tasks per node
---
 env/WCOSS2.env                   |  4 ++--
 parm/config/gfs/config.resources | 18 ++++++++++++++++--
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/env/WCOSS2.env b/env/WCOSS2.env
index d2dae3ba93..cea24fb26b 100755
--- a/env/WCOSS2.env
+++ b/env/WCOSS2.env
@@ -272,12 +272,12 @@ elif [[ "${step}" = "postsnd" ]]; then
     export OMP_NUM_THREADS=1
 
     export NTHREADS_POSTSND=${NTHREADS1}
-    export mpmd_opt="-ppn 21 ${mpmd_opt}"
-
     export NTHREADS_POSTSNDCFP=${threads_per_task_postsndcfp:-1}
     [[ ${NTHREADS_POSTSNDCFP} -gt ${max_threads_per_task} ]] && export NTHREADS_POSTSNDCFP=${max_threads_per_task}
     export APRUN_POSTSNDCFP="${launcher} -np ${ntasks_postsndcfp} ${mpmd_opt}"
 
+    export mpmd_opt="-ppn ${tasks_per_node} ${mpmd_opt}"
+
 elif [[ "${step}" = "awips" ]]; then
 
     export NTHREADS_AWIPS=${NTHREADS1}
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index a89c72e951..afc5939fcd 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -1208,9 +1208,23 @@ case ${step} in
   "postsnd")
     walltime="02:00:00"
     export ntasks=141
-    threads_per_task=6
-    export tasks_per_node=21 
     export ntasks_postsndcfp=9
+    case ${CASE} in
+      "C768")
+        tasks_per_node=21
+        threads_per_task=6
+        memory="23GB"
+        ;;
+      "C1152")
+        tasks_per_node=9
+        threads_per_task=14
+        memory="50GB"
+        ;;
+      *)
+        tasks_per_node=21
+        threads_per_task=6
+        ;;
+    esac
     export tasks_per_node_postsndcfp=1
     postsnd_req_cores=$(( tasks_per_node * threads_per_task ))
     if (( postsnd_req_cores > max_tasks_per_node )); then

From 2602eac32fe9b538310ae25f154d219d8400fa0b Mon Sep 17 00:00:00 2001
From: mingshichen-noaa <48537176+mingshichen-noaa@users.noreply.github.com>
Date: Mon, 16 Sep 2024 09:58:07 -0400
Subject: [PATCH 07/21] Update global atmos upp job to use COMIN/COMOUT (#2867)

NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global-workflow
Unified Post Processor (UPP) task.
Refs: https://github.com/NOAA-EMC/global-workflow/issues/2451
---
 jobs/JGLOBAL_ATMOS_UPP        |  7 +++++--
 parm/post/upp.yaml            | 28 ++++++++++++++--------------
 scripts/exglobal_atmos_upp.py |  2 +-
 ush/python/pygfs/task/upp.py  |  6 +++---
 4 files changed, 23 insertions(+), 20 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_UPP b/jobs/JGLOBAL_ATMOS_UPP
index 1aa62cdbb3..0e70e97025 100755
--- a/jobs/JGLOBAL_ATMOS_UPP
+++ b/jobs/JGLOBAL_ATMOS_UPP
@@ -12,8 +12,11 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "upp" -c "base upp"
 ##############################################
 
 # Construct COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS COM_ATMOS_HISTORY COM_ATMOS_MASTER
-if [[ ! -d ${COM_ATMOS_MASTER} ]]; then mkdir -m 775 -p "${COM_ATMOS_MASTER}"; fi
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+   COMIN_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL \
+   COMOUT_ATMOS_MASTER:COM_ATMOS_MASTER_TMPL
+if [[ ! -d ${COMOUT_ATMOS_MASTER} ]]; then mkdir -p "${COMOUT_ATMOS_MASTER}"; fi
 
 
 ###############################################################
diff --git a/parm/post/upp.yaml b/parm/post/upp.yaml
index 41dbb7defb..dd9aed3358 100644
--- a/parm/post/upp.yaml
+++ b/parm/post/upp.yaml
@@ -19,12 +19,12 @@ analysis:
   data_in:
     copy:
       - ["{{ PARMgfs }}/post/gfs/postxconfig-NT-gfs-anl.txt", "{{ DATA }}/postxconfig-NT.txt"]
-      - ["{{ COM_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmanl.nc", "{{ DATA }}/{{ atmos_filename }}"]
-      - ["{{ COM_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcanl.nc", "{{ DATA }}/{{ flux_filename }}"]
+      - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmanl.nc", "{{ DATA }}/{{ atmos_filename }}"]
+      - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcanl.nc", "{{ DATA }}/{{ flux_filename }}"]
   data_out:
     copy:
-      - ["{{ DATA }}/GFSPRS.GrbF00", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2anl"]
-      - ["{{ DATA }}/GFSPRS.GrbF00.idx", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2ianl"]
+      - ["{{ DATA }}/GFSPRS.GrbF00", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2anl"]
+      - ["{{ DATA }}/GFSPRS.GrbF00.idx", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2ianl"]
 
 forecast:
   config:
@@ -36,14 +36,14 @@ forecast:
       {% else %}
       - ["{{ PARMgfs }}/post/gfs/postxconfig-NT-gfs-two.txt", "{{ DATA }}/postxconfig-NT.txt"]
       {% endif %}
-      - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
-      - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
+      - ["{{ COMIN_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
+      - ["{{ COMIN_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
   data_out:
     copy:
-      - ["{{ DATA }}/GFSPRS.GrbF{{ '%02d' % forecast_hour }}", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2f{{ '%03d' % forecast_hour }}"]
-      - ["{{ DATA }}/GFSFLX.GrbF{{ '%02d' % forecast_hour }}", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfluxgrbf{{ '%03d' % forecast_hour }}.grib2"]
-      - ["{{ DATA }}/GFSPRS.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2if{{ '%03d' % forecast_hour }}"]
-      - ["{{ DATA }}/GFSFLX.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfluxgrbf{{ '%03d' % forecast_hour }}.grib2.idx"]
+      - ["{{ DATA }}/GFSPRS.GrbF{{ '%02d' % forecast_hour }}", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2f{{ '%03d' % forecast_hour }}"]
+      - ["{{ DATA }}/GFSFLX.GrbF{{ '%02d' % forecast_hour }}", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfluxgrbf{{ '%03d' % forecast_hour }}.grib2"]
+      - ["{{ DATA }}/GFSPRS.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.grb2if{{ '%03d' % forecast_hour }}"]
+      - ["{{ DATA }}/GFSFLX.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfluxgrbf{{ '%03d' % forecast_hour }}.grib2.idx"]
 
 goes:
   config:
@@ -82,9 +82,9 @@ goes:
       - ["{{ 'CRTM_FIX' | getenv }}/AerosolCoeff.bin", "{{ DATA }}/"]
       - ["{{ 'CRTM_FIX' | getenv }}/CloudCoeff.bin", "{{ DATA }}/"]
       - ["{{ PARMgfs }}/post/gfs/postxconfig-NT-gfs-goes.txt", "{{ DATA }}/postxconfig-NT.txt"]
-      - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
-      - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
+      - ["{{ COMIN_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
+      - ["{{ COMIN_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
   data_out:
     copy:
-      - ["{{ DATA }}/GFSGOES.GrbF{{ '%02d' % forecast_hour }}", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.special.grb2f{{ '%03d' % forecast_hour }}"]
-      - ["{{ DATA }}/GFSGOES.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COM_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.special.grb2if{{ '%03d' % forecast_hour }}"]
+      - ["{{ DATA }}/GFSGOES.GrbF{{ '%02d' % forecast_hour }}", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.special.grb2f{{ '%03d' % forecast_hour }}"]
+      - ["{{ DATA }}/GFSGOES.GrbF{{ '%02d' % forecast_hour }}.idx", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.special.grb2if{{ '%03d' % forecast_hour }}"]
diff --git a/scripts/exglobal_atmos_upp.py b/scripts/exglobal_atmos_upp.py
index 6cdbc1bc51..f87f06d2c9 100755
--- a/scripts/exglobal_atmos_upp.py
+++ b/scripts/exglobal_atmos_upp.py
@@ -19,7 +19,7 @@ def main():
 
     # Pull out all the configuration keys needed to run the rest of UPP steps
     keys = ['HOMEgfs', 'DATA', 'current_cycle', 'RUN', 'NET',
-            'COM_ATMOS_ANALYSIS', 'COM_ATMOS_HISTORY', 'COM_ATMOS_MASTER',
+            'COMIN_ATMOS_ANALYSIS', 'COMIN_ATMOS_HISTORY', 'COMOUT_ATMOS_MASTER',
             'upp_run',
             'APRUN_UPP',
             'forecast_hour', 'valid_datetime',
diff --git a/ush/python/pygfs/task/upp.py b/ush/python/pygfs/task/upp.py
index 1b37b845f6..70955a7276 100644
--- a/ush/python/pygfs/task/upp.py
+++ b/ush/python/pygfs/task/upp.py
@@ -249,7 +249,7 @@ def _call_executable(exec_cmd: Executable) -> None:
     @logit(logger)
     def finalize(upp_run: Dict, upp_yaml: Dict) -> None:
         """Perform closing actions of the task.
-        Copy data back from the DATA/ directory to COM/
+        Copy data back from the DATA/ directory to COMOUT/
 
         Parameters
         ----------
@@ -259,6 +259,6 @@ def finalize(upp_run: Dict, upp_yaml: Dict) -> None:
             Fully resolved upp.yaml dictionary
         """
 
-        # Copy "upp_run" specific generated data to COM/ directory
-        logger.info(f"Copy '{upp_run}' processed data to COM/ directory")
+        # Copy "upp_run" specific generated data to COMOUT/ directory
+        logger.info(f"Copy '{upp_run}' processed data to COMOUT/ directory")
         FileHandler(upp_yaml[upp_run].data_out).sync()

From 7588d2bd17ef345216ae096d088b5470b6f31bcd Mon Sep 17 00:00:00 2001
From: Kate Friedman <kate.friedman@noaa.gov>
Date: Tue, 17 Sep 2024 20:59:59 -0400
Subject: [PATCH 08/21] Update to obsproc/v1.2.0 and prepobs/v1.1.0 (#2903)

This PR updates the `develop` branch to use the newer operational
`obsproc/v1.2.0` and `prepobs/v1.1.0`. The obsproc/prepobs installs in
glopara space on supported platforms use tags cut from the `dev/gfsv17`
branches in the respective repos. The installation of `prepobs/v1.1.0`
on WCOSS2 is called "gfsv17_v1.1.0" to help avoid GFSv16 users using it
instead of the operational module.

Also, the `HOMEobsproc` path is updated to set an empty default for
`obsproc_run_ver`. This both removes the need to set a default (and
constantly update it, which is duplication) and avoid the unset variable
error when the fcst jobs use their own load module script that does not
know `obsproc_run_ver`:
```
export HOMEobsproc="${BASE_GIT:-}/obsproc/v${obsproc_run_ver:-}"
```

This PR also reverts the prepobs and fit2obs installs on MSU back to the
glopara space from the temporary `/work/noaa/global/kfriedma/glopara`
space installs.

Lastly, this PR also includes updates to complete issue #2844 (merge
`build.spack.ver` and `run.spack.ver`).

Resolves #2291
Resolves #2840
Resolves #2844
---
 modulefiles/module_base.gaea.lua      |  6 ++----
 modulefiles/module_base.hercules.lua  |  6 ++----
 modulefiles/module_base.jet.lua       |  2 +-
 modulefiles/module_base.orion.lua     |  6 ++----
 modulefiles/module_base.wcoss2.lua    |  2 +-
 parm/config/gfs/config.base           |  2 +-
 versions/build.gaea.ver               |  3 +--
 versions/build.hera.ver               |  2 +-
 versions/build.hercules.ver           |  2 +-
 versions/build.jet.ver                |  2 +-
 versions/build.noaacloud.ver          |  2 +-
 versions/build.orion.ver              |  2 +-
 versions/build.s4.ver                 |  2 +-
 versions/build.spack.ver              | 27 ---------------------------
 versions/run.gaea.ver                 |  2 +-
 versions/run.hera.ver                 |  2 +-
 versions/run.hercules.ver             |  3 +--
 versions/run.jet.ver                  |  2 +-
 versions/run.noaacloud.ver            |  2 +-
 versions/run.orion.ver                |  3 +--
 versions/run.s4.ver                   |  2 +-
 versions/run.wcoss2.ver               |  6 +++---
 versions/{run.spack.ver => spack.ver} | 17 ++++++++++++++---
 workflow/hosts/orion.yaml             |  2 +-
 24 files changed, 41 insertions(+), 66 deletions(-)
 delete mode 100644 versions/build.spack.ver
 rename versions/{run.spack.ver => spack.ver} (68%)

diff --git a/modulefiles/module_base.gaea.lua b/modulefiles/module_base.gaea.lua
index b08e79c274..f379225380 100644
--- a/modulefiles/module_base.gaea.lua
+++ b/modulefiles/module_base.gaea.lua
@@ -38,10 +38,8 @@ load(pathJoin("py-xarray", (os.getenv("py_xarray_ver") or "None")))
 setenv("WGRIB2","wgrib2")
 setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 
---prepend_path("MODULEPATH", pathJoin("/gpfs/f5/ufs-ard/world-shared/global/glopara/data/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
---load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
-prepend_path("MODULEPATH", pathJoin("/gpfs/f5/ufs-ard/world-shared/global/glopara/data/git/prepobs/v1.1.0", "modulefiles"))
-load(pathJoin("prepobs", "1.1.0"))
+prepend_path("MODULEPATH", pathJoin("/gpfs/f5/ufs-ard/world-shared/global/glopara/data/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
+load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
 prepend_path("MODULEPATH", pathJoin("/gpfs/f5/ufs-ard/world-shared/global/glopara/data/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
 load(pathJoin("fit2obs", (os.getenv("fit2obs_ver") or "None")))
diff --git a/modulefiles/module_base.hercules.lua b/modulefiles/module_base.hercules.lua
index fdc5f58698..4245b0d6f9 100644
--- a/modulefiles/module_base.hercules.lua
+++ b/modulefiles/module_base.hercules.lua
@@ -43,12 +43,10 @@ setenv("WGRIB2","wgrib2")
 setenv("WGRIB","wgrib")
 setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 
---prepend_path("MODULEPATH", pathJoin"/work/noaa/global/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles")
-prepend_path("MODULEPATH", pathJoin("/work/noaa/global/kfriedma/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git_rocky9/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
---prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
-prepend_path("MODULEPATH", pathJoin("/work/noaa/global/kfriedma/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git_rocky9/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
 load(pathJoin("fit2obs", (os.getenv("fit2obs_ver") or "None")))
 
 whatis("Description: GFS run environment")
diff --git a/modulefiles/module_base.jet.lua b/modulefiles/module_base.jet.lua
index 76320688b0..2f00c301df 100644
--- a/modulefiles/module_base.jet.lua
+++ b/modulefiles/module_base.jet.lua
@@ -49,7 +49,7 @@ setenv("WGRIB2","wgrib2")
 setenv("WGRIB","wgrib")
 setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 
-prepend_path("MODULEPATH", pathJoin("/lfs4/HFIP/hfv3gfs/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/lfs5/HFIP/hfv3gfs/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
 prepend_path("MODULEPATH", pathJoin("/lfs4/HFIP/hfv3gfs/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
diff --git a/modulefiles/module_base.orion.lua b/modulefiles/module_base.orion.lua
index 5cee9e5e31..e7b51ed563 100644
--- a/modulefiles/module_base.orion.lua
+++ b/modulefiles/module_base.orion.lua
@@ -42,12 +42,10 @@ setenv("WGRIB2","wgrib2")
 setenv("WGRIB","wgrib")
 setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 
---prepend_path("MODULEPATH", pathJoin"/work/noaa/global/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles")
-prepend_path("MODULEPATH", pathJoin("/work/noaa/global/kfriedma/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git_rocky9/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
---prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
-prepend_path("MODULEPATH", pathJoin("/work/noaa/global/kfriedma/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/work/noaa/global/glopara/git_rocky9/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
 load(pathJoin("fit2obs", (os.getenv("fit2obs_ver") or "None")))
 
 whatis("Description: GFS run environment")
diff --git a/modulefiles/module_base.wcoss2.lua b/modulefiles/module_base.wcoss2.lua
index 49d5abc678..830ea78b05 100644
--- a/modulefiles/module_base.wcoss2.lua
+++ b/modulefiles/module_base.wcoss2.lua
@@ -36,7 +36,7 @@ setenv("HPC_OPT", "/apps/ops/para/libs")
 load(pathJoin("met", (os.getenv("met_ver") or "None")))
 load(pathJoin("metplus", (os.getenv("metplus_ver") or "None")))
 
-prepend_path("MODULEPATH", pathJoin("/lfs/h2/emc/global/save/emc.global/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/lfs/h2/emc/global/save/emc.global/git/prepobs/gfsv17_v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
 prepend_path("MODULEPATH", pathJoin("/lfs/h2/emc/global/save/emc.global/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 81b18030fa..784c334d82 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -95,7 +95,7 @@ export MODE="@MODE@" # cycled/forecast-only
 # Build paths relative to $HOMEgfs
 export FIXgsi="${HOMEgfs}/fix/gsi"
 export HOMEpost="${HOMEgfs}"
-export HOMEobsproc="${BASE_GIT:-}/obsproc/v${obsproc_run_ver:-1.1.2}"
+export HOMEobsproc="${BASE_GIT:-}/obsproc/v${obsproc_run_ver:-}"
 
 # CONVENIENT utility scripts and other environment parameters
 export NCP="/bin/cp -p"
diff --git a/versions/build.gaea.ver b/versions/build.gaea.ver
index b92fe8c1db..8b6e641eb6 100644
--- a/versions/build.gaea.ver
+++ b/versions/build.gaea.ver
@@ -1,6 +1,5 @@
 export stack_intel_ver=2023.1.0
 export stack_cray_mpich_ver=8.1.25
 export spack_env=gsi-addon-dev
-
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/ncrc/proj/epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.hera.ver b/versions/build.hera.ver
index 337d5c32da..70afb90a29 100644
--- a/versions/build.hera.ver
+++ b/versions/build.hera.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
 export spack_env=gsi-addon-dev-rocky8
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.hercules.ver b/versions/build.hercules.ver
index cab0c92111..2d7185d5e7 100644
--- a/versions/build.hercules.ver
+++ b/versions/build.hercules.ver
@@ -2,5 +2,5 @@ export stack_intel_ver=2021.9.0
 export stack_impi_ver=2021.9.0
 export intel_mkl_ver=2023.1.0
 export spack_env=gsi-addon-env
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.jet.ver b/versions/build.jet.ver
index 55c0ea0bd1..e103725d41 100644
--- a/versions/build.jet.ver
+++ b/versions/build.jet.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
 export spack_env=gsi-addon-dev
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.noaacloud.ver b/versions/build.noaacloud.ver
index ba47313675..fc288b76b5 100644
--- a/versions/build.noaacloud.ver
+++ b/versions/build.noaacloud.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.3.0
 export stack_impi_ver=2021.3.0
 export spack_env=gsi-addon-env
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/contrib/spack-stack/spack-stack-${spack_stack_ver}/envs/gsi-addon-env/install/modulefiles/Core"
diff --git a/versions/build.orion.ver b/versions/build.orion.ver
index 834ecfc166..29e02f0873 100644
--- a/versions/build.orion.ver
+++ b/versions/build.orion.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.9.0
 export stack_impi_ver=2021.9.0
 export spack_env=gsi-addon-env-rocky9
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.s4.ver b/versions/build.s4.ver
index e2731ccfb3..e2641c124f 100644
--- a/versions/build.s4.ver
+++ b/versions/build.s4.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.0
 export spack_env=gsi-addon-env
-source "${HOMEgfs:-}/versions/build.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/data/prod/jedi/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/build.spack.ver b/versions/build.spack.ver
deleted file mode 100644
index 808f85dd16..0000000000
--- a/versions/build.spack.ver
+++ /dev/null
@@ -1,27 +0,0 @@
-export spack_stack_ver=1.6.0
-
-export cmake_ver=3.23.1
-
-export jasper_ver=2.0.32
-export libpng_ver=1.6.37
-export zlib_ver=1.2.13
-export esmf_ver=8.5.0
-export fms_ver=2023.02.01
-
-export hdf5_ver=1.14.0
-export netcdf_c_ver=4.9.2
-export netcdf_fortran_ver=4.6.1
-
-export bacio_ver=2.4.1
-export nemsio_ver=2.5.4
-export sigio_ver=2.3.2
-export w3emc_ver=2.10.0
-export bufr_ver=11.7.0
-export g2_ver=3.4.5
-export sp_ver=2.5.0
-export ip_ver=4.3.0
-export gsi_ncdiag_ver=1.1.2
-export g2tmpl_ver=1.10.2
-export crtm_ver=2.4.0.1
-export wgrib2_ver=2.0.8
-export grib_util_ver=1.3.0
diff --git a/versions/run.gaea.ver b/versions/run.gaea.ver
index c3aceb445d..81aa70df57 100644
--- a/versions/run.gaea.ver
+++ b/versions/run.gaea.ver
@@ -4,5 +4,5 @@ export spack_env=gsi-addon-dev
 
 export perl_ver=5.38.2
 
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/ncrc/proj/epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.hera.ver b/versions/run.hera.ver
index 34f81bfe96..6ebc64d9f2 100644
--- a/versions/run.hera.ver
+++ b/versions/run.hera.ver
@@ -9,5 +9,5 @@ export R_ver=3.6.1
 export gempak_ver=7.17.0
 export perl_ver=5.38.0
 
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.hercules.ver b/versions/run.hercules.ver
index ee8e4f8aea..2d7185d5e7 100644
--- a/versions/run.hercules.ver
+++ b/versions/run.hercules.ver
@@ -2,6 +2,5 @@ export stack_intel_ver=2021.9.0
 export stack_impi_ver=2021.9.0
 export intel_mkl_ver=2023.1.0
 export spack_env=gsi-addon-env
-
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.jet.ver b/versions/run.jet.ver
index 3aa586ee42..1e41fd0036 100644
--- a/versions/run.jet.ver
+++ b/versions/run.jet.ver
@@ -10,5 +10,5 @@ export gempak_ver=7.4.2
 # Adding perl as a module; With Rocky8, perl packages will not be from the OS
 export perl_ver=5.38.0
 
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.noaacloud.ver b/versions/run.noaacloud.ver
index 4c9ac3cd42..1fc3779b2e 100644
--- a/versions/run.noaacloud.ver
+++ b/versions/run.noaacloud.ver
@@ -2,7 +2,7 @@ export stack_intel_ver=2021.3.0
 export stack_impi_ver=2021.3.0
 export spack_env=gsi-addon-env
 
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/contrib/spack-stack/spack-stack-${spack_stack_ver}/envs/gsi-addon-env/install/modulefiles/Core"
 
 export cdo_ver=2.2.0
diff --git a/versions/run.orion.ver b/versions/run.orion.ver
index 112636fb20..29e02f0873 100644
--- a/versions/run.orion.ver
+++ b/versions/run.orion.ver
@@ -1,6 +1,5 @@
 export stack_intel_ver=2021.9.0
 export stack_impi_ver=2021.9.0
 export spack_env=gsi-addon-env-rocky9
-
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/work/noaa/epic/role-epic/spack-stack/orion/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.s4.ver b/versions/run.s4.ver
index 6d0f4cbaca..43e690e19b 100644
--- a/versions/run.s4.ver
+++ b/versions/run.s4.ver
@@ -4,5 +4,5 @@ export spack_env=gsi-addon-env
 
 export ncl_ver=6.4.0-precompiled
 
-source "${HOMEgfs:-}/versions/run.spack.ver"
+source "${HOMEgfs:-}/versions/spack.ver"
 export spack_mod_path="/data/prod/jedi/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.wcoss2.ver b/versions/run.wcoss2.ver
index 7f653dd50e..f5b11b3a6f 100644
--- a/versions/run.wcoss2.ver
+++ b/versions/run.wcoss2.ver
@@ -44,10 +44,10 @@ export metplus_ver=3.1.1
 
 # Development-only below
 
-export obsproc_run_ver=1.1.2
-export prepobs_run_ver=1.0.2
+export obsproc_run_ver=1.2.0
+export prepobs_run_ver=1.1.0
 
 export ens_tracker_ver=feature-GFSv17_com_reorg
-export fit2obs_ver=1.1.2
+export fit2obs_ver=1.1.4
 export mos_ver=5.4.3
 export mos_shared_ver=2.7.2
diff --git a/versions/run.spack.ver b/versions/spack.ver
similarity index 68%
rename from versions/run.spack.ver
rename to versions/spack.ver
index 4a17d0ef27..1f553134f0 100644
--- a/versions/run.spack.ver
+++ b/versions/spack.ver
@@ -1,8 +1,12 @@
 export spack_stack_ver=1.6.0
+export cmake_ver=3.23.1
 export python_ver=3.11.6
 
 export jasper_ver=2.0.32
 export libpng_ver=1.6.37
+export zlib_ver=1.2.13
+export esmf_ver=8.5.0
+export fms_ver=2023.02.01
 export cdo_ver=2.2.0
 export nco_ver=5.0.6
 
@@ -10,7 +14,14 @@ export hdf5_ver=1.14.0
 export netcdf_c_ver=4.9.2
 export netcdf_fortran_ver=4.6.1
 
+export bacio_ver=2.4.1
+export nemsio_ver=2.5.4
+export sigio_ver=2.3.2
+export w3emc_ver=2.10.0
 export bufr_ver=11.7.0
+export g2_ver=3.4.5
+export sp_ver=2.5.0
+export ip_ver=4.3.0
 export gsi_ncdiag_ver=1.1.2
 export g2tmpl_ver=1.10.2
 export crtm_ver=2.4.0.1
@@ -29,8 +40,8 @@ export met_ver=9.1.3
 export metplus_ver=3.1.1
 export py_xarray_ver=2023.7.0
 
-export obsproc_run_ver=1.1.2
-export prepobs_run_ver=1.0.2
+export obsproc_run_ver=1.2.0
+export prepobs_run_ver=1.1.0
 
 export ens_tracker_ver=feature-GFSv17_com_reorg
-export fit2obs_ver=1.1.2
+export fit2obs_ver=1.1.4
diff --git a/workflow/hosts/orion.yaml b/workflow/hosts/orion.yaml
index 81daea6168..4ec78fc8cc 100644
--- a/workflow/hosts/orion.yaml
+++ b/workflow/hosts/orion.yaml
@@ -1,4 +1,4 @@
-BASE_GIT: '/work/noaa/global/glopara/git'
+BASE_GIT: '/work/noaa/global/glopara/git_rocky9'
 DMPDIR: '/work/noaa/rstprod/dump'
 BASE_IC: '/work/noaa/global/glopara/data/ICSDIR'
 PACKAGEROOT: '/work/noaa/global/glopara/nwpara'

From c6e32621a71e71d250c64c5349d9249cfeec2cf4 Mon Sep 17 00:00:00 2001
From: Jiarui Dong <Jiarui.Dong@noaa.gov>
Date: Thu, 19 Sep 2024 12:43:21 -0400
Subject: [PATCH 09/21] Remove the GTS BUFR2IODA part of the snow obs prep job
 (#2900)

This PR removed the GTS BUFR2IODA part of the snow obs prep job, and
replaced it with a direct read from BUFR snow data at runtime by the
JEDI executable.

Depends on NOAA-EMC/GDASApp#1276
---------

Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
---
 parm/config/gfs/config.prepsnowobs     |  3 -
 parm/config/gfs/config.snowanl         |  1 +
 scripts/exglobal_prep_snow_obs.py      |  1 -
 sorc/gdas.cd                           |  2 +-
 ush/python/pygfs/task/snow_analysis.py | 84 ++------------------------
 5 files changed, 8 insertions(+), 83 deletions(-)

diff --git a/parm/config/gfs/config.prepsnowobs b/parm/config/gfs/config.prepsnowobs
index 60ca16ce9e..20bdd89ddf 100644
--- a/parm/config/gfs/config.prepsnowobs
+++ b/parm/config/gfs/config.prepsnowobs
@@ -8,11 +8,8 @@ echo "BEGIN: config.prepsnowobs"
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepsnowobs
 
-export GTS_OBS_LIST="${PARMgfs}/gdas/snow/prep/prep_gts.yaml.j2"
 export IMS_OBS_LIST="${PARMgfs}/gdas/snow/prep/prep_ims.yaml.j2"
 
-export BUFR2IODAX="${EXECgfs}/bufr2ioda.x"
-
 export CALCFIMSEXE="${EXECgfs}/calcfIMS.exe"
 export FIMS_NML_TMPL="${PARMgfs}/gdas/snow/prep/fims.nml.j2"
 
diff --git a/parm/config/gfs/config.snowanl b/parm/config/gfs/config.snowanl
index a2984f190b..b1460dfa67 100644
--- a/parm/config/gfs/config.snowanl
+++ b/parm/config/gfs/config.snowanl
@@ -9,6 +9,7 @@ echo "BEGIN: config.snowanl"
 source "${EXPDIR}/config.resources" snowanl
 
 export OBS_LIST="${PARMgfs}/gdas/snow/obs/lists/gdas_snow.yaml.j2"
+export GTS_SNOW_STAGE_YAML="${PARMgfs}/gdas/snow/obs/config/bufr2ioda_mapping.yaml.j2"
 
 # Name of the JEDI executable and its yaml template
 export JEDIEXE="${EXECgfs}/gdas.x"
diff --git a/scripts/exglobal_prep_snow_obs.py b/scripts/exglobal_prep_snow_obs.py
index a6a9070151..aa1eb1bb7d 100755
--- a/scripts/exglobal_prep_snow_obs.py
+++ b/scripts/exglobal_prep_snow_obs.py
@@ -20,6 +20,5 @@
 
     # Instantiate the snow prepare task
     SnowAnl = SnowAnalysis(config)
-    SnowAnl.prepare_GTS()
     if SnowAnl.task_config.cyc == 0:
         SnowAnl.prepare_IMS()
diff --git a/sorc/gdas.cd b/sorc/gdas.cd
index faa95efb18..7c1c181359 160000
--- a/sorc/gdas.cd
+++ b/sorc/gdas.cd
@@ -1 +1 @@
-Subproject commit faa95efb18f0f52acab2cf09b17f78406f9b48b1
+Subproject commit 7c1c181359c2c1952bab3dc1c481bbdb361aa472
diff --git a/ush/python/pygfs/task/snow_analysis.py b/ush/python/pygfs/task/snow_analysis.py
index 9656b00a8e..4b991d2b34 100644
--- a/ush/python/pygfs/task/snow_analysis.py
+++ b/ush/python/pygfs/task/snow_analysis.py
@@ -54,83 +54,6 @@ def __init__(self, config):
         # Extend task_config with local_dict
         self.task_config = AttrDict(**self.task_config, **local_dict)
 
-    @logit(logger)
-    def prepare_GTS(self) -> None:
-        """Prepare the GTS data for a global snow analysis
-
-        This method will prepare GTS data for a global snow analysis using JEDI.
-        This includes:
-        - processing GTS bufr snow depth observation data to IODA format
-
-        Parameters
-        ----------
-        Analysis: parent class for GDAS task
-
-        Returns
-        ----------
-        None
-        """
-
-        # create a temporary dict of all keys needed in this method
-        localconf = AttrDict()
-        keys = ['HOMEgfs', 'DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV',
-                'OPREFIX', 'CASE', 'OCNRES', 'ntiles']
-        for key in keys:
-            localconf[key] = self.task_config[key]
-
-        # Read and render the GTS_OBS_LIST yaml
-        logger.info(f"Reading {self.task_config.GTS_OBS_LIST}")
-        prep_gts_config = parse_j2yaml(self.task_config.GTS_OBS_LIST, localconf)
-        logger.debug(f"{self.task_config.GTS_OBS_LIST}:\n{pformat(prep_gts_config)}")
-
-        # copy the GTS obs files from COM_OBS to DATA/obs
-        logger.info("Copying GTS obs for bufr2ioda.x")
-        FileHandler(prep_gts_config.gtsbufr).sync()
-
-        logger.info("Link BUFR2IODAX into DATA/")
-        exe_src = self.task_config.BUFR2IODAX
-        exe_dest = os.path.join(localconf.DATA, os.path.basename(exe_src))
-        if os.path.exists(exe_dest):
-            rm_p(exe_dest)
-        os.symlink(exe_src, exe_dest)
-
-        # Create executable instance
-        exe = Executable(self.task_config.BUFR2IODAX)
-
-        def _gtsbufr2iodax(exe, yaml_file):
-            if not os.path.isfile(yaml_file):
-                logger.exception(f"FATAL ERROR: {yaml_file} not found")
-                raise FileNotFoundError(yaml_file)
-
-            logger.info(f"Executing {exe}")
-            try:
-                exe(yaml_file)
-            except OSError:
-                raise OSError(f"Failed to execute {exe} {yaml_file}")
-            except Exception:
-                raise WorkflowException(f"An error occured during execution of {exe} {yaml_file}")
-
-        # Loop over entries in prep_gts_config.bufr2ioda keys
-        # 1. generate bufr2ioda YAML files
-        # 2. execute bufr2ioda.x
-        for name in prep_gts_config.bufr2ioda.keys():
-            gts_yaml = os.path.join(self.task_config.DATA, f"bufr_{name}_snow.yaml")
-            logger.info(f"Generate BUFR2IODA YAML file: {gts_yaml}")
-            temp_yaml = parse_j2yaml(prep_gts_config.bufr2ioda[name], localconf)
-            save_as_yaml(temp_yaml, gts_yaml)
-            logger.info(f"Wrote bufr2ioda YAML to: {gts_yaml}")
-
-            # execute BUFR2IODAX to convert {name} bufr data into IODA format
-            _gtsbufr2iodax(exe, gts_yaml)
-
-        # Ensure the IODA snow depth GTS file is produced by the IODA converter
-        # If so, copy to COM_OBS/
-        try:
-            FileHandler(prep_gts_config.gtsioda).sync()
-        except OSError as err:
-            logger.exception(f"{self.task_config.BUFR2IODAX} failed to produce GTS ioda files")
-            raise OSError(err)
-
     @logit(logger)
     def prepare_IMS(self) -> None:
         """Prepare the IMS data for a global snow analysis
@@ -248,7 +171,7 @@ def initialize(self) -> None:
 
         # create a temporary dict of all keys needed in this method
         localconf = AttrDict()
-        keys = ['DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV',
+        keys = ['PARMgfs', 'DATA', 'current_cycle', 'COM_OBS', 'COM_ATMOS_RESTART_PREV',
                 'OPREFIX', 'CASE', 'OCNRES', 'ntiles']
         for key in keys:
             localconf[key] = self.task_config[key]
@@ -268,6 +191,11 @@ def initialize(self) -> None:
         logger.info("Staging ensemble backgrounds")
         FileHandler(self.get_ens_bkg_dict(localconf)).sync()
 
+        # stage GTS bufr2ioda mapping YAML files
+        logger.info(f"Staging GTS bufr2ioda mapping YAML files from {self.task_config.GTS_SNOW_STAGE_YAML}")
+        gts_mapping_list = parse_j2yaml(self.task_config.GTS_SNOW_STAGE_YAML, localconf)
+        FileHandler(gts_mapping_list).sync()
+
         # Write out letkfoi YAML file
         save_as_yaml(self.task_config.jedi_config, self.task_config.jedi_yaml)
         logger.info(f"Wrote letkfoi YAML to: {self.task_config.jedi_yaml}")

From 3c86873acfc2afed19dd38e72c47782ace60f610 Mon Sep 17 00:00:00 2001
From: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri, 20 Sep 2024 07:16:55 -0400
Subject: [PATCH 10/21] Adjust C768 resources for Hera (#2819)

This modifies the resources for gdasfcst (everywhere) and enkfgdaseupd
(Hera only). For the fcst job, the number of write tasks is increased to
prevent out of memory errors from the inline post. For the eupd, the
number of tasks is decreased to prevent out of memory errors. The
runtime for the eupd job was just over 10 minutes.

Resolves #2506
Resolves #2498
Resolves #2916

---------

Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
---
 jobs/JGFS_ATMOS_CYCLONE_GENESIS       |  5 -----
 jobs/JGFS_ATMOS_CYCLONE_TRACKER       |  5 -----
 parm/config/gfs/config.base           |  7 +++++++
 parm/config/gfs/config.resources.HERA | 16 ++++++++++++++--
 parm/config/gfs/config.resources.S4   |  2 +-
 parm/config/gfs/config.ufs            |  2 +-
 sorc/gsi_utils.fd                     |  2 +-
 7 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/jobs/JGFS_ATMOS_CYCLONE_GENESIS b/jobs/JGFS_ATMOS_CYCLONE_GENESIS
index de130bf9aa..a80bcc1153 100755
--- a/jobs/JGFS_ATMOS_CYCLONE_GENESIS
+++ b/jobs/JGFS_ATMOS_CYCLONE_GENESIS
@@ -3,11 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis" -c "base genesis"
 
-# Hack to temporary skip this as the tracker has not been build
-#   on Hercules Rocky 9 yet
-# TODO: Remove this after tracker has been built for Rocky 9 #2639
-if [[ "${machine}" == 'HERCULES' ]]; then exit 0; fi
-
 ##############################################
 # Set variables used in the exglobal script
 ##############################################
diff --git a/jobs/JGFS_ATMOS_CYCLONE_TRACKER b/jobs/JGFS_ATMOS_CYCLONE_TRACKER
index 067de2c4aa..24fe33f8ca 100755
--- a/jobs/JGFS_ATMOS_CYCLONE_TRACKER
+++ b/jobs/JGFS_ATMOS_CYCLONE_TRACKER
@@ -3,11 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "tracker" -c "base tracker"
 
-# Hack to temporary skip this as the tracker has not been build
-#   on Hercules Rocky 9 yet
-# TODO: Remove this after tracker has been built for Rocky 9 #2639
-if [[ "${machine}" == 'HERCULES' ]]; then exit 0; fi
-
 export COMPONENT="atmos"
 
 
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 784c334d82..27fcbdd055 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -492,4 +492,11 @@ if [[ "${machine}" =~ "PW" ]]; then
    export DO_WAVE="NO"
 fi
 
+# The tracker and genesis are not installed on Orion/Hercules yet; this requires spack-stack builds of the package.
+# TODO: we should place these in workflow/hosts/[orion|hercules].yaml.
+if [[ "${machine}" == "ORION" || "${machine}" == "HERCULES" ]]; then
+   export DO_TRACKER="NO"
+   export DO_GENESIS="NO"
+fi
+
 echo "END: config.base"
diff --git a/parm/config/gfs/config.resources.HERA b/parm/config/gfs/config.resources.HERA
index e79d4c5b0a..d1b09fcc32 100644
--- a/parm/config/gfs/config.resources.HERA
+++ b/parm/config/gfs/config.resources.HERA
@@ -5,8 +5,9 @@
 case ${step} in
   "anal")
     if [[ "${CASE}" == "C384" ]]; then
-      export ntasks=270
-      export threads_per_task_anal=8
+      export ntasks_gdas=270
+      export ntasks_gfs=270
+      export threads_per_task=8
       export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     fi
     ;;
@@ -26,6 +27,10 @@ case ${step} in
 
   "eupd")
     case ${CASE} in
+      "C768")
+        export ntasks=80
+        export threads_per_task=20
+        ;;
       "C384")
         export ntasks=80
         ;;
@@ -43,6 +48,13 @@ case ${step} in
     export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 
+  "upp")
+    if (( "${CASE:1}" >= 768 )); then
+       # Run fewer tasks per node for memory
+       tasks_per_node=20
+    fi
+    ;;
+
   *)
     ;;
 esac
diff --git a/parm/config/gfs/config.resources.S4 b/parm/config/gfs/config.resources.S4
index 1af64bf250..817494c7cd 100644
--- a/parm/config/gfs/config.resources.S4
+++ b/parm/config/gfs/config.resources.S4
@@ -32,7 +32,7 @@ case ${step} in
       *)
         ;;
     esac
-    export tasks_node=$(( max_tasks_per_node / threads_per_task ))
+    export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 
   "eobs")
diff --git a/parm/config/gfs/config.ufs b/parm/config/gfs/config.ufs
index babbe1f2dd..6309c4073b 100644
--- a/parm/config/gfs/config.ufs
+++ b/parm/config/gfs/config.ufs
@@ -281,7 +281,7 @@ case "${fv3_res}" in
           export rf_cutoff=100.0
           export fv_sg_adj=450
           export WRITE_GROUP_GDAS=2
-          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GDAS=10
+          export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GDAS=15
           export WRITE_GROUP_GFS=4
           export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20 #Note this should be 10 for WCOSS2
         fi
diff --git a/sorc/gsi_utils.fd b/sorc/gsi_utils.fd
index 9382fd01c2..a6ea311e5c 160000
--- a/sorc/gsi_utils.fd
+++ b/sorc/gsi_utils.fd
@@ -1 +1 @@
-Subproject commit 9382fd01c2a626c8934c3f553d420a45de2b4dec
+Subproject commit a6ea311e5c82369d255e3afdc99c1bce0c9a3014

From 7bdb3626118d8e33705dac44269f77729ccdb86a Mon Sep 17 00:00:00 2001
From: mingshichen-noaa <48537176+mingshichen-noaa@users.noreply.github.com>
Date: Sat, 21 Sep 2024 02:15:17 -0400
Subject: [PATCH 11/21] Update global atmos vminmon job with COMIN/COMOUT for
 COM prefix (#2939)

NCO has requested that each COM variable specify whether it is an input
or an output. This completes that process for the global minimization
monitor job.

Refs #2451
---
 jobs/JGLOBAL_ATMOS_VMINMON | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/jobs/JGLOBAL_ATMOS_VMINMON b/jobs/JGLOBAL_ATMOS_VMINMON
index 8ad9b91792..26cdc73c95 100755
--- a/jobs/JGLOBAL_ATMOS_VMINMON
+++ b/jobs/JGLOBAL_ATMOS_VMINMON
@@ -17,16 +17,18 @@ export gcyc=${GDATE:8:2}
 #############################################
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_MINMON
-YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx COM_ATMOS_MINMON_PREV:COM_ATMOS_MINMON_TMPL
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+	COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+	COMOUT_ATMOS_MINMON:COM_ATMOS_MINMON_TMPL
 
-export gsistat="${COM_ATMOS_ANALYSIS}/${RUN}.t${cyc}z.gsistat"
-export M_TANKverf=${M_TANKverf:-${COM_ATMOS_MINMON}}
-export M_TANKverfM1=${M_TANKverfM1:-${COM_ATMOS_MINMON_PREV}}
+YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+	COMIN_ATMOS_MINMON_PREV:COM_ATMOS_MINMON_TMPL
 
-if [[ ! -d ${M_TANKverf} ]]; then mkdir -p -m 775 "${M_TANKverf}" ; fi
-if [[ ! -d ${M_TANKverfM1} ]]; then mkdir -p -m 775 "${M_TANKverfM1}" ; fi
+export gsistat="${COMIN_ATMOS_ANALYSIS}/${RUN}.t${cyc}z.gsistat"
+export M_TANKverf=${M_TANKverf:-${COMOUT_ATMOS_MINMON}}
+export M_TANKverfM1=${M_TANKverfM1:-${COMIN_ATMOS_MINMON_PREV}}
+
+if [[ ! -d ${M_TANKverf} ]]; then mkdir -p "${M_TANKverf}" ; fi
 
 ########################################################
 # Execute the script.

From fe57bb4df5dc3ab53d1f7e2ad2d3c77d734bd2fa Mon Sep 17 00:00:00 2001
From: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Mon, 23 Sep 2024 01:14:26 -0400
Subject: [PATCH 12/21] Remove need for a ice_prod dependency check script 
 (#2809)

# Description
The main purpose of this PR is to remove the need for an ice_prod
dependency check script `ush/check_ice_netcdf.sh`. The original purpose
of the ice_prod dependency check script is to check for special case
dependencies where `( cyc + FHMIN ) % FHOUT_ICE )) =! 0` (more details
on this issue can be found in issue #2674 ). A bugfix for these special
cases is expected to come from a PR in the ufs-weather-model.

Resolves #2721
Refs #2721, #2674
---
 ush/check_ice_netcdf.sh                    | 43 ----------------------
 ush/forecast_predet.sh                     | 11 +-----
 ush/python/pygfs/task/oceanice_products.py | 16 +-------
 workflow/rocoto/gefs_tasks.py              | 20 +++-------
 4 files changed, 9 insertions(+), 81 deletions(-)
 delete mode 100755 ush/check_ice_netcdf.sh

diff --git a/ush/check_ice_netcdf.sh b/ush/check_ice_netcdf.sh
deleted file mode 100755
index 9d2d945a8b..0000000000
--- a/ush/check_ice_netcdf.sh
+++ /dev/null
@@ -1,43 +0,0 @@
-#! /usr/bin/env bash
-
-yyyy=${1?}
-mm=${2?}
-dd=${3?}
-cyc=${4?}
-fhr=${5?}
-ROTDIR=${6?}
-member=${7?}
-FHOUT_ICE_GFS=${8?}
-
-fhri=$((10#${fhr}))
-
-#Will need to consider fhmin in the future to calculate the offset if we are to stick with this approach. 
-((offset = ( cyc ) % FHOUT_ICE_GFS))
-
-if (( offset != 0  )); then
-  (( fhri = fhri - cyc ))
-  fhr3=$(printf %03i "${fhri}")
-  if (( fhri <= FHOUT_ICE_GFS  )); then
-    (( interval = FHOUT_ICE_GFS - cyc )) 
-    ncfile=${ROTDIR}/gefs.${yyyy}${mm}${dd}/${cyc}/mem${member}/model/ice/history/gefs.ice.t${cyc}z.${interval}hr_avg.f${fhr3}.nc
-  else
-    ncfile=${ROTDIR}/gefs.${yyyy}${mm}${dd}/${cyc}/mem${member}/model/ice/history/gefs.ice.t${cyc}z.${FHOUT_ICE_GFS}hr_avg.f${fhr3}.nc
-  fi
-else
-  ncfile=${ROTDIR}/gefs.${yyyy}${mm}${dd}/${cyc}/mem${member}/model/ice/history/gefs.ice.t${cyc}z.${FHOUT_ICE_GFS}hr_avg.f${fhr}.nc
-fi
-
-#Check if netcdf file exists.
-if [[ ! -f "${ncfile}" ]];then
-  rc=1
-else
-  #Check if netcdf file is older than 2 minutes.
-  ncage="$(find "${ncfile}" -mmin -2)"
-  if [[ -n "${ncage}" ]]; then
-    rc=1
-  else
-    rc=0
-  fi
-fi
-
-exit "${rc}"
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 9e08a12dd8..d7c04ea699 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -642,15 +642,8 @@ CICE_predet(){
 
   # CICE does not have a concept of high frequency output like FV3
   # Convert output settings into an explicit list for CICE
-  if (( $(( ( cyc + FHMIN ) % FHOUT_ICE )) == 0 )); then
-    # shellcheck disable=SC2312
-    mapfile -t CICE_OUTPUT_FH < <(seq "${FHMIN}" "${FHOUT_ICE}" "${FHMAX}") || exit 10
-  else
-    CICE_OUTPUT_FH=("${FHMIN}")
-    # shellcheck disable=SC2312
-    mapfile -t -O "${#CICE_OUTPUT_FH[@]}" CICE_OUTPUT_FH < <(seq "$(( FHMIN + $(( ( cyc + FHMIN ) % FHOUT_ICE )) ))" "${FHOUT_ICE}" "${FHMAX}") || exit 10
-    CICE_OUTPUT_FH+=("${FHMAX}")
-  fi
+  # shellcheck disable=SC2312
+  mapfile -t CICE_OUTPUT_FH < <(seq "${FHMIN}" "${FHOUT_ICE}" "${FHMAX}") || exit 10
 
   # Fix files
   ${NCP} "${FIXgfs}/cice/${ICERES}/${CICE_GRID}" "${DATA}/"
diff --git a/ush/python/pygfs/task/oceanice_products.py b/ush/python/pygfs/task/oceanice_products.py
index 98b57ae801..39ec53b100 100644
--- a/ush/python/pygfs/task/oceanice_products.py
+++ b/ush/python/pygfs/task/oceanice_products.py
@@ -58,22 +58,10 @@ def __init__(self, config: Dict[str, Any]) -> None:
 
         valid_datetime = add_to_datetime(self.task_config.current_cycle, to_timedelta(f"{self.task_config.FORECAST_HOUR}H"))
 
+        forecast_hour = self.task_config.FORECAST_HOUR
         if self.task_config.COMPONENT == 'ice':
-            offset = int(self.task_config.current_cycle.strftime("%H")) % self.task_config.FHOUT_ICE_GFS
-            # For CICE cases where offset is not 0, forecast_hour needs to be adjusted based on the offset.
-            # TODO: Consider FHMIN when calculating offset.
-            if offset != 0:
-                forecast_hour = self.task_config.FORECAST_HOUR - int(self.task_config.current_cycle.strftime("%H"))
-                # For the first forecast hour, the interval may be different from the intervals of subsequent forecast hours
-                if forecast_hour <= self.task_config.FHOUT_ICE_GFS:
-                    interval = self.task_config.FHOUT_ICE_GFS - int(self.task_config.current_cycle.strftime("%H"))
-                else:
-                    interval = self.task_config.FHOUT_ICE_GFS
-            else:
-                forecast_hour = self.task_config.FORECAST_HOUR
-                interval = self.task_config.FHOUT_ICE_GFS
+            interval = self.task_config.FHOUT_ICE_GFS
         if self.task_config.COMPONENT == 'ocean':
-            forecast_hour = self.task_config.FORECAST_HOUR
             interval = self.task_config.FHOUT_OCN_GFS
 
         # TODO: This is a bit of a hack, but it works for now
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index 8a4f148f24..3b72677a58 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -213,21 +213,11 @@ def _atmosoceaniceprod(self, component: str):
         history_path = self._template_to_rocoto_cycstring(self._base[history_path_tmpl], {'MEMDIR': 'mem#member#'})
         deps = []
         data = f'{history_path}/{history_file_tmpl}'
-        if component in ['ocean']:
-            dep_dict = {'type': 'data', 'data': data, 'age': 120}
-            deps.append(rocoto.add_dependency(dep_dict))
-            dep_dict = {'type': 'metatask', 'name': 'fcst_mem#member#'}
-            deps.append(rocoto.add_dependency(dep_dict))
-            dependencies = rocoto.create_dependency(dep=deps, dep_condition='or')
-        elif component in ['ice']:
-            command = f"{self.HOMEgfs}/ush/check_ice_netcdf.sh @Y @m @d @H #fhr# &ROTDIR; #member# {fhout_ice_gfs}"
-            dep_dict = {'type': 'sh', 'command': command}
-            deps.append(rocoto.add_dependency(dep_dict))
-            dependencies = rocoto.create_dependency(dep=deps)
-        else:
-            dep_dict = {'type': 'data', 'data': data, 'age': 120}
-            deps.append(rocoto.add_dependency(dep_dict))
-            dependencies = rocoto.create_dependency(dep=deps)
+        dep_dict = {'type': 'data', 'data': data, 'age': 120}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dep_dict = {'type': 'metatask', 'name': 'fcst_mem#member#'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep=deps, dep_condition='or')
 
         postenvars = self.envars.copy()
         postenvar_dict = {'ENSMEM': '#member#',

From ec634926f3b1ba1984b0735e17b76869659ceabe Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Mon, 23 Sep 2024 11:15:27 -0400
Subject: [PATCH 13/21] Refine issue and PR templates (#2947)

Refines the issue and PR templates to cover some shortcomings and
pitfalls we have identified.

The fix file issue template is expanded to cover other data sets managed
under "glopara".

Resolves #2589
---
 .github/ISSUE_TEMPLATE/NCO_bug_report.yml    |   2 +-
 .github/ISSUE_TEMPLATE/bug_report.yml        |  14 +-
 .github/ISSUE_TEMPLATE/feature_request.yml   |  17 ++-
 .github/ISSUE_TEMPLATE/fix_file.yml          |  97 --------------
 .github/ISSUE_TEMPLATE/production_update.yml |  29 ++--
 .github/ISSUE_TEMPLATE/static_data.yml       | 134 +++++++++++++++++++
 .github/pull_request_template.md             |  63 +++++----
 7 files changed, 212 insertions(+), 144 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/fix_file.yml
 create mode 100644 .github/ISSUE_TEMPLATE/static_data.yml

diff --git a/.github/ISSUE_TEMPLATE/NCO_bug_report.yml b/.github/ISSUE_TEMPLATE/NCO_bug_report.yml
index cc53205807..79632779aa 100644
--- a/.github/ISSUE_TEMPLATE/NCO_bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/NCO_bug_report.yml
@@ -1,4 +1,4 @@
-name: NCO Bug report
+name: NCO Bug Report
 description: Report something that is incorrect or broken
 labels: ["nco-bug", "triage"]
 assignees:
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 216293781c..d43d2eb3d7 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,4 +1,4 @@
-name: Bug report
+name: Bug Report
 description: Report something that is incorrect or broken
 labels: ["bug", "triage"]
 
@@ -9,6 +9,8 @@ body:
         Your bug may already be reported!
         Please search on the [Issue tracker](https://github.com/NOAA-EMC/global-workflow/issues) before creating one.
 
+        Is this actually a workflow bug? If not, please open an issue in the appropriate repository first.
+
   - type: textarea
     id: current_behavior
     attributes:
@@ -46,6 +48,13 @@ body:
     validations:
       required: true
 
+  - type: input
+    id: hash
+    attributes:
+      label: What global-workflow hash are you using?
+    validations:
+      required: true
+
   - type: textarea
     id: reproduction_steps
     attributes:
@@ -63,8 +72,9 @@ body:
     attributes:
       label: Additional information
       description: Provide context or any additional information about the bug.
+      placeholder: Optional
     validations:
-      required: true
+      required: false
 
   - type: textarea
     id: propsed_implementation
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
index 3aed58c520..7e0ddb2459 100644
--- a/.github/ISSUE_TEMPLATE/feature_request.yml
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,4 +1,4 @@
-name: Feature request
+name: Feature Request
 description: Request new capability
 labels: ["feature", "triage"]
 
@@ -10,8 +10,7 @@ body:
         - Something is wrong or broken
         - It is a request from NCO
         - It is initiating a production update
-        - Files need to be updated or added to fix
-
+        - Files need to be updated in a directory managed by workflow CMs under "glopara"
 
         Please search on the [Issue tracker](https://github.com/NOAA-EMC/global-workflow/issues) to make sure the feature has not already been requested to avoid duplicates.
   
@@ -34,7 +33,17 @@ body:
     id: criteria
     attributes:
       label: Acceptance Criteria
-      placeholder: What does it mean for this issue to be complete?
+      description: |
+        A checklist of criteria to be satisfied before this feature is considered complete.
+
+        Examples:
+          - Forecast with option X completes successfully
+          - File X produced
+          - Output unchanged
+      placeholder: |
+        - [ ] Criterion #1
+        - [ ] Criterion #2
+        - [ ] Criterion #3
     validations:
       required: true
   
diff --git a/.github/ISSUE_TEMPLATE/fix_file.yml b/.github/ISSUE_TEMPLATE/fix_file.yml
deleted file mode 100644
index 3f5b69cd1d..0000000000
--- a/.github/ISSUE_TEMPLATE/fix_file.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-name: Fix File Update
-description: Request fix files be added or updated
-labels: ["Fix Files", "triage"]
-assignees:
-  - KateFriedman-NOAA
-  - WalterKolczynski-NOAA
-
-body:
-  - type: dropdown
-    attributes:
-      label: Target fix directory
-      options:
-        - NEW
-        - aer
-        - am
-        - chem
-        - cice
-        - cpl
-        - datm
-        - gdas/crtm
-        - gdas/fv3jedi
-        - gdas/gsibec
-        - gldas
-        - glwu
-        - gsi
-        - lut
-        - mom6
-        - orog
-        - raw
-        - reg2grb2
-        - sfc_climo
-        - ugwd
-        - verif
-        - wave
-      multiple: true
-    validations:
-      required: true
-
-  - type: checkboxes
-    attributes:
-      label: Type of change
-      options:
-        - label: Update existing files
-        - label: Remove files
-        - label: Add new files to existing directory
-        - label: Add new fix directory
-    validations:
-      required: true
-
-  - type: dropdown
-    attributes:
-      label: Any workflow changes needed?
-      description: |
-        Any change other than adding files to an existing directory will require at least a new fix version.
-      options:
-        - No change needed
-        - Fix version only
-        - Fix version + additional changes
-    validations:
-      required: true
-
-  - type: textarea
-    attributes:
-      label: Related issues
-      description: Please link any related issues in other repositories
-      placeholder: NOAA-EMC/repo#1234
-    validations:
-      required: false
-
-  - type: input
-    attributes:
-      label: Pickup location
-      description: |
-        Please provide a path to the data on either Hera or WCOSS.
-
-        If this requires a version update, please provide the *entire* directory, including unchanged files from current fix.
-      placeholder: '/path/to/new/fix'
-    validations:
-      required: true
-
-  - type: input
-    attributes:
-      label: Size
-      description: How much bigger/smaller is the new set from the existing set (in MB)?
-      placeholder: '0'
-    validations:
-      required: true
-
-  - type: markdown
-    attributes:
-      value: |
-        # Tasks
-        - [ ] Discuss needs with global-workflow developer assigned to request.
-        - [ ] Add/update/remove fix file(s) in fix sets on supported platforms (global-workflow assignee task).
-        - [ ] Update "Fix File Management" spreadsheet (https://docs.google.com/spreadsheets/d/1BeIvcz6TO3If4YCqkUK-oz_kGS9q2wTjwLS-BBemSEY/edit?usp=sharing).
-        - [ ] Make related workflow/component updates.
-
diff --git a/.github/ISSUE_TEMPLATE/production_update.yml b/.github/ISSUE_TEMPLATE/production_update.yml
index ac9ada505a..cb1fb588d8 100644
--- a/.github/ISSUE_TEMPLATE/production_update.yml
+++ b/.github/ISSUE_TEMPLATE/production_update.yml
@@ -33,18 +33,19 @@ body:
     validations:
       required: true
 
-  - type: markdown
+  - type: checkboxes
     attributes:
-      value: |
-        ** Tasks **
-        - [ ] Create release branch
-        - [ ] Make workflow changes for upgrade in release branch (add additional checklist items as needed)
-        - [ ] Create release notes
-        - [ ] Cut hand-off tag for CDF
-        - [ ] Submit CDF to NCO
-        - [ ] Implementation into operations complete
-        - [ ] Merge release branch into operational branch
-        - [ ] Cut version tag from operational branch
-        - [ ] Release new version tag
-        - [ ] Announce to users
-        - [ ] Update Read-The-Docs operations status version in develop
+      label: Tasks
+      description: List of tasks to complete update. For use after issue is created.
+      options:
+        - label: Create release branch
+        - label: Make workflow changes for upgrade in release branch (add additional checklist items as needed)
+        - label: Create release notes
+        - label: Cut hand-off tag for CDF
+        - label: Submit CDF to NCO
+        - label: Implementation into operations complete
+        - label: Merge release branch into operational branch
+        - label: Cut version tag from operational branch
+        - label: Release new version tag
+        - label: Announce to users
+        - label: Update Read-The-Docs operations status version in develop
diff --git a/.github/ISSUE_TEMPLATE/static_data.yml b/.github/ISSUE_TEMPLATE/static_data.yml
new file mode 100644
index 0000000000..f29f155cf8
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/static_data.yml
@@ -0,0 +1,134 @@
+name: Static Data Update
+description: Request static data be added or updated
+labels: ["Static Data Mgmt"]
+assignees:
+  - KateFriedman-NOAA
+  - WalterKolczynski-NOAA
+
+body:
+  - type: dropdown
+    attributes:
+      label: Type of static data
+      description: |
+        - Fix: large static files needed to run global-workflow
+        - Initial conditions: ICs needed to run one of global-workflow's included tests
+        - Experimental data: Temporary datasets needed for development that will be replaced by other sources for operations (e.g. data that will be in DCOM)
+      options:
+        - Fix
+        - Initial conditions
+        - Experimental data
+    validations:
+      required: true
+
+  - type: dropdown
+    attributes:
+      label: Target directory
+      options:
+        - "Fix: aer"
+        - "Fix: am"
+        - "Fix: chem"
+        - "Fix: cice"
+        - "Fix: cpl"
+        - "Fix: datm"
+        - "Fix: gdas/crtm"
+        - "Fix: gdas/fv3jedi"
+        - "Fix: gdas/gsibec"
+        - "Fix: gldas"
+        - "Fix: glwu"
+        - "Fix: gsi"
+        - "Fix: lut"
+        - "Fix: mom6"
+        - "Fix: orog"
+        - "Fix: raw"
+        - "Fix: reg2grb2"
+        - "Fix: sfc_climo"
+        - "Fix: ugwd"
+        - "Fix: verif"
+        - "Fix: wave"
+        - "Fix: *NEW*"
+        - "ICs: C48/C48 mx500"
+        - "ICs: C96/C48"
+        - "ICs: C96 mx100"
+        - "ICs: C384/C192"
+        - "ICs: C384 mx025"
+        - "ICs: C768 mx025"
+        - "ICs: C1152 mx025"
+        - "ICs: *NEW RESOLUTION*"
+        - "Exp Data: GOCART emissions"
+        - "Exp Data: JEDI obs"
+        - "Exp Data: *NEW*"
+      multiple: true
+    validations:
+      required: true
+
+  - type: checkboxes
+    attributes:
+      label: Type of change
+      options:
+        - label: Update existing files (Version update needed)
+        - label: Remove files (Version update needed)
+        - label: Add new files to existing directory
+        - label: Add new directory (Version update needed if fix)
+    validations:
+      required: true
+
+  - type: dropdown
+    attributes:
+      label: Any workflow changes needed?
+      description: |
+        ANY fix or IC change other than adding files will require at least a new version.
+      options:
+        - No change needed
+        - Fix/IC version update only
+        - Fix/IC version update + additional changes
+        - Non-version changes only
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: |
+        Please list all related issues. If this request requires a workflow update (including a fix version update), please open a *separate* global-workflow issue to track the change.
+      description: Please link any related issues
+      placeholder: NOAA-EMC/repo#1234
+    validations:
+      required: false
+
+  - type: input
+    attributes:
+      label: Pickup location
+      description: |
+        Please provide a path to the data on either Hera or WCOSS.
+
+        If this requires a version update, please provide a CLEAN copy of the *entire* directory, including the structure and unchanged files from current directory.
+
+        If this is just adding additional files, you may provide just the new files. The directory structure should still match the target.
+      placeholder: '/path/to/new/data'
+    validations:
+      required: true
+
+  - type: input
+    attributes:
+      label: Size
+      description: How much data needs to be copied (size of pickup location in MB)?
+      placeholder: '0'
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional information
+      description: |
+        Please provide any additional information needed for this request. If this is a new directory, please provide a short description and a point of contact.
+    validations:
+      required: false
+
+  - type: markdown
+    attributes:
+      value: |
+        # Tasks
+        - [ ] Discuss needs with global-workflow developer assigned to request
+        - [ ] Stage a CLEAN copy of data on Hera or WCOSS in the location provided above
+        - [ ] [global-workflow CM] Update data in "glopara"-managed space on supported platforms
+        - [ ] [Fix only] Update "Fix File Management" [spreadsheet](https://docs.google.com/spreadsheets/d/1BeIvcz6TO3If4YCqkUK-oz_kGS9q2wTjwLS-BBemSEY/edit?usp=sharing)
+        - [ ] Make related workflow/component updates (if any)
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index 3f8fe65065..9a1d61eb30 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -1,19 +1,28 @@
-<!-- PLEASE READ -->
-<!-- Any PRs not following this template will be closed -->
 <!--
-    Please use a short (<60 char), descriptive title above. It should complete the sentence "If merged, this PR will _____". Capitalize the first word and do not end with a period.
+  *** PLEASE READ ***
 
-    PRs should meet these guidelines:
-    - Each PR should address ONE topic and have an associated issue.
-    - No hard-coded paths or personal directories.
-    - No temporary or backup files should be committed (including logs).
-    - Any code that you disabled by being commented out should be removed or reenabled.
+  Any PRs not following this template will be closed.
 
-    Please delete all these comments before submitting the PR.
+  Please delete all these comments before submitting the PR.
+
+  Please use a short (<60 char), descriptive title for the PR title above. It should complete the sentence "If merged, this PR will _____". Capitalize the first word and do not end with a period.
+
+  No content should appear above the "Description" header.
+
+  If this PR is not merge-ready (e.g. it depends on other PRs not yet merged), please mark it as draft until it is ready.
+
+  PRs should meet these guidelines:
+  - Each PR should address ONE topic and have an associated issue.
+  - No hard-coded paths or personal directories.
+  - No temporary or backup files should be committed (including logs).
+  - Any code that you disabled by being commented out should be removed or reenabled.
 -->
 # Description
-<!-- This description will become the commit message for the PR-->
-<!-- Please use this format for your description:
+<!-- This description will become the commit message for the PR. -->
+<!--
+  Solely pointing to an issue is not an adequate description!
+
+  Please use this format for your description:
 
   Describe your changes. Focus on the *what* and *why*. The *how* will be evident from the changes. In particular, be sure to note any interface changes, such as command line syntax, that will need to be communicated to users.
 
@@ -23,27 +32,27 @@
   Refs #4321
   Refs NOAA-EMC/repo#5678
 -->
+<!-- For more on writing good commit messages, see https://cbea.ms/git-commit/ -->
 
 # Type of change
-<!-- Delete all except one -->
-- Bug fix (fixes something broken)
-- New feature (adds functionality)
-- Maintenance (code refactor, clean-up, new CI test, etc.)
+- [ ] Bug fix (fixes something broken)
+- [ ] New feature (adds functionality)
+- [ ] Maintenance (code refactor, clean-up, new CI test, etc.)
 
 # Change characteristics
+<!-- Choose YES or NO from each of the following and delete the other -->
 - Is this a breaking change (a change in existing functionality)? YES/NO
 - Does this change require a documentation update? YES/NO
 - Does this change require an update to any of the following submodules? YES/NO (If YES, please add a link to any PRs that are pending.)
-  - [ ] EMC verif-global
-  - [ ] GDAS
-  - [ ] GFS-utils
-  - [ ] GSI
-  - [ ] GSI-monitor
-  - [ ] GSI-utils
-  - [ ] UFS-utils
-  - [ ] UFS-weather-model
-  - [ ] wxflow
-
+  - [ ] EMC verif-global <!-- NOAA-EMC/EMC_verif-global#1234 -->
+  - [ ] GDAS <!-- NOAA-EMC/GDASApp#1234 -->
+  - [ ] GFS-utils <!-- NOAA-EMC/gfs-utils#1234 -->
+  - [ ] GSI <!-- NOAA-EMC/GSI#1234 -->
+  - [ ] GSI-monitor <!-- NOAA-EMC/GSI-Monitor#1234 -->
+  - [ ] GSI-utils <!-- NOAA-EMC/GSI-Utils#1234 -->
+  - [ ] UFS-utils <!-- ufs-community/UFS_UTILS#1234 -->
+  - [ ] UFS-weather-model <!-- ufs-community/ufs-weather-model#1234 -->
+  - [ ] wxflow <!-- NOAA-EMC/wxflow#1234 -->
 
 # How has this been tested?
 <!-- Please list any test you conducted, including the machine.
@@ -59,6 +68,8 @@ Example:
 - [ ] My code follows the style guidelines of this project
 - [ ] I have performed a self-review of my own code
 - [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have documented my code, including function, input, and output descriptions
 - [ ] My changes generate no new warnings
 - [ ] New and existing tests pass with my changes
-- [ ] I have made corresponding changes to the documentation if necessary
+- [ ] This change is covered by an existing CI test or a new one has been added
+- [ ] I have made corresponding changes to the system documentation if necessary

From 7088a91e4f5461d96d97429f67c8a3519db6d3d0 Mon Sep 17 00:00:00 2001
From: AntonMFernando-NOAA
 <167725623+AntonMFernando-NOAA@users.noreply.github.com>
Date: Wed, 25 Sep 2024 10:47:03 -0400
Subject: [PATCH 14/21] Add an archive task to GEFS system to archive files in
 HPSS (#2895)

- This task is an extension of the arch job previously merged that
archives files in ROTDIR (#2816
https://github.com/AntonMFernando-NOAA/global-workflow/commit/2816c3b69d87425c538baa1215ba29719bdcde47)
- This feature adds an archive task to GEFS system to archive files in
HPSSARCH and LOCALARCH.
  Resolves #2698
  Refs #2816 #2772 #832
---------

Co-authored-by: David Huber <david.huber@noaa.gov>
---
 parm/archive/gefs_extracted_atmos.yaml.j2 | 86 +++++++++++++++++++++++
 parm/archive/gefs_extracted_ice.yaml.j2   | 33 +++++++++
 parm/archive/gefs_extracted_ocean.yaml.j2 | 40 +++++++++++
 parm/archive/gefs_extracted_wave.yaml.j2  | 51 ++++++++++++++
 parm/archive/master_gefs.yaml.j2          | 12 ++++
 parm/config/gefs/yaml/defaults.yaml       |  1 -
 parm/config/gfs/config.resources          | 11 +--
 parm/config/gfs/config.resources.GAEA     |  5 ++
 parm/config/gfs/config.resources.HERA     |  5 ++
 parm/config/gfs/config.resources.JET      |  5 ++
 parm/config/gfs/config.resources.ORION    |  6 ++
 parm/config/gfs/config.resources.S4       |  6 ++
 scripts/exglobal_archive.py               |  5 +-
 ush/python/pygfs/task/archive.py          |  3 -
 workflow/applications/gefs.py             |  4 +-
 workflow/rocoto/gefs_tasks.py             | 30 ++++++--
 16 files changed, 286 insertions(+), 17 deletions(-)
 create mode 100644 parm/archive/gefs_extracted_atmos.yaml.j2
 create mode 100644 parm/archive/gefs_extracted_ice.yaml.j2
 create mode 100644 parm/archive/gefs_extracted_ocean.yaml.j2
 create mode 100644 parm/archive/gefs_extracted_wave.yaml.j2
 create mode 100644 parm/archive/master_gefs.yaml.j2

diff --git a/parm/archive/gefs_extracted_atmos.yaml.j2 b/parm/archive/gefs_extracted_atmos.yaml.j2
new file mode 100644
index 0000000000..7ceba551bf
--- /dev/null
+++ b/parm/archive/gefs_extracted_atmos.yaml.j2
@@ -0,0 +1,86 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+{% set head = RUN + ".t" + cycle_HH + "z." %}
+
+gefs_atmos:
+    name: "GEFS_ATMOS"
+    target: "{{ ATARDIR }}/{{ cycle_YMDH }}/gefs_atmos.tar"
+    required:
+#select mem%03d and ensstat files required
+{% set members = ["ensstat"] %}
+{% for mem_nm in range(0, NMEM_ENS + 1) %}
+    {% do members.append("mem" ~ '%03d' % mem_nm ) %}
+{% endfor %}
+
+{% if REPLAY_ICS %}
+    {% set ofst_hr = OFFSET_START_HOUR %}
+{% else %}
+    {% set ofst_hr = FHMIN_GFS %}
+{% endif %}
+
+{% for mem in members %}
+    {% for res in ['0p25', '0p50', '1p00'] %}
+        {% set tmpl_dict = ({ '${ROTDIR}':ROTDIR,
+                              '${RUN}':RUN,
+                              '${YMD}':cycle_YMD,
+                              '${HH}':cycle_HH,
+                              '${GRID}':res,
+                              '${MEMDIR}':mem }) %}
+
+        {% set COMIN_ATMOS_GRIB = COM_ATMOS_GRIB_GRID_TMPL | replace_tmpl(tmpl_dict) %}
+
+# Select pgrb and grib files to copy to the atardir
+        {% if path_exists(COMIN_ATMOS_GRIB) %}
+            {% if FHMAX_HF_GFS  == 0 %}
+                {% for fhr in range(ofst_hr, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
+                    {% if mem=="ensstat" %}
+                        {% set file_name = head ~ "mean.pres_." ~ res ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2" %}
+                        {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                        - "{{ file_path | relpath(ROTDIR)}}"
+                    {% else %}
+                        {% set file_name = head ~ "pgrb2." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                        {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                        - "{{ file_path | relpath(ROTDIR)}}"
+                        {% set file_name = head ~ "pgrb2b." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                        {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                        - "{{ file_path | relpath(ROTDIR)}}"
+                    {% endif %}
+                {% endfor %}
+            {% else %}
+                 {% if res == "0p25" %}
+                    {% for fhr in range(ofst_hr, FHMAX_HF_GFS + FHOUT_HF_GFS, FHOUT_HF_GFS) %}
+                        {% if mem=="ensstat" %}
+                            {% set file_name = head ~ "mean.pres_." ~ res ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2" %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                        {% else %}
+                            {% set file_name = head ~ "pgrb2." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                            {% set file_name = head ~ "pgrb2b." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                        {% endif %}
+                    {% endfor %}
+                {% endif %}
+                {% if res == "0p50" %}
+                    {% for fhr in range(FHMAX_HF_GFS + FHOUT_GFS, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
+                        {% if mem=="ensstat" %}
+                            {% set file_name = head ~ "mean.pres_." ~ res ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2" %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                        {% else %}
+                            {% set file_name = head ~ "pgrb2." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                            {% set file_name = head ~ "pgrb2b." ~ res ~ ".f" ~ '%03d'|format(fhr) %}
+                            {% set file_path = COMIN_ATMOS_GRIB ~ "/" ~ file_name %}
+                            - "{{ file_path | relpath(ROTDIR)}}"
+                        {% endif %}
+                    {% endfor %}
+                {% endif %}
+            {% endif %}
+        {% endif %}
+    {% endfor %}
+{% endfor %}
diff --git a/parm/archive/gefs_extracted_ice.yaml.j2 b/parm/archive/gefs_extracted_ice.yaml.j2
new file mode 100644
index 0000000000..786d502f23
--- /dev/null
+++ b/parm/archive/gefs_extracted_ice.yaml.j2
@@ -0,0 +1,33 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+{% set head = RUN + ".ice.t" + cycle_HH + "z." %}
+
+gefs_ice:
+    name: "GEFS_ICE"
+    target: "{{ ATARDIR }}/{{ cycle_YMDH }}/gefs_ice.tar"
+    required:
+#select mem%03d and ensstat files required
+{% set members = [] %}
+{% for mem_nm in range(0, NMEM_ENS + 1) %}
+    {% do members.append("mem" ~ '%03d' % mem_nm ) %}
+{% endfor %}
+
+{% for mem in members %}
+    {% set tmpl_dict = ({ '${ROTDIR}':ROTDIR,
+                          '${RUN}':RUN,
+                          '${YMD}':cycle_YMD,
+                          '${HH}':cycle_HH,
+                          '${MEMDIR}':mem }) %}
+
+    {% set COMIN_ICE_HISTORY = COM_ICE_HISTORY_TMPL | replace_tmpl(tmpl_dict) %}
+
+# Select netcdf files to copy to the atardir
+    {% if path_exists(COMIN_ICE_HISTORY) %}
+        {% for fhr in range(FHMIN_GFS + FHOUT_ICE_GFS, FHMAX_GFS + FHOUT_ICE_GFS, FHOUT_ICE_GFS) %}
+            {% set file_name = head ~ FHOUT_ICE_GFS ~ "hr_avg" ~ ".f" ~ '%03d'|format(fhr) ~ ".nc" %}
+            {% set file_path = COMIN_ICE_HISTORY ~ "/" ~ file_name %}
+            - "{{ file_path | relpath(ROTDIR)}}"
+        {% endfor %}
+    {% endif %}
+{% endfor %}
diff --git a/parm/archive/gefs_extracted_ocean.yaml.j2 b/parm/archive/gefs_extracted_ocean.yaml.j2
new file mode 100644
index 0000000000..e5e3b36e3b
--- /dev/null
+++ b/parm/archive/gefs_extracted_ocean.yaml.j2
@@ -0,0 +1,40 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+{% set head = RUN + ".ocean.t" + cycle_HH + "z." %}
+
+gefs_ocean:
+    name: "GEFS_OCEAN"
+    target: "{{ ATARDIR }}/{{ cycle_YMDH }}/gefs_ocean.tar"
+    required:
+#select mem%03d and ensstat files required
+{% set members = [] %}
+{% for mem_nm in range(0, NMEM_ENS + 1) %}
+    {% do members.append("mem" ~ '%03d' % mem_nm ) %}
+{% endfor %}
+
+{% if OCNRES == "025" %}
+    {% set res = "1p00" %}
+{% else %}
+    {% set res = (OCNRES|string())[0] ~ "p" ~ (OCNRES|string())[-2:] %}
+{% endif %}
+
+{% for mem in members %}
+    {% set tmpl_dict = ({ '${ROTDIR}':ROTDIR,
+                          '${RUN}':RUN,
+                          '${YMD}':cycle_YMD,
+                          '${HH}':cycle_HH,
+                          '${MEMDIR}':mem }) %}
+
+    {% set COMIN_OCEAN_NETCDF = COM_OCEAN_NETCDF_TMPL | replace_tmpl(tmpl_dict) %}
+
+    # Select netcdf files to copy to the atardir
+    {% set netcdf_grid_dir = COMIN_OCEAN_NETCDF ~ "/" ~ res %}
+    {% if path_exists(netcdf_grid_dir) %}
+        {% for fhr in range(FHMIN_GFS + FHOUT_OCN_GFS, FHMAX_GFS + FHOUT_OCN_GFS, FHOUT_OCN_GFS) %}
+            {% set file_name = head ~ res ~ ".f" ~ '%03d'|format(fhr) ~ ".nc" %}
+            {% set file_path = netcdf_grid_dir ~ "/" ~ file_name %}
+            - "{{ file_path | relpath(ROTDIR)}}"
+        {% endfor %}
+    {% endif %}
+{% endfor %}
diff --git a/parm/archive/gefs_extracted_wave.yaml.j2 b/parm/archive/gefs_extracted_wave.yaml.j2
new file mode 100644
index 0000000000..e0aa07c816
--- /dev/null
+++ b/parm/archive/gefs_extracted_wave.yaml.j2
@@ -0,0 +1,51 @@
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+{% set head = RUN + "wave.t" + cycle_HH + "z." %}
+
+gefs_wave:
+    name: "GEFS_WAVE"
+    target: "{{ ATARDIR }}/{{ cycle_YMDH }}/gefs_wave.tar"
+    required:
+{% if REPLAY_ICS %}
+    {% set ofst_hr = OFFSET_START_HOUR %}
+{% else %}
+    {% set ofst_hr = FHMIN_GFS %}
+{% endif %}
+
+{% set res = (waveGRD[-3:])[0] ~ "p" ~ (waveGRD[-3:])[-2:] %}
+
+#select mem%03d and ensstat files required
+{% set members = [] %}
+{% for mem_nm in range(0, NMEM_ENS + 1) %}
+    {% do members.append("mem" ~ '%03d' % mem_nm ) %}
+{% endfor %}
+
+{% for mem in members %}
+    {% set tmpl_dict = ({ '${ROTDIR}':ROTDIR,
+                          '${RUN}':RUN,
+                          '${YMD}':cycle_YMD,
+                          '${HH}':cycle_HH,
+                          '${MEMDIR}':mem }) %}
+
+    {% set COMIN_WAVE_GRID = COM_WAVE_GRID_TMPL | replace_tmpl(tmpl_dict) %}
+    # Select grib2 files to copy to the atardir
+    {% if path_exists(COMIN_WAVE_GRID) %}
+        {% for fhr in range(ofst_hr, FHMAX_GFS + FHOUT_WAV, FHOUT_WAV) %}
+            {% set file_name = head ~ "global." ~ res ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2" %}
+            {% set file_path = COMIN_WAVE_GRID ~ "/" ~ file_name %}
+        - "{{ file_path | relpath(ROTDIR)}}"
+        {% endfor %}
+    {% endif %}
+
+    {% set COMIN_WAVE_STATION = COM_WAVE_STATION_TMPL | replace_tmpl(tmpl_dict) %}
+    # Select station files to copy to the atardir
+    {% if path_exists(COMIN_WAVE_STATION) %}
+        {% set file_path = COMIN_WAVE_STATION ~ "/" ~ RUN ~ "wave.t" ~ cycle_HH ~ "z.spec_tar.gz" %}
+        - "{{ file_path | relpath(ROTDIR)}}"
+        {% set file_path = COMIN_WAVE_STATION ~ "/" ~ RUN ~ "wave.t" ~ cycle_HH ~ "z.cbull_tar" %}
+        - "{{ file_path | relpath(ROTDIR)}}"
+        {% set file_path = COMIN_WAVE_STATION ~ "/" ~ RUN ~ "wave.t" ~ cycle_HH ~ "z.bull_tar" %}
+        - "{{ file_path | relpath(ROTDIR)}}"
+    {% endif %}
+{% endfor %}
diff --git a/parm/archive/master_gefs.yaml.j2 b/parm/archive/master_gefs.yaml.j2
new file mode 100644
index 0000000000..5dc046dcfd
--- /dev/null
+++ b/parm/archive/master_gefs.yaml.j2
@@ -0,0 +1,12 @@
+# Set variables/lists needed to parse the gefs templates
+{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set cycle_YMD = current_cycle | to_YMD %}
+{% set cycle_YMDH = current_cycle | to_YMDH %}
+
+datasets:
+{% filter indent(width=4) %}
+    {% include "gefs_extracted_atmos.yaml.j2" %}
+    {% include "gefs_extracted_ocean.yaml.j2" %}
+    {% include "gefs_extracted_ice.yaml.j2" %}
+    {% include "gefs_extracted_wave.yaml.j2" %}
+{% endfilter %}
diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
index 5ecf690e18..382e60ee12 100644
--- a/parm/config/gefs/yaml/defaults.yaml
+++ b/parm/config/gefs/yaml/defaults.yaml
@@ -14,5 +14,4 @@ base:
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"
-  HPSSARCH: "NO"
   LOCALARCH: "NO"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index afc5939fcd..0479543ebc 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -38,6 +38,7 @@ echo "BEGIN: config.resources"
 case ${machine} in
   "WCOSS2")
               max_tasks_per_node=128
+              # WCOSS2 nodes have 512GB of RAM, but only 500GB are reservable
               # shellcheck disable=SC2034
               mem_node_max="500GB"
     ;;
@@ -54,12 +55,12 @@ case ${machine} in
   "ORION")
               max_tasks_per_node=40
               # shellcheck disable=SC2034
-              mem_node_max="192GB"
+              mem_node_max="180GB"
     ;;
   "HERCULES")
               max_tasks_per_node=80
               # shellcheck disable=SC2034
-              mem_node_max="512GB"
+              mem_node_max="500GB"
     ;;
   "JET")
     case ${PARTITION_BATCH} in
@@ -145,10 +146,10 @@ export max_tasks_per_node
 case ${step} in
   "prep")
     walltime='00:30:00'
-    ntasks=4
-    tasks_per_node=2
+    ntasks=14
+    tasks_per_node=14
     threads_per_task=1
-    memory="40GB"
+    memory="${mem_node_max}"
     ;;
 
   "prepsnowobs")
diff --git a/parm/config/gfs/config.resources.GAEA b/parm/config/gfs/config.resources.GAEA
index a4d4ddfece..c50601da00 100644
--- a/parm/config/gfs/config.resources.GAEA
+++ b/parm/config/gfs/config.resources.GAEA
@@ -3,6 +3,11 @@
 # Gaea-specific job resources
 
 case ${step} in
+  "prep")
+    # Run on two nodes (requires ~400GB total)
+    tasks_per_node=7
+    ;;
+
   "eobs")
     # The number of tasks and cores used must be the same for eobs
     # See https://github.com/NOAA-EMC/global-workflow/issues/2092 for details
diff --git a/parm/config/gfs/config.resources.HERA b/parm/config/gfs/config.resources.HERA
index d1b09fcc32..ac3067d9f9 100644
--- a/parm/config/gfs/config.resources.HERA
+++ b/parm/config/gfs/config.resources.HERA
@@ -3,6 +3,11 @@
 # Hera-specific job resources
 
 case ${step} in
+  "prep")
+    # Run on 7 nodes for memory requirement
+    tasks_per_node=2
+    ;;
+
   "anal")
     if [[ "${CASE}" == "C384" ]]; then
       export ntasks_gdas=270
diff --git a/parm/config/gfs/config.resources.JET b/parm/config/gfs/config.resources.JET
index 47b953c0f4..bbd308f439 100644
--- a/parm/config/gfs/config.resources.JET
+++ b/parm/config/gfs/config.resources.JET
@@ -3,6 +3,11 @@
 # Jet-specific job resources
 
 case ${step} in
+  "prep")
+    # Run on 7 nodes for memory requirement
+    tasks_per_node=2
+    ;;
+
   "anal")
     if [[ "${CASE}" == "C384" ]]; then
       export ntasks=270
diff --git a/parm/config/gfs/config.resources.ORION b/parm/config/gfs/config.resources.ORION
index 6b42d780d4..d761df7b73 100644
--- a/parm/config/gfs/config.resources.ORION
+++ b/parm/config/gfs/config.resources.ORION
@@ -3,6 +3,12 @@
 # Orion-specific job resources
 
 case ${step} in
+  "prep")
+    # Run on 2 nodes for memory requirement
+    # This may not be enough and may need to run on more nodes.
+    export tasks_per_node=7
+    ;;
+
   "anal")
     # TODO:
     # On Orion, after Rocky 9 upgrade, GSI performance is degraded.
diff --git a/parm/config/gfs/config.resources.S4 b/parm/config/gfs/config.resources.S4
index 817494c7cd..fa64068e81 100644
--- a/parm/config/gfs/config.resources.S4
+++ b/parm/config/gfs/config.resources.S4
@@ -3,6 +3,12 @@
 # S4-specific job resources
 
 case ${step} in
+  "prep")
+    # Run on two nodes for memory requirement
+    # This may not be enough memory.  Decrease tasks/node to 2 if necessary.
+    tasks_per_node=7
+    ;;
+
   "anal")
     case ${CASE} in
       "C384")
diff --git a/scripts/exglobal_archive.py b/scripts/exglobal_archive.py
index 793fa1c1ac..4ee9e5ed0e 100755
--- a/scripts/exglobal_archive.py
+++ b/scripts/exglobal_archive.py
@@ -30,8 +30,9 @@ def main():
             'FHOUT_HF_WAV', 'FHMAX_WAV', 'FHMAX_HF_WAV', 'FHMAX_WAV_GFS',
             'restart_interval_gdas', 'restart_interval_gfs',
             'AERO_ANL_RUN', 'AERO_FCST_RUN', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
-            'NMEM_ENS', 'DO_JEDIATMVAR', 'DO_VRFY_OCEANDA', 'FHMAX_FITS',
-            'IAUFHRS', 'DO_FIT2OBS', 'NET']
+            'NMEM_ENS', 'DO_JEDIATMVAR', 'DO_VRFY_OCEANDA', 'FHMAX_FITS', 'waveGRD',
+            'IAUFHRS', 'DO_FIT2OBS', 'NET', 'FHOUT_HF_GFS', 'FHMAX_HF_GFS', 'REPLAY_ICS',
+            'OFFSET_START_HOUR']
 
     archive_dict = AttrDict()
     for key in keys:
diff --git a/ush/python/pygfs/task/archive.py b/ush/python/pygfs/task/archive.py
index 14cd015601..d138474e9a 100644
--- a/ush/python/pygfs/task/archive.py
+++ b/ush/python/pygfs/task/archive.py
@@ -114,9 +114,6 @@ def configure(self, arch_dict: Dict[str, Any]) -> (Dict[str, Any], List[Dict[str
             self.tar_cmd = ""
             return arcdir_set, []
 
-        if arch_dict.NET == "gefs":
-            raise NotImplementedError("GEFS archiving is not yet implemented!")
-
         master_yaml = "master_" + arch_dict.RUN + ".yaml.j2"
 
         parsed_sets = parse_j2yaml(os.path.join(archive_parm, master_yaml),
diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py
index afb4072596..c15786a2e8 100644
--- a/workflow/applications/gefs.py
+++ b/workflow/applications/gefs.py
@@ -80,8 +80,8 @@ def get_task_names(self):
             tasks += ['wavepostpnt']
 
         if self.do_extractvars:
-            tasks += ['extractvars']
+            tasks += ['extractvars', 'arch']
 
-        tasks += ['arch', 'cleanup']
+        tasks += ['cleanup']
 
         return {f"{self.run}": tasks}
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index 3b72677a58..e214bb8c19 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -560,10 +560,32 @@ def arch(self):
 
     def cleanup(self):
         deps = []
-        dep_dict = {'type': 'task', 'name': 'arch'}
-        deps.append(rocoto.add_dependency(dep_dict))
-
-        dependencies = rocoto.create_dependency(dep=deps)
+        if self.app_config.do_extractvars:
+            dep_dict = {'type': 'task', 'name': 'arch'}
+            deps.append(rocoto.add_dependency(dep_dict))
+            dependencies = rocoto.create_dependency(dep=deps)
+        else:
+            dep_dict = {'type': 'metatask', 'name': 'atmos_prod'}
+            deps.append(rocoto.add_dependency(dep_dict))
+            dep_dict = {'type': 'metatask', 'name': 'atmos_ensstat'}
+            deps.append(rocoto.add_dependency(dep_dict))
+            if self.app_config.do_ice:
+                dep_dict = {'type': 'metatask', 'name': 'ice_prod'}
+                deps.append(rocoto.add_dependency(dep_dict))
+            if self.app_config.do_ocean:
+                dep_dict = {'type': 'metatask', 'name': 'ocean_prod'}
+                deps.append(rocoto.add_dependency(dep_dict))
+            if self.app_config.do_wave:
+                dep_dict = {'type': 'metatask', 'name': 'wave_post_grid'}
+                deps.append(rocoto.add_dependency(dep_dict))
+                dep_dict = {'type': 'metatask', 'name': 'wave_post_pnt'}
+                deps.append(rocoto.add_dependency(dep_dict))
+                if self.app_config.do_wave_bnd:
+                    dep_dict = {'type': 'metatask', 'name': 'wave_post_bndpnt'}
+                    deps.append(rocoto.add_dependency(dep_dict))
+                    dep_dict = {'type': 'metatask', 'name': 'wave_post_bndpnt_bull'}
+                    deps.append(rocoto.add_dependency(dep_dict))
+            dependencies = rocoto.create_dependency(dep=deps, dep_condition='and')
 
         resources = self.get_resource('cleanup')
         task_name = 'cleanup'

From a694cf148a639dac524cce5ad6d93d81aebb8a47 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@gmail.com>
Date: Thu, 26 Sep 2024 11:05:05 -0400
Subject: [PATCH 15/21] Move the variational scripts to this repository (#2920)

This PR "moves and refactors" the variational DA `exscripts` that were
in the `GDASapp` to this repository. The ens. var. feature will be
replicated/moved in a subsequent PR.

Issues have been opened to address reviewer comments at a later time in separate PRs
---------

Co-authored-by: Kate.Friedman <Kate.Friedman@noaa.gov>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 ci/cases/gfsv17/ocnanal.yaml                  |   2 +-
 env/CONTAINER.env                             |   4 +-
 env/HERA.env                                  |  10 +-
 env/HERCULES.env                              |   8 +-
 env/JET.env                                   |   6 +-
 env/ORION.env                                 |   9 +-
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT        |  58 ---
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST         |  49 --
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY         |   2 +-
 ...RUN => JGLOBAL_MARINE_ANALYSIS_CHECKPOINT} |  13 +-
 jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE         |  43 ++
 ...REP => JGLOBAL_MARINE_ANALYSIS_INITIALIZE} |  36 +-
 jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL      |  38 ++
 jobs/JGLOBAL_MARINE_BMAT                      |  16 +-
 .../{ocnanalrun.sh => marineanlchkpt.sh}      |   4 +-
 .../{ocnanalchkpt.sh => marineanlfinal.sh}    |   4 +-
 .../{ocnanalprep.sh => marineanlinit.sh}      |   2 +-
 .../{ocnanalpost.sh => marineanlvar.sh}       |   4 +-
 parm/archive/gdas.yaml.j2                     |   8 +-
 parm/config/gefs/config.base                  |   3 +
 parm/config/gfs/config.base                   |   3 +
 parm/config/gfs/config.marineanl              |  20 +
 parm/config/gfs/config.marineanlchkpt         |  11 +
 parm/config/gfs/config.marineanlfinal         |  10 +
 parm/config/gfs/config.marineanlinit          |  10 +
 parm/config/gfs/config.marineanlvar           |  11 +
 parm/config/gfs/config.marinebmat             |   8 +
 parm/config/gfs/config.ocnanal                |  20 -
 parm/config/gfs/config.ocnanalchkpt           |  11 -
 parm/config/gfs/config.ocnanalpost            |  10 -
 parm/config/gfs/config.ocnanalprep            |  10 -
 parm/config/gfs/config.ocnanalrun             |  11 -
 parm/config/gfs/config.prepoceanobs           |   2 +-
 parm/config/gfs/config.resources              |  10 +-
 parm/config/gfs/yaml/defaults.yaml            |   4 +-
 .../exglobal_marine_analysis_checkpoint.py    |  29 ++
 scripts/exglobal_marine_analysis_finalize.py  |  27 +
 .../exglobal_marine_analysis_initialize.py    |  24 +
 .../exglobal_marine_analysis_variational.py   |  24 +
 sorc/gdas.cd                                  |   2 +-
 sorc/link_workflow.sh                         |   2 +-
 ush/python/pygfs/task/marine_analysis.py      | 485 ++++++++++++++++++
 ush/python/pygfs/task/marine_bmat.py          |  78 ++-
 ush/python/pygfs/utils/marine_da_utils.py     | 122 ++++-
 workflow/applications/gfs_cycled.py           |   8 +-
 workflow/hosts/awspw.yaml                     |   1 +
 workflow/hosts/azurepw.yaml                   |   1 +
 workflow/hosts/gaea.yaml                      |   1 +
 workflow/hosts/googlepw.yaml                  |   1 +
 workflow/hosts/hera.yaml                      |   1 +
 workflow/hosts/hercules.yaml                  |   1 +
 workflow/hosts/jet.yaml                       |   1 +
 workflow/hosts/orion.yaml                     |   1 +
 workflow/hosts/s4.yaml                        |   1 +
 workflow/hosts/wcoss2.yaml                    |   1 +
 workflow/rocoto/gfs_tasks.py                  |  44 +-
 workflow/rocoto/tasks.py                      |   2 +-
 57 files changed, 993 insertions(+), 334 deletions(-)
 delete mode 100755 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
 delete mode 100755 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN => JGLOBAL_MARINE_ANALYSIS_CHECKPOINT} (65%)
 create mode 100755 jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP => JGLOBAL_MARINE_ANALYSIS_INITIALIZE} (60%)
 create mode 100755 jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
 rename jobs/rocoto/{ocnanalrun.sh => marineanlchkpt.sh} (82%)
 rename jobs/rocoto/{ocnanalchkpt.sh => marineanlfinal.sh} (82%)
 rename jobs/rocoto/{ocnanalprep.sh => marineanlinit.sh} (89%)
 rename jobs/rocoto/{ocnanalpost.sh => marineanlvar.sh} (82%)
 create mode 100644 parm/config/gfs/config.marineanl
 create mode 100644 parm/config/gfs/config.marineanlchkpt
 create mode 100644 parm/config/gfs/config.marineanlfinal
 create mode 100644 parm/config/gfs/config.marineanlinit
 create mode 100644 parm/config/gfs/config.marineanlvar
 delete mode 100644 parm/config/gfs/config.ocnanal
 delete mode 100644 parm/config/gfs/config.ocnanalchkpt
 delete mode 100644 parm/config/gfs/config.ocnanalpost
 delete mode 100644 parm/config/gfs/config.ocnanalprep
 delete mode 100644 parm/config/gfs/config.ocnanalrun
 create mode 100755 scripts/exglobal_marine_analysis_checkpoint.py
 create mode 100755 scripts/exglobal_marine_analysis_finalize.py
 create mode 100755 scripts/exglobal_marine_analysis_initialize.py
 create mode 100755 scripts/exglobal_marine_analysis_variational.py
 create mode 100644 ush/python/pygfs/task/marine_analysis.py

diff --git a/ci/cases/gfsv17/ocnanal.yaml b/ci/cases/gfsv17/ocnanal.yaml
index 483250db10..d559f544e4 100644
--- a/ci/cases/gfsv17/ocnanal.yaml
+++ b/ci/cases/gfsv17/ocnanal.yaml
@@ -16,7 +16,7 @@ base:
   FHMAX_GFS: 240
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
 
-ocnanal:
+marineanl:
   SOCA_INPUT_FIX_DIR: {{ HOMEgfs }}/fix/gdas/soca/1440x1080x75/soca
   SOCA_OBS_LIST: {{ HOMEgfs }}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
   SOCA_NINNER: 100
diff --git a/env/CONTAINER.env b/env/CONTAINER.env
index c40543794b..ba01fcf0dd 100755
--- a/env/CONTAINER.env
+++ b/env/CONTAINER.env
@@ -26,7 +26,7 @@ ulimit -s unlimited
 ulimit -a
 
 
-if [ "${step}" = "ocnanalrun" ]; then
+if [ "${step}" = "marineanlvar" ]; then
     export NTHREADS_OCNANAL=1
-    export APRUN_OCNANAL="${launcher} -n 2"
+    export APRUN_MARINEANLVAR="${launcher} -n 2"
 fi
diff --git a/env/HERA.env b/env/HERA.env
index 0d77547b5b..09743967b5 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -138,17 +138,15 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
-    export APRUN_OCNANAL="${APRUN_default}"
-
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
-
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 
diff --git a/env/HERCULES.env b/env/HERCULES.env
index 0138e33645..9ec112c699 100755
--- a/env/HERCULES.env
+++ b/env/HERCULES.env
@@ -133,10 +133,10 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN_default}"
  ;;
- "ocnanalrun")
+ "marineanlvar")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
  ;;
 "ocnanalecen")
 
@@ -148,12 +148,12 @@ case ${step} in
     [[ ${NTHREADS_OCNANALECEN} -gt ${max_threads_per_task} ]] && export NTHREADS_OCNANALECEN=${max_threads_per_task}
     export APRUN_OCNANALECEN="${launcher} -n ${ntasks_ocnanalecen} --cpus-per-task=${NTHREADS_OCNANALECEN}"
 ;;
- "ocnanalchkpt")
+ "marineanlchkpt")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
  ;;
  "anal" | "analcalc")
 
diff --git a/env/JET.env b/env/JET.env
index f2b018d2d7..dbc249d4d6 100755
--- a/env/JET.env
+++ b/env/JET.env
@@ -69,7 +69,7 @@ elif [[ "${step}" = "atmensanlsol" ]]; then
 
     export NTHREADS_ATMENSANLSOL=${NTHREADSmax}
     export APRUN_ATMENSANLSOL="${APRUN_default}"
-	
+
 elif [[ "${step}" = "atmensanlletkf" ]]; then
 
     export NTHREADS_ATMENSANLLETKF=${NTHREADSmax}
@@ -121,10 +121,10 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 
diff --git a/env/ORION.env b/env/ORION.env
index e8c1bcbf58..1bc7eb60d4 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -130,18 +130,19 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export NTHREADS_MARINEBMAT=${NTHREADSmax}
     export APRUN_MARINEBMAT="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    export APRUN_OCNANAL="${APRUN_default}"
+    export APRUN_MARINEANLVAR="${APRUN_default}"
 
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
+
+    export APRUN_MARINEANLCHKPT="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
deleted file mode 100755
index 875fe9d0ee..0000000000
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/bash
-source "${HOMEgfs}/ush/preamble.sh"
-export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnanalchkpt"
-
-
-##############################################
-# Set variables used in the script
-##############################################
-# Ignore possible spelling error (nothing is misspelled)
-# shellcheck disable=SC2153
-GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export GDATE
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP=${GDUMP:-"gdas"}
-
-export GPREFIX="${GDUMP}.t${gcyc}z."
-# Ignore possible spelling error (nothing is misspelled)
-# shellcheck disable=SC2153
-export APREFIX="${RUN}.t${cyc}z."
-
-# Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS
-
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
-
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-###############################################################
-# Run relevant script
-
-EXSCRIPT=${GDASOCNCHKPTSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_chkpt.sh}
-${EXSCRIPT}
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
-##############################################
-# End JOB SPECIFIC work
-##############################################
-
-##############################################
-# Final processing
-##############################################
-if [[ -e "${pgmout}" ]] ; then
-  cat "${pgmout}"
-fi
-
-##########################################
-# Do not remove the Temporary working directory (do this in POST)
-##########################################
-cd "${DATAROOT}" || exit 1
-
-exit 0
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
deleted file mode 100755
index 00597f14f8..0000000000
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/bin/bash
-source "${HOMEgfs}/ush/preamble.sh"
-export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
-
-
-##############################################
-# Set variables used in the script
-##############################################
-# TODO remove this CDUMP declaration when the GDAS script
-#      exgdas_global_marine_analysis_post.py is updated to look for RUN instead
-#      of CDUMP.
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export CDATE=${CDATE:-${PDY}${cyc}}
-export GDUMP=${GDUMP:-"gdas"}
-
-# Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OCEAN_ANALYSIS COM_ICE_ANALYSIS COM_ICE_RESTART
-
-mkdir -p "${COM_OCEAN_ANALYSIS}"
-mkdir -p "${COM_ICE_ANALYSIS}"
-mkdir -p "${COM_ICE_RESTART}"
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-# Add UFSDA to PYTHONPATH
-ufsdaPATH="${HOMEgfs}/sorc/gdas.cd/ush/"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${ufsdaPATH}"
-export PYTHONPATH
-
-###############################################################
-# Run relevant script
-###############################################################
-
-EXSCRIPT=${GDASOCNPOSTPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_post.py}
-${EXSCRIPT}
-status=$?
-[[ ${status} -ne 0 ]] && exit "${status}"
-
-##########################################
-# Remove the Temporary working directory
-##########################################
-cd "${DATAROOT}" || exit 1
-[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
-
-exit 0
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
index 0d90c46184..31df1e45c7 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
@@ -1,6 +1,6 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base ocnanal marineanlinit"
 
 
 ##############################################
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
similarity index 65%
rename from jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
rename to jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
index 5871497223..8cd7b1ab7c 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
@@ -1,8 +1,9 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl marineanlchkpt"
 
 
 ##############################################
@@ -13,11 +14,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalr
 # Begin JOB SPECIFIC work
 ##############################################
 
-
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNRUNSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_run.sh}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_checkpoint.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -33,9 +33,4 @@ if [[ -e "${pgmout}" ]] ; then
   cat "${pgmout}"
 fi
 
-##########################################
-# Do not remove the Temporary working directory (do this in POST)
-##########################################
-cd "${DATAROOT}" || exit 1
-
 exit 0
diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
new file mode 100755
index 0000000000..2614639184
--- /dev/null
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
@@ -0,0 +1,43 @@
+#!/bin/bash
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlfinal" -c "base marineanl marineanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL
+
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+   COMOUT_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \
+   COMOUT_ICE_ANALYSIS:COM_ICE_ANALYSIS_TMPL \
+   COMOUT_ICE_RESTART:COM_ICE_RESTART_TMPL
+
+mkdir -p "${COMOUT_OCEAN_ANALYSIS}"
+mkdir -p "${COMOUT_ICE_ANALYSIS}"
+mkdir -p "${COMOUT_ICE_RESTART}"
+
+###############################################################
+# Run relevant script
+###############################################################
+
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_finalize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+
+exit 0
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
similarity index 60%
rename from jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
rename to jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
index 664df3aad6..eb167af94d 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
@@ -1,7 +1,9 @@
 #!/bin/bash
+
 source "${HOMEgfs}/ush/preamble.sh"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base marineanl marineanlinit"
 
 
 ##############################################
@@ -10,42 +12,30 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanal
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export GDATE
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
+gPDY=${GDATE:0:8}
+gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 
-export OPREFIX="${RUN}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${RUN}.t${cyc}z."
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
 
 # Generate COM variables from templates
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-   COM_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
-   COM_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
-   COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
+   COMIN_OCEAN_HISTORY_PREV:COM_OCEAN_HISTORY_TMPL \
+   COMIN_ICE_HISTORY_PREV:COM_ICE_HISTORY_TMPL \
+   COMIN_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
 
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
    COMIN_OCEAN_BMATRIX:COM_OCEAN_BMATRIX_TMPL \
    COMIN_ICE_BMATRIX:COM_ICE_BMATRIX_TMPL
 
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
-# Add UFSDA to PYTHONPATH
-ufsdaPATH="${HOMEgfs}/sorc/gdas.cd/ush/"
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python$(detect_py_ver)/"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${ufsdaPATH}:${pyiodaPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNPREPPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_prep.py}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_initialize.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
new file mode 100755
index 0000000000..7780353294
--- /dev/null
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
@@ -0,0 +1,38 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlvar" -c "base marineanl marineanlvar"
+
+##############################################
+# Set variables used in the script
+##############################################
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASMARINERUNSH:-${SCRgfs}/exglobal_marine_analysis_variational.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/JGLOBAL_MARINE_BMAT b/jobs/JGLOBAL_MARINE_BMAT
index 3dacec9278..3189df0463 100755
--- a/jobs/JGLOBAL_MARINE_BMAT
+++ b/jobs/JGLOBAL_MARINE_BMAT
@@ -2,17 +2,17 @@
 
 source "${HOMEgfs}/ush/preamble.sh"
 
-if (( 10#${ENSMEM:-0} > 0 )); then
-  export DATAjob="${DATAROOT}/${RUN}marinebmat.${PDY:-}${cyc}"
-  export DATA="${DATAjob}/${jobid}"
-  # Create the directory to hold ensemble perturbations
-  export DATAenspert="${DATAjob}/enspert"
-  if [[ ! -d "${DATAenspert}" ]]; then mkdir -p "${DATAenspert}"; fi
-fi
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/${jobid}"
+# Create the directory to hold ensemble perturbations
+export DATAens="${DATAjob}/ensdata"
+export DATAstaticb="${DATAjob}/staticb"
+if [[ ! -d "${DATAens}" ]]; then mkdir -p "${DATAens}"; fi
+if [[ ! -d "${DATAstaticb}" ]]; then mkdir -p "${DATAstaticb}"; fi
 
 # source config.base, config.ocnanal and config.marinebmat
 # and pass marinebmat to ${machine}.env
-source "${HOMEgfs}/ush/jjob_header.sh" -e "marinebmat" -c "base ocnanal marinebmat"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marinebmat" -c "base marineanl marinebmat"
 
 ##############################################
 # Set variables used in the script
diff --git a/jobs/rocoto/ocnanalrun.sh b/jobs/rocoto/marineanlchkpt.sh
similarity index 82%
rename from jobs/rocoto/ocnanalrun.sh
rename to jobs/rocoto/marineanlchkpt.sh
index 5f998af989..69e10a7fa8 100755
--- a/jobs/rocoto/ocnanalrun.sh
+++ b/jobs/rocoto/marineanlchkpt.sh
@@ -8,11 +8,11 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalrun"
+export job="marineanlchkpt"
 export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
 status=$?
 exit "${status}"
diff --git a/jobs/rocoto/ocnanalchkpt.sh b/jobs/rocoto/marineanlfinal.sh
similarity index 82%
rename from jobs/rocoto/ocnanalchkpt.sh
rename to jobs/rocoto/marineanlfinal.sh
index ae98bc8e88..8f0c8fa3a3 100755
--- a/jobs/rocoto/ocnanalchkpt.sh
+++ b/jobs/rocoto/marineanlfinal.sh
@@ -8,11 +8,11 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalchkpt"
+export job="marineanlfinal"
 export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
 status=$?
 exit "${status}"
diff --git a/jobs/rocoto/ocnanalprep.sh b/jobs/rocoto/marineanlinit.sh
similarity index 89%
rename from jobs/rocoto/ocnanalprep.sh
rename to jobs/rocoto/marineanlinit.sh
index 3830fe1c39..953fc0dcfd 100755
--- a/jobs/rocoto/ocnanalprep.sh
+++ b/jobs/rocoto/marineanlinit.sh
@@ -14,6 +14,6 @@ export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
 status=$?
 exit "${status}"
diff --git a/jobs/rocoto/ocnanalpost.sh b/jobs/rocoto/marineanlvar.sh
similarity index 82%
rename from jobs/rocoto/ocnanalpost.sh
rename to jobs/rocoto/marineanlvar.sh
index b99a4e05ca..35a21a2bcb 100755
--- a/jobs/rocoto/ocnanalpost.sh
+++ b/jobs/rocoto/marineanlvar.sh
@@ -8,11 +8,11 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalpost"
+export job="marineanlvar"
 export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+"${HOMEgfs}/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL"
 status=$?
 exit "${status}"
diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
index 56e47e595a..030678f31f 100644
--- a/parm/archive/gdas.yaml.j2
+++ b/parm/archive/gdas.yaml.j2
@@ -21,11 +21,11 @@ gdas:
         - "logs/{{ cycle_YMDH }}/{{ RUN }}atmanlupp.log"
             {% if DO_JEDIOCNVAR %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}prepoceanobs.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalprep.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlinit.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marinebmat.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalrun.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalpost.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalchkpt.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlvar.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlfinal.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlchkpt.log"
                 {% if DOHYBVAR %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalecen.log"
                 {% endif %}
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index 883957ed0c..a0bd8b3bd1 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -48,6 +48,9 @@ export NOSCRUB="@NOSCRUB@"
 # Base directories for various builds
 export BASE_GIT="@BASE_GIT@"
 
+# Base directory for staged data
+export BASE_DATA="@BASE_DATA@"
+
 # Toggle to turn on/off GFS downstream processing.
 export DO_BUFRSND="@DO_BUFRSND@"     # BUFR sounding products
 export DO_GEMPAK="@DO_GEMPAK@"       # GEMPAK products
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 27fcbdd055..7fa8245057 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -63,6 +63,9 @@ export NOSCRUB="@NOSCRUB@"
 # Base directories for various builds
 export BASE_GIT="@BASE_GIT@"
 
+# Base directory for staged data
+export BASE_DATA="@BASE_DATA@"
+
 # Toggle to turn on/off GFS downstream processing.
 export DO_GOES="@DO_GOES@"               # GOES products
 export DO_BUFRSND="@DO_BUFRSND@"         # BUFR sounding products
diff --git a/parm/config/gfs/config.marineanl b/parm/config/gfs/config.marineanl
new file mode 100644
index 0000000000..a19fc015e2
--- /dev/null
+++ b/parm/config/gfs/config.marineanl
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+########## config.marineanl ##########
+# configuration common to all ocean analysis tasks
+
+echo "BEGIN: config.marineanl"
+
+export MARINE_OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
+export MARINE_OBS_LIST_YAML=@SOCA_OBS_LIST@
+export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
+export SOCA_NINNER=@SOCA_NINNER@
+export DOMAIN_STACK_SIZE=116640000  #TODO: Make the stack size resolution dependent
+export SOCA_ENS_BKG_STAGE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_ens_bkg_stage.yaml.j2"
+export SOCA_FIX_YAML_TMPL="${PARMgfs}/gdas/soca/soca_fix_stage_${OCNRES}.yaml.j2"
+export MARINE_UTILITY_YAML_TMPL="${PARMgfs}/gdas/soca/soca_utils_stage.yaml.j2"
+export MARINE_ENSDA_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/ensda/stage_ens_mem.yaml.j2"
+export MARINE_DET_STAGE_BKG_YAML_TMPL="${PARMgfs}/gdas/soca/soca_det_bkg_stage.yaml.j2"
+export MARINE_JCB_GDAS_ALGO="${PARMgfs}/gdas/jcb-gdas/algorithm/marine"
+
+echo "END: config.marineanl"
diff --git a/parm/config/gfs/config.marineanlchkpt b/parm/config/gfs/config.marineanlchkpt
new file mode 100644
index 0000000000..7dd6ff79b2
--- /dev/null
+++ b/parm/config/gfs/config.marineanlchkpt
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+########## config.marineanlchkpt ##########
+# Marine Analysis specific
+
+echo "BEGIN: config.marineanlchkpt"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marineanlchkpt
+
+echo "END: config.marineanlchkpt"
diff --git a/parm/config/gfs/config.marineanlfinal b/parm/config/gfs/config.marineanlfinal
new file mode 100644
index 0000000000..ccde289088
--- /dev/null
+++ b/parm/config/gfs/config.marineanlfinal
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+########## config.marineanlfinal ##########
+# Post Ocn Analysis specific
+
+echo "BEGIN: config.marineanlfinal"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marineanlfinal
+echo "END: config.marineanlfinal"
diff --git a/parm/config/gfs/config.marineanlinit b/parm/config/gfs/config.marineanlinit
new file mode 100644
index 0000000000..01489fc0b8
--- /dev/null
+++ b/parm/config/gfs/config.marineanlinit
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+########## config.marineanlinit ##########
+# Pre Marine Analysis specific
+
+echo "BEGIN: config.marineanlinit"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marineanlinit
+echo "END: config.marineanlinit"
diff --git a/parm/config/gfs/config.marineanlvar b/parm/config/gfs/config.marineanlvar
new file mode 100644
index 0000000000..5ed6d444eb
--- /dev/null
+++ b/parm/config/gfs/config.marineanlvar
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+########## config.marineanlvar ##########
+# Marine Analysis specific
+
+echo "BEGIN: config.marineanlvar"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" marineanlvar
+
+echo "END: config.marineanlvar"
diff --git a/parm/config/gfs/config.marinebmat b/parm/config/gfs/config.marinebmat
index d88739dced..00352737d0 100644
--- a/parm/config/gfs/config.marinebmat
+++ b/parm/config/gfs/config.marinebmat
@@ -8,4 +8,12 @@ echo "BEGIN: config.marinebmat"
 # Get task specific resources
 . "${EXPDIR}/config.resources" marinebmat
 
+export BERROR_DIAGB_YAML="${PARMgfs}/gdas/soca/berror/soca_diagb.yaml.j2"
+export BERROR_VTSCALES_YAML="${PARMgfs}/gdas/soca/berror/soca_vtscales.yaml.j2"
+export BERROR_DIFFV_YAML="${PARMgfs}/gdas/soca/berror/soca_parameters_diffusion_vt.yaml.j2"
+export BERROR_HZSCALES_YAML="${PARMgfs}/gdas/soca/berror/soca_setcorscales.yaml"
+export BERROR_DIFFH_YAML="${PARMgfs}/gdas/soca/berror/soca_parameters_diffusion_hz.yaml.j2"
+export BERROR_ENS_RECENTER_YAML="${PARMgfs}/gdas/soca/berror/soca_ensb.yaml.j2"
+export BERROR_HYB_WEIGHTS_YAML="${PARMgfs}/gdas/soca/berror/soca_ensweights.yaml.j2"
+
 echo "END: config.marinebmat"
diff --git a/parm/config/gfs/config.ocnanal b/parm/config/gfs/config.ocnanal
deleted file mode 100644
index 4d58f2dedf..0000000000
--- a/parm/config/gfs/config.ocnanal
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanal ##########
-# configuration common to all ocean analysis tasks
-
-echo "BEGIN: config.ocnanal"
-
-export OBS_YAML_DIR="${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config"
-export OBS_LIST=@SOCA_OBS_LIST@  # TODO(GA): doesn't look necessary as is to have
-export OBS_YAML="${OBS_LIST}"    #           OBS_LIST and OBS_YAML pick one or add logic
-export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
-export SOCA_NINNER=@SOCA_NINNER@
-export DOMAIN_STACK_SIZE=116640000  #TODO: Make the stack size resolution dependent
-export SOCA_ENS_BKG_STAGE_YAML_TMPL="${PARMgfs}/gdas/soca/soca_ens_bkg_stage.yaml.j2"
-export SOCA_FIX_YAML_TMPL="${PARMgfs}/gdas/soca/soca_fix_stage_${OCNRES}.yaml.j2"
-
-export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin  # TODO(GA): remove once analysis "run"
-                                                   #          and "checkpoint" are refactored
-
-echo "END: config.ocnanal"
diff --git a/parm/config/gfs/config.ocnanalchkpt b/parm/config/gfs/config.ocnanalchkpt
deleted file mode 100644
index c059fdba42..0000000000
--- a/parm/config/gfs/config.ocnanalchkpt
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalchkpt ##########
-# Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalchkpt"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalchkpt
-
-echo "END: config.ocnanalchkpt"
diff --git a/parm/config/gfs/config.ocnanalpost b/parm/config/gfs/config.ocnanalpost
deleted file mode 100644
index bc4d945865..0000000000
--- a/parm/config/gfs/config.ocnanalpost
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalpost ##########
-# Post Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalpost"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalpost
-echo "END: config.ocnanalpost"
diff --git a/parm/config/gfs/config.ocnanalprep b/parm/config/gfs/config.ocnanalprep
deleted file mode 100644
index 225eb089c3..0000000000
--- a/parm/config/gfs/config.ocnanalprep
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalprep ##########
-# Pre Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalprep"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalprep
-echo "END: config.ocnanalprep"
diff --git a/parm/config/gfs/config.ocnanalrun b/parm/config/gfs/config.ocnanalrun
deleted file mode 100644
index 5345b6c684..0000000000
--- a/parm/config/gfs/config.ocnanalrun
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalrun ##########
-# Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalrun"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalrun
-
-echo "END: config.ocnanalrun"
diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 746ce79257..0963a5c42d 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -8,7 +8,7 @@ export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
 export SOCA_INPUT_FIX_DIR=@SOCA_INPUT_FIX_DIR@
 
-export OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
+export MARINE_OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
 export OBSPREP_YAML=@OBSPREP_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@
 export OBS_YAML=${OBS_LIST}
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 0479543ebc..d512f1f885 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -26,7 +26,7 @@ if (( $# != 1 )); then
     echo "waveinit waveprep wavepostsbs wavepostbndpnt wavepostbndpntbll wavepostpnt"
     echo "wavegempak waveawipsbulls waveawipsgridded"
     echo "postsnd awips gempak npoess"
-    echo "ocnanalprep prepoceanobs marinebmat ocnanalrun ocnanalecen marineanalletkf ocnanalchkpt ocnanalpost ocnanalvrfy"
+    echo "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
     exit 1
 
 fi
@@ -506,7 +506,7 @@ case ${step} in
     memory="3072M"
     ;;
 
-  "ocnanalprep")
+  "marineanlinit")
     walltime="00:10:00"
     ntasks=1
     threads_per_task=1
@@ -541,7 +541,7 @@ case ${step} in
     tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 
-  "ocnanalrun")
+  "marineanlvar")
     ntasks=16
     case ${OCNRES} in
       "025")
@@ -632,7 +632,7 @@ case ${step} in
     ;;
 
 
-  "ocnanalchkpt")
+  "marineanlchkpt")
     walltime="00:10:00"
     ntasks=1
     threads_per_task=1
@@ -656,7 +656,7 @@ case ${step} in
     esac
     ;;
 
-  "ocnanalpost")
+  "marineanlfinal")
     walltime="00:30:00"
     ntasks=${max_tasks_per_node}
     threads_per_task=1
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index 05e1b24012..dfc67d1237 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -52,7 +52,7 @@ snowanl:
   IO_LAYOUT_X: 1
   IO_LAYOUT_Y: 1
 
-ocnanal:
+marineanl:
   SOCA_INPUT_FIX_DIR: "${FIXgfs}/gdas/soca/72x35x25/soca"
   SOCA_OBS_LIST: "${PARMgfs}/gdas/soca/obs/obs_list.yaml"  # TODO: This is also repeated in oceanprepobs
   SOCA_NINNER: 100
@@ -61,4 +61,4 @@ prepoceanobs:
   SOCA_INPUT_FIX_DIR: "${FIXgfs}/gdas/soca/72x35x25/soca"
   SOCA_OBS_LIST: "${PARMgfs}/gdas/soca/obs/obs_list.yaml"  # TODO: This is also repeated in ocnanal
   OBSPREP_YAML: "${PARMgfs}/gdas/soca/obsprep/obsprep_config.yaml"
-  DMPDIR: "/scratch1/NCEPDEV/global/glopara/data/experimental_obs"
+  DMPDIR: "${BASE_DATA}/experimental_obs"
diff --git a/scripts/exglobal_marine_analysis_checkpoint.py b/scripts/exglobal_marine_analysis_checkpoint.py
new file mode 100755
index 0000000000..84b180b287
--- /dev/null
+++ b/scripts/exglobal_marine_analysis_checkpoint.py
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# exglobal_marine_analysis_checkpoint.py
+# This script creates a MarineAnalysis object
+# and runs the checkpoint methods which inserts
+# the seaice analysis into the CICE6 restart or
+# create a soca MOM6 IAU increment
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_analysis import MarineAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Create a MarineAnalysis object
+    MarineAnl = MarineAnalysis(config)
+
+    # Prepare the SOCA increment for MOM6 IAU
+    MarineAnl.checkpoint_mom6_iau('socaincr2mom6.yaml')
+
+    # Insert the seaice analysis into the CICE6 restarts in 2 sequential stages
+    MarineAnl.checkpoint_cice6('soca_2cice_arctic.yaml')
+    MarineAnl.checkpoint_cice6('soca_2cice_antarctic.yaml')
diff --git a/scripts/exglobal_marine_analysis_finalize.py b/scripts/exglobal_marine_analysis_finalize.py
new file mode 100755
index 0000000000..daa3fbb487
--- /dev/null
+++ b/scripts/exglobal_marine_analysis_finalize.py
@@ -0,0 +1,27 @@
+#!/usr/bin/env python3
+# exglobal_marine_analysis_finalize.py
+# This script creates an MarineAnalysis object
+# and makes copies of the variational analysis output
+# to the COMROOT
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_analysis import MarineAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Create a MarineAnalysis object
+    MarineAnl = MarineAnalysis(config)
+
+    # Make a copy of the analysis output to the COMROOT
+    MarineAnl.finalize()
+
+    # Compute the observation space statistics
+    MarineAnl.obs_space_stats()
diff --git a/scripts/exglobal_marine_analysis_initialize.py b/scripts/exglobal_marine_analysis_initialize.py
new file mode 100755
index 0000000000..37e45a5b73
--- /dev/null
+++ b/scripts/exglobal_marine_analysis_initialize.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# exglobal_marine_analysis_initialize.py
+# This script creates an MarineAnalysis object
+# and runs the initialize method
+# which create and stage the runtime directory
+# and create the YAML configuration
+# for a global marine variational analysis
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_analysis import MarineAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Create a MarineAnalysis object
+    MarineAnl = MarineAnalysis(config)
+    MarineAnl.initialize()
diff --git a/scripts/exglobal_marine_analysis_variational.py b/scripts/exglobal_marine_analysis_variational.py
new file mode 100755
index 0000000000..e03c56b1e5
--- /dev/null
+++ b/scripts/exglobal_marine_analysis_variational.py
@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+# exglobal_marine_analysis_variational.py
+# This script creates an MarineAnalysis object
+# and runs the execute method
+# which executes the global marine variational analysis
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs.task.marine_analysis import MarineAnalysis
+
+# Initialize root logger
+logger = Logger(level='DEBUG', colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Create a MarineAnalysis object
+    MarineAnl = MarineAnalysis(config)
+
+    # Run the variational application
+    MarineAnl.variational()
diff --git a/sorc/gdas.cd b/sorc/gdas.cd
index 7c1c181359..55e895f1dc 160000
--- a/sorc/gdas.cd
+++ b/sorc/gdas.cd
@@ -1 +1 @@
-Subproject commit 7c1c181359c2c1952bab3dc1c481bbdb361aa472
+Subproject commit 55e895f1dcf4e6be36eb0eb4c8a7995d429157e0
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 270a8bb1c9..9426a09ce9 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -275,7 +275,6 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   done
 fi
 
-
 #------------------------------
 #--add DA Monitor file (NOTE: ensure to use correct version)
 #------------------------------
@@ -372,6 +371,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
                        "gdas_incr_handler.x" \
                        "gdas_obsprovider2ioda.x" \
                        "gdas_socahybridweights.x" \
+                       "gdassoca_obsstats.x" \
                        "gdasapp_land_ensrecenter.x" \
                        "bufr2ioda.x" \
                        "calcfIMS.exe" \
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
new file mode 100644
index 0000000000..4e4311b906
--- /dev/null
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -0,0 +1,485 @@
+#!/usr/bin/env python3
+
+import copy
+import os
+from logging import getLogger
+import pygfs.utils.marine_da_utils as mdau
+import glob
+import re
+import netCDF4
+from multiprocessing import Process
+import subprocess
+import yaml
+from jcb import render
+
+from wxflow import (AttrDict,
+                    FileHandler,
+                    add_to_datetime, to_timedelta, to_YMD,
+                    parse_j2yaml,
+                    logit,
+                    Executable,
+                    Task,
+                    save_as_yaml,
+                    Template, TemplateConstants, YAMLFile)
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+def parse_obs_list_file(obs_list_yaml_path):
+    # Get the list of observation types from the obs_list.yaml
+    obs_types = []
+    with open(obs_list_yaml_path, 'r') as file:
+        for line in file:
+            # Remove leading/trailing whitespace and check if the line is uncommented
+            line = line.strip()
+            if line.startswith('- !INC') and not line.startswith('#'):
+                # Extract the type using regex
+                match = re.search(r'\$\{MARINE_OBS_YAML_DIR\}/(.+)\.yaml', line)
+                if match:
+                    obs_types.append(str(match.group(1)))
+    return obs_types
+
+
+class MarineAnalysis(Task):
+    """
+    Class for global marine analysis tasks
+    """
+    @logit(logger, name="MarineAnalysis")
+    def __init__(self, config):
+        super().__init__(config)
+        _calc_scale_exec = os.path.join(self.task_config.HOMEgfs, 'ush', 'soca', 'calc_scales.py')
+        _window_begin = add_to_datetime(self.task_config.current_cycle, -to_timedelta(f"{self.task_config.assim_freq}H") / 2)
+        _window_end = add_to_datetime(self.task_config.current_cycle, to_timedelta(f"{self.task_config.assim_freq}H") / 2)
+
+        # compute the relative path from self.task_config.DATA to self.task_config.DATAenspert
+        if self.task_config.NMEM_ENS > 0:
+            _enspert_relpath = os.path.relpath(self.task_config.DATAenspert, self.task_config.DATA)
+        else:
+            _enspert_relpath = None
+
+        # Create a local dictionary that is repeatedly used across this class
+        local_dict = AttrDict(
+            {
+                'PARMsoca': os.path.join(self.task_config.PARMgfs, 'gdas', 'soca'),
+                'MARINE_WINDOW_BEGIN': _window_begin,
+                'MARINE_WINDOW_BEGIN_ISO': _window_begin.strftime('%Y-%m-%dT%H:%M:%SZ'),
+                'MARINE_WINDOW_END': _window_end,
+                'MARINE_WINDOW_LENGTH': f"PT{self.task_config['assim_freq']}H",
+                'MARINE_WINDOW_MIDDLE': self.task_config.current_cycle,
+                'MARINE_WINDOW_MIDDLE_ISO': self.task_config.current_cycle.strftime('%Y-%m-%dT%H:%M:%SZ'),
+                'ENSPERT_RELPATH': _enspert_relpath,
+                'CALC_SCALE_EXEC': _calc_scale_exec,
+                'OPREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z."
+            }
+        )
+
+        # Extend task_config with local_dict
+        self.task_config.update(local_dict)
+
+    @logit(logger)
+    def initialize(self: Task) -> None:
+        """Initialize the marine analysis
+
+        This method will initialize the marine analysis.
+        This includes:
+        - staging the deterministic backgrounds (middle of window)
+        - staging SOCA fix files
+        - staging static ensemble members (optional)
+        - staging ensemble members (optional)
+        - generating the YAML files for the JEDI and GDASApp executables
+        - creating output directories
+        """
+        super().initialize()
+
+        # prepare the directory structure to run SOCA
+        self._prep_scratch_dir()
+
+        # fetch observations from COMROOT
+        # TODO(G.V. or A.E.): Keep a copy of the obs in the scratch fs after the obs prep job
+        self._fetch_observations()
+
+        # stage the ocean and ice backgrounds for FGAT
+        bkg_list = parse_j2yaml(self.task_config.MARINE_DET_STAGE_BKG_YAML_TMPL, self.task_config)
+        FileHandler(bkg_list).sync()
+
+        # stage the soca grid
+        FileHandler({'copy': [[os.path.join(self.task_config.COMIN_OCEAN_BMATRIX, 'soca_gridspec.nc'),
+                               os.path.join(self.task_config.DATA, 'soca_gridspec.nc')]]}).sync()
+
+        # link the flow dependent static B resources from the B-matrix task of the same cycle
+        os.symlink('../staticb', 'staticb')
+
+        # hybrid EnVAR case
+        if self.task_config.DOHYBVAR == "YES" or self.task_config.NMEM_ENS > 2:
+            # stage ensemble membersfiles for use in hybrid background error
+            logger.debug(f"Stage ensemble members for the hybrid background error")
+            mdau.stage_ens_mem(self.task_config)
+
+        # prepare the yaml configuration to run the SOCA variational application
+        self._prep_variational_yaml()
+
+        # prepare the yaml configuration to run the SOCA to MOM6 IAU increment
+        self._prep_checkpoint()
+
+    @logit(logger)
+    def _fetch_observations(self: Task) -> None:
+        """Fetch observations from COMIN_OBS
+
+        This method will fetch the observations for the cycle and check the
+        list against what is available for the cycle.
+        """
+
+        # get the list of observations
+        obs_list_config = YAMLFile(self.task_config.MARINE_OBS_LIST_YAML)
+        obs_list_config = Template.substitute_structure(obs_list_config, TemplateConstants.DOLLAR_PARENTHESES, self.task_config)
+        obs_list_config = {'observations': obs_list_config}
+        logger.info(f"{obs_list_config}")
+
+        obs_files = []
+        for ob in obs_list_config['observations']['observers']:
+            logger.info(f"******** {self.task_config.OPREFIX}{ob['obs space']['name'].lower()}.{to_YMD(self.task_config.PDY)}{self.task_config.cyc}.nc4")
+            obs_files.append(f"{self.task_config.OPREFIX}{ob['obs space']['name'].lower()}.{to_YMD(self.task_config.PDY)}{self.task_config.cyc}.nc4")
+        obs_list = []
+
+        # copy obs from COM_OBS to DATA/obs
+        for obs_file in obs_files:
+            logger.info(f"******* {obs_file}")
+            obs_src = os.path.join(self.task_config.COM_OBS, obs_file)
+            obs_dst = os.path.join(self.task_config.DATA, 'obs', obs_file)
+            logger.info(f"******* {obs_src}")
+            if os.path.exists(obs_src):
+                logger.info(f"******* fetching {obs_file}")
+                obs_list.append([obs_src, obs_dst])
+            else:
+                logger.info(f"******* {obs_file} is not in the database")
+
+        FileHandler({'copy': obs_list}).sync()
+
+    @logit(logger)
+    def _prep_scratch_dir(self: Task) -> None:
+        """Create and stage all the resources needed to run SOCA/JEDI, including the necesssary
+           directory structure to run the SOCA variational application
+        """
+        logger.info(f"---------------- Setup runtime environement")
+
+        anl_dir = self.task_config.DATA
+
+        # create analysis directories
+        diags = os.path.join(anl_dir, 'diags')            # output dir for soca DA obs space
+        obs_in = os.path.join(anl_dir, 'obs')             # input      "           "
+        anl_out = os.path.join(anl_dir, 'Data')           # output dir for soca DA
+        FileHandler({'mkdir': [diags, obs_in, anl_out]}).sync()
+
+        # stage fix files
+        logger.info(f"Staging SOCA fix files from {self.task_config.SOCA_INPUT_FIX_DIR}")
+        soca_fix_list = parse_j2yaml(self.task_config.SOCA_FIX_YAML_TMPL, self.task_config)
+        FileHandler(soca_fix_list).sync()
+
+        # prepare the MOM6 input.nml
+        mdau.prep_input_nml(self.task_config)
+
+        # stage the soca utility yamls (gridgen, fields and ufo mapping yamls)
+        logger.info(f"Staging SOCA utility yaml files from {self.task_config.PARMsoca}")
+        soca_utility_list = parse_j2yaml(self.task_config.MARINE_UTILITY_YAML_TMPL, self.task_config)
+        FileHandler(soca_utility_list).sync()
+
+    @logit(logger)
+    def _prep_variational_yaml(self: Task) -> None:
+        """Create the yaml configuration to run the SOCA variational application
+        """
+
+        # prepare background list for the pseudo model, check bkg date for consistency
+        mdau.gen_bkg_list(bkg_path='./bkg',
+                          window_begin=self.task_config.MARINE_WINDOW_BEGIN,
+                          yaml_name='bkg_list.yaml')
+
+        # Make a copy of the env config before modifying to avoid breaking something else
+        envconfig_jcb = copy.deepcopy(self.task_config)
+        logger.info(f"---------------- Prepare the yaml configuration")
+        logger.info(f"{envconfig_jcb}")       # Prepare the yaml configuration
+
+        # Add the things to the envconfig in order to template JCB files
+        envconfig_jcb['PARMgfs'] = self.task_config.PARMgfs
+        envconfig_jcb['nmem_ens'] = self.task_config.NMEM_ENS
+        envconfig_jcb['berror_model'] = 'marine_background_error_static_diffusion'
+        if self.task_config.NMEM_ENS > 3:
+            envconfig_jcb['berror_model'] = 'marine_background_error_hybrid_diffusion_diffusion'
+        envconfig_jcb['DATA'] = self.task_config.DATA
+        envconfig_jcb['OPREFIX'] = self.task_config.OPREFIX
+        envconfig_jcb['PDY'] = os.getenv('PDY')
+        envconfig_jcb['cyc'] = os.getenv('cyc')
+        envconfig_jcb['SOCA_NINNER'] = self.task_config.SOCA_NINNER
+        envconfig_jcb['obs_list'] = ['adt_rads_all']
+
+        # Write obs_list_short
+        save_as_yaml(parse_obs_list_file(self.task_config.MARINE_OBS_LIST_YAML), 'obs_list_short.yaml')
+        os.environ['OBS_LIST_SHORT'] = 'obs_list_short.yaml'
+
+        # Render the JCB configuration files
+        jcb_base_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-base.yaml')
+        jcb_algo_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-3dfgat.yaml.j2')
+
+        jcb_base_config = YAMLFile(path=jcb_base_yaml)
+        jcb_base_config = Template.substitute_structure(jcb_base_config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig_jcb.get)
+        jcb_base_config = Template.substitute_structure(jcb_base_config, TemplateConstants.DOLLAR_PARENTHESES, envconfig_jcb.get)
+        jcb_algo_config = YAMLFile(path=jcb_algo_yaml)
+        jcb_algo_config = Template.substitute_structure(jcb_algo_config, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig_jcb.get)
+        jcb_algo_config = Template.substitute_structure(jcb_algo_config, TemplateConstants.DOLLAR_PARENTHESES, envconfig_jcb.get)
+
+        # Override base with the application specific config
+        jcb_config = {**jcb_base_config, **jcb_algo_config}
+
+        # convert datetime to string
+        jcb_config['window_begin'] = self.task_config.MARINE_WINDOW_BEGIN.strftime('%Y-%m-%dT%H:%M:%SZ')
+        jcb_config['window_middle'] = self.task_config.MARINE_WINDOW_MIDDLE.strftime('%Y-%m-%dT%H:%M:%SZ')
+
+        # Render the full JEDI configuration file using JCB
+        jedi_config = render(jcb_config)
+
+        # Save the JEDI configuration file
+        var_yaml_jcb = 'var.yaml'
+        mdau.clean_empty_obsspaces(jedi_config, target=var_yaml_jcb, app='var')
+
+    def _prep_checkpoint(self: Task) -> None:
+        """Create the yaml configuration to run the SOCA to MOM6 IAU increment
+        """
+        # prepare the socaincr2mom6.yaml
+        logger.info("Generate the SOCA to MOM6 IAU increment YAML file")
+        data = {'marine_window_begin': self.task_config.MARINE_WINDOW_BEGIN_ISO,
+                'marine_window_middle': self.task_config.MARINE_WINDOW_MIDDLE_ISO}
+        soca2mom6inc_config = parse_j2yaml(path=os.path.join(self.task_config.MARINE_JCB_GDAS_ALGO, 'socaincr2mom6.yaml.j2'),
+                                           data=data)
+        soca2mom6inc_config.save(os.path.join(self.task_config.DATA, 'socaincr2mom6.yaml'))
+
+        # prepare the SOCA to CICE YAML file
+        logger.info("Generate the SOCA to CICE RST YAML file")
+
+        # set the restart date, dependent on the cycling type
+        if self.task_config.DOIAU:
+            # forecast initialized at the begining of the DA window
+            fcst_begin = self.task_config.MARINE_WINDOW_BEGIN_ISO
+            rst_date = self.task_config.MARINE_WINDOW_BEGIN.strftime('%Y%m%d.%H%M%S')
+        else:
+            # forecast initialized at the middle of the DA window
+            fcst_begin = self.task_config.MARINE_WINDOW_MIDDLE_ISO
+            rst_date = self.task_config.MARINE_WINDOW_MIDDLE.strftime('%Y%m%d.%H%M%S')
+
+        # make a copy of the CICE6 restart
+        ice_rst = os.path.join(self.task_config.COMIN_ICE_RESTART_PREV, f'{rst_date}.cice_model.res.nc')
+        ice_rst_ana = os.path.join(self.task_config.DATA, 'Data', rst_date + '.cice_model.res.nc')
+        FileHandler({'copy': [[ice_rst, ice_rst_ana]]}).sync()
+
+        # prepare the necessary configuration for the SOCA to CICE application
+        soca2cice_param = AttrDict({
+            "ocn_ana": f"./Data/ocn.3dvarfgat_pseudo.an.{self.task_config.MARINE_WINDOW_MIDDLE_ISO}.nc",
+            "ice_ana": f"./Data/ice.3dvarfgat_pseudo.an.{self.task_config.MARINE_WINDOW_MIDDLE_ISO}.nc",
+            "ice_rst": ice_rst_ana,
+            "fcst_begin": fcst_begin
+        })
+        logger.debug(f"{soca2cice_param}")
+
+        # render the SOCA to CICE YAML file for the Arctic and Antarctic
+        logger.info("render the SOCA to CICE YAML file for the Arctic and Antarctic")
+        varchgyamls = ['soca_2cice_arctic.yaml', 'soca_2cice_antarctic.yaml']
+        for varchgyaml in varchgyamls:
+            soca2cice_config = parse_j2yaml(path=os.path.join(self.task_config.MARINE_JCB_GDAS_ALGO, f'{varchgyaml}.j2'),
+                                            data=soca2cice_param)
+            soca2cice_config.save(os.path.join(self.task_config.DATA, varchgyaml))
+
+    @logit(logger)
+    def variational(self: Task) -> None:
+        # link gdas_soca_gridgen.x
+        mdau.link_executable(self.task_config, 'gdas.x')
+        exec_cmd = Executable(self.task_config.APRUN_MARINEANLVAR)
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('soca')
+        exec_cmd.add_default_arg('variational')
+        exec_cmd.add_default_arg('var.yaml')
+
+        mdau.run(exec_cmd)
+
+    @logit(logger)
+    def checkpoint_cice6(self: Task, soca2ciceyaml) -> None:
+        # link gdas_soca_gridgen.x
+        mdau.link_executable(self.task_config, 'gdas.x')
+        exec_cmd = Executable(self.task_config.APRUN_MARINEANLCHKPT)
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('soca')
+        exec_cmd.add_default_arg('convertstate')
+        exec_cmd.add_default_arg(soca2ciceyaml)
+
+        mdau.run(exec_cmd)
+
+    @logit(logger)
+    def checkpoint_mom6_iau(self: Task, socaincr2mom6yaml) -> None:
+        # link gdas_incr_handler.x
+        mdau.link_executable(self.task_config, 'gdas_incr_handler.x')
+        exec_cmd = Executable(self.task_config.APRUN_MARINEANLCHKPT)
+        exec_name = os.path.join(self.task_config.DATA, 'gdas_incr_handler.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg(socaincr2mom6yaml)
+
+        mdau.run(exec_cmd)
+
+    @logit(logger)
+    def finalize(self: Task) -> None:
+        """Finalize the marine analysis job
+           This method saves the results of the deterministic variational analysis to the COMROOT
+        """
+
+        def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
+            files = glob.glob(os.path.join(dir_in, wc))
+            for file_src in files:
+                file_dst = os.path.join(dir_out, os.path.basename(file_src))
+                fh_list.append([file_src, file_dst])
+            return fh_list
+
+        # variables of convenience
+        com_ocean_analysis = self.task_config.COMOUT_OCEAN_ANALYSIS
+        com_ice_analysis = self.task_config.COMOUT_ICE_ANALYSIS
+        com_ice_restart = self.task_config.COMOUT_ICE_RESTART
+        anl_dir = self.task_config.DATA
+        cdate = self.task_config.CDATE
+        pdy = self.task_config.PDY
+        staticsoca_dir = self.task_config.SOCA_INPUT_FIX_DIR
+        RUN = self.task_config.RUN
+        cyc = str(self.task_config.cyc).zfill(2)
+        bcyc = str(self.task_config.MARINE_WINDOW_BEGIN.hour).zfill(2)
+        bdate = self.task_config.MARINE_WINDOW_BEGIN_ISO
+        mdate = self.task_config.MARINE_WINDOW_MIDDLE_ISO
+        nmem_ens = int(self.task_config.NMEM_ENS)
+
+        logger.info(f"---------------- Copy from RUNDIR to COMOUT")
+
+        post_file_list = []
+
+        # Make a copy the IAU increment
+        post_file_list.append([os.path.join(anl_dir, 'inc.nc'),
+                               os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocninc.nc')])
+
+        domains = ['ocn', 'ice']
+        for domain in domains:
+            '''
+            # Copy of the diagonal of the background error for the cycle
+            post_file_list.append([os.path.join(anl_dir, f'{domain}.bkgerr_stddev.incr.{mdate}.nc'),
+                                   os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.bkgerr_stddev.nc')])
+
+            # Copy the recentering error
+            if nmem_ens > 2:
+                post_file_list.append([os.path.join(anl_dir, 'static_ens', f'{domain}.ssh_recentering_error.incr.{bdate}.nc'),
+                                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.recentering_error.nc')])
+            '''
+
+            # Copy the ice and ocean increments
+            post_file_list.append([os.path.join(anl_dir, 'Data', f'{domain}.3dvarfgat_pseudo.incr.{mdate}.nc'),
+                                   os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}.incr.nc')])
+
+            # Copy the analysis at the start of the window
+            post_file_list.append([os.path.join(anl_dir, 'Data', f'{domain}.3dvarfgat_pseudo.an.{mdate}.nc'),
+                                   os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.{domain}ana.nc')])
+
+        # Copy of the ssh diagnostics
+        '''
+        if nmem_ens > 2:
+            for string in ['ssh_steric_stddev', 'ssh_unbal_stddev', 'ssh_total_stddev', 'steric_explained_variance']:
+                post_file_list.append([os.path.join(anl_dir, 'static_ens', f'ocn.{string}.incr.{bdate}.nc'),
+                                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.{string}.nc')])
+        '''
+
+        # Copy DA grid (computed for the start of the window)
+        post_file_list.append([os.path.join(anl_dir, 'soca_gridspec.nc'),
+                               os.path.join(com_ocean_analysis, f'{RUN}.t{bcyc}z.ocngrid.nc')])
+
+        # Copy the CICE analysis restart
+        if os.getenv('DOIAU') == "YES":
+            cice_rst_date = self.task_config.MARINE_WINDOW_BEGIN.strftime('%Y%m%d.%H%M%S')
+        else:
+            cice_rst_date = cdate.strftime('%Y%m%d.%H%M%S')
+
+        post_file_list.append([os.path.join(anl_dir, 'Data', f'{cice_rst_date}.cice_model.res.nc'),
+                               os.path.join(com_ice_analysis, f'{cice_rst_date}.cice_model_anl.res.nc')])
+
+        FileHandler({'copy': post_file_list}).sync()
+
+        # create COM sub-directories
+        FileHandler({'mkdir': [os.path.join(com_ocean_analysis, 'diags'),
+                               os.path.join(com_ocean_analysis, 'bump'),
+                               os.path.join(com_ocean_analysis, 'yaml')]}).sync()
+
+        # ioda output files
+        fh_list = list_all_files(os.path.join(anl_dir, 'diags'),
+                                 os.path.join(com_ocean_analysis, 'diags'))
+
+        # yaml configurations
+        fh_list = list_all_files(os.path.join(anl_dir),
+                                 os.path.join(com_ocean_analysis, 'yaml'), wc='*.yaml', fh_list=fh_list)
+
+        FileHandler({'copy': fh_list}).sync()
+
+    @logit(logger)
+    def obs_space_stats(self: Task) -> None:
+        """Observation space statistics
+           This method computes a few basic statistics on the observation spaces
+        """
+
+        # obs space statistics
+        logger.info(f"---------------- Compute basic stats")
+        diags_list = glob.glob(os.path.join(os.path.join(self.task_config.COMOUT_OCEAN_ANALYSIS, 'diags', '*.nc4')))
+        obsstats_j2yaml = str(os.path.join(self.task_config.PARMgfs, 'gdas', 'soca', 'obs', 'obs_stats.yaml.j2'))
+
+        # function to create a minimalist ioda obs sapce
+        def create_obs_space(data):
+            os_dict = {"obs space": {
+                       "name": data["obs_space"],
+                       "obsdatain": {
+                           "engine": {"type": "H5File", "obsfile": data["obsfile"]}
+                       },
+                       "simulated variables": [data["variable"]]
+                       },
+                       "variable": data["variable"],
+                       "experiment identifier": data["pslot"],
+                       "csv output": data["csv_output"]
+                       }
+            return os_dict
+
+        # get the experiment id
+        pslot = self.task_config.PSLOT
+
+        # iterate through the obs spaces and generate the yaml for gdassoca_obsstats.x
+        obs_spaces = []
+        for obsfile in diags_list:
+
+            # define an obs space name
+            obs_space = re.sub(r'\.\d{10}\.nc4$', '', os.path.basename(obsfile))
+
+            # get the variable name, assume 1 variable per file
+            nc = netCDF4.Dataset(obsfile, 'r')
+            variable = next(iter(nc.groups["ObsValue"].variables))
+            nc.close()
+
+            # filling values for the templated yaml
+            data = {'obs_space': os.path.basename(obsfile),
+                    'obsfile': obsfile,
+                    'pslot': pslot,
+                    'variable': variable,
+                    'csv_output': os.path.join(self.task_config.COMOUT_OCEAN_ANALYSIS,
+                                               f"{self.task_config.OPREFIX}ocn.{obs_space}.stats.csv")}
+            obs_spaces.append(create_obs_space(data))
+
+        # create the yaml
+        data = {'obs_spaces': obs_spaces}
+        conf = parse_j2yaml(path=obsstats_j2yaml, data=data)
+        stats_yaml = 'diag_stats.yaml'
+        conf.save(stats_yaml)
+
+        # run the application
+        mdau.link_executable(self.task_config, 'gdassoca_obsstats.x')
+        command = f"{os.getenv('launcher')} -n 1"
+        exec_cmd = Executable(command)
+        exec_name = os.path.join(self.task_config.DATA, 'gdassoca_obsstats.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg(stats_yaml)
+
+        mdau.run(exec_cmd)
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 4770583934..93329f05ac 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -26,29 +26,24 @@ def __init__(self, config):
         super().__init__(config)
         _home_gdas = os.path.join(self.task_config.HOMEgfs, 'sorc', 'gdas.cd')
         _calc_scale_exec = os.path.join(self.task_config.HOMEgfs, 'ush', 'soca', 'calc_scales.py')
-        _window_begin = add_to_datetime(self.task_config.current_cycle, -to_timedelta(f"{self.task_config.assim_freq}H") / 2)
-        _window_end = add_to_datetime(self.task_config.current_cycle, to_timedelta(f"{self.task_config.assim_freq}H") / 2)
+        _window_begin = add_to_datetime(self.task_config.current_cycle,
+                                        -to_timedelta(f"{self.task_config.assim_freq}H") / 2)
+        _window_end = add_to_datetime(self.task_config.current_cycle,
+                                      to_timedelta(f"{self.task_config.assim_freq}H") / 2)
 
         # compute the relative path from self.task_config.DATA to self.task_config.DATAenspert
-        if self.task_config.NMEM_ENS > 0:
-            _enspert_relpath = os.path.relpath(self.task_config.DATAenspert, self.task_config.DATA)
-        else:
-            _enspert_relpath = None
+        _enspert_relpath = os.path.relpath(self.task_config.DATAens, self.task_config.DATA)
 
         # Create a local dictionary that is repeatedly used across this class
         local_dict = AttrDict(
             {
-                'HOMEgdas': _home_gdas,
+                'PARMsoca': os.path.join(self.task_config.PARMgfs, 'gdas', 'soca'),
                 'MARINE_WINDOW_BEGIN': _window_begin,
                 'MARINE_WINDOW_END': _window_end,
                 'MARINE_WINDOW_MIDDLE': self.task_config.current_cycle,
-                'BERROR_YAML_DIR': os.path.join(_home_gdas, 'parm', 'soca', 'berror'),
-                'UTILITY_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_utils_stage.yaml.j2'),
-                'MARINE_ENSDA_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'ensda', 'stage_ens_mem.yaml.j2'),
-                'MARINE_DET_STAGE_BKG_YAML_TMPL': os.path.join(_home_gdas, 'parm', 'soca', 'soca_det_bkg_stage.yaml.j2'),
                 'ENSPERT_RELPATH': _enspert_relpath,
                 'CALC_SCALE_EXEC': _calc_scale_exec,
-                'APREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",
+                'APREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z."
             }
         )
 
@@ -61,7 +56,7 @@ def initialize(self: Task) -> None:
 
         This method will initialize a global B-Matrix.
         This includes:
-        - staging the deterministic backgrounds (middle of window)
+        - staging the deterministic backgrounds
         - staging SOCA fix files
         - staging static ensemble members (optional)
         - staging ensemble members (optional)
@@ -84,39 +79,35 @@ def initialize(self: Task) -> None:
         FileHandler(bkg_list).sync()
 
         # stage the soca utility yamls (gridgen, fields and ufo mapping yamls)
-        logger.info(f"Staging SOCA utility yaml files from {self.task_config.HOMEgfs}/parm/gdas/soca")
-        soca_utility_list = parse_j2yaml(self.task_config.UTILITY_YAML_TMPL, self.task_config)
+        logger.info(f"Staging SOCA utility yaml files")
+        soca_utility_list = parse_j2yaml(self.task_config.MARINE_UTILITY_YAML_TMPL, self.task_config)
         FileHandler(soca_utility_list).sync()
 
         # generate the variance partitioning YAML file
-        logger.debug("Generate variance partitioning YAML file")
-        diagb_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_diagb.yaml.j2'),
-                                    data=self.task_config)
+        logger.info(f"Generate variance partitioning YAML file from {self.task_config.BERROR_DIAGB_YAML}")
+        diagb_config = parse_j2yaml(path=self.task_config.BERROR_DIAGB_YAML, data=self.task_config)
         diagb_config.save(os.path.join(self.task_config.DATA, 'soca_diagb.yaml'))
 
         # generate the vertical decorrelation scale YAML file
-        logger.debug("Generate the vertical correlation scale YAML file")
-        vtscales_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_vtscales.yaml.j2'),
-                                       data=self.task_config)
+        logger.info(f"Generate the vertical correlation scale YAML file from {self.task_config.BERROR_VTSCALES_YAML}")
+        vtscales_config = parse_j2yaml(path=self.task_config.BERROR_VTSCALES_YAML, data=self.task_config)
         vtscales_config.save(os.path.join(self.task_config.DATA, 'soca_vtscales.yaml'))
 
         # generate vertical diffusion scale YAML file
-        logger.debug("Generate vertical diffusion YAML file")
-        diffvz_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_parameters_diffusion_vt.yaml.j2'),
-                                     data=self.task_config)
+        logger.info(f"Generate vertical diffusion YAML file from {self.task_config.BERROR_DIFFV_YAML}")
+        diffvz_config = parse_j2yaml(path=self.task_config.BERROR_DIFFV_YAML, data=self.task_config)
         diffvz_config.save(os.path.join(self.task_config.DATA, 'soca_parameters_diffusion_vt.yaml'))
 
         # generate the horizontal diffusion YAML files
         if True:  # TODO(G): skip this section once we have optimized the scales
             # stage the correlation scale configuration
-            logger.debug("Generate correlation scale YAML file")
-            FileHandler({'copy': [[os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_setcorscales.yaml'),
+            logger.info(f"Generate correlation scale YAML file from {self.task_config.BERROR_HZSCALES_YAML}")
+            FileHandler({'copy': [[self.task_config.BERROR_HZSCALES_YAML,
                                    os.path.join(self.task_config.DATA, 'soca_setcorscales.yaml')]]}).sync()
 
             # generate horizontal diffusion scale YAML file
-            logger.debug("Generate horizontal diffusion scale YAML file")
-            diffhz_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_parameters_diffusion_hz.yaml.j2'),
-                                         data=self.task_config)
+            logger.info(f"Generate horizontal diffusion scale YAML file from {self.task_config.BERROR_DIFFH_YAML}")
+            diffhz_config = parse_j2yaml(path=self.task_config.BERROR_DIFFH_YAML, data=self.task_config)
             diffhz_config.save(os.path.join(self.task_config.DATA, 'soca_parameters_diffusion_hz.yaml'))
 
         # hybrid EnVAR case
@@ -127,19 +118,20 @@ def initialize(self: Task) -> None:
 
             # generate ensemble recentering/rebalancing YAML file
             logger.debug("Generate ensemble recentering YAML file")
-            ensrecenter_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_ensb.yaml.j2'),
-                                              data=self.task_config)
+            ensrecenter_config = parse_j2yaml(path=self.task_config.BERROR_ENS_RECENTER_YAML, data=self.task_config)
             ensrecenter_config.save(os.path.join(self.task_config.DATA, 'soca_ensb.yaml'))
 
             # generate ensemble weights YAML file
-            logger.debug("Generate ensemble recentering YAML file: {self.task_config.abcd_yaml}")
-            hybridweights_config = parse_j2yaml(path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_ensweights.yaml.j2'),
-                                                data=self.task_config)
+            logger.debug("Generate hybrid-weigths YAML file")
+            hybridweights_config = parse_j2yaml(path=self.task_config.BERROR_HYB_WEIGHTS_YAML, data=self.task_config)
             hybridweights_config.save(os.path.join(self.task_config.DATA, 'soca_ensweights.yaml'))
 
-        # need output dir for ensemble perturbations and static B-matrix
-        logger.debug("Create empty diagb directories to receive output from executables")
-        FileHandler({'mkdir': [os.path.join(self.task_config.DATA, 'diagb')]}).sync()
+        # create the symbolic link to the static B-matrix directory
+        link_target = os.path.join(self.task_config.DATAstaticb)
+        link_name = os.path.join(self.task_config.DATA, 'staticb')
+        if os.path.exists(link_name):
+            os.remove(link_name)
+        os.symlink(link_target, link_name)
 
     @logit(logger)
     def gridgen(self: Task) -> None:
@@ -290,12 +282,12 @@ def finalize(self: Task) -> None:
         logger.info(f"Copying the diffusion coefficient files to the ROTDIR")
         diffusion_coeff_list = []
         for diff_type in ['hz', 'vt']:
-            src = os.path.join(self.task_config.DATA, f"{diff_type}_ocean.nc")
+            src = os.path.join(self.task_config.DATAstaticb, f"{diff_type}_ocean.nc")
             dest = os.path.join(self.task_config.COMOUT_OCEAN_BMATRIX,
                                 f"{self.task_config.APREFIX}{diff_type}_ocean.nc")
             diffusion_coeff_list.append([src, dest])
 
-        src = os.path.join(self.task_config.DATA, f"hz_ice.nc")
+        src = os.path.join(self.task_config.DATAstaticb, f"hz_ice.nc")
         dest = os.path.join(self.task_config.COMOUT_ICE_BMATRIX,
                             f"{self.task_config.APREFIX}hz_ice.nc")
         diffusion_coeff_list.append([src, dest])
@@ -308,13 +300,17 @@ def finalize(self: Task) -> None:
         window_end_iso = self.task_config.MARINE_WINDOW_END.strftime('%Y-%m-%dT%H:%M:%SZ')
 
         # ocean diag B
-        src = os.path.join(self.task_config.DATA, 'diagb', f"ocn.bkgerr_stddev.incr.{window_end_iso}.nc")
+        os.rename(os.path.join(self.task_config.DATAstaticb, f"ocn.bkgerr_stddev.incr.{window_end_iso}.nc"),
+                  os.path.join(self.task_config.DATAstaticb, f"ocn.bkgerr_stddev.nc"))
+        src = os.path.join(self.task_config.DATAstaticb, f"ocn.bkgerr_stddev.nc")
         dst = os.path.join(self.task_config.COMOUT_OCEAN_BMATRIX,
                            f"{self.task_config.APREFIX}ocean.bkgerr_stddev.nc")
         diagb_list.append([src, dst])
 
         # ice diag B
-        src = os.path.join(self.task_config.DATA, 'diagb', f"ice.bkgerr_stddev.incr.{window_end_iso}.nc")
+        os.rename(os.path.join(self.task_config.DATAstaticb, f"ice.bkgerr_stddev.incr.{window_end_iso}.nc"),
+                  os.path.join(self.task_config.DATAstaticb, f"ice.bkgerr_stddev.nc"))
+        src = os.path.join(self.task_config.DATAstaticb, f"ice.bkgerr_stddev.nc")
         dst = os.path.join(self.task_config.COMOUT_ICE_BMATRIX,
                            f"{self.task_config.APREFIX}ice.bkgerr_stddev.nc")
         diagb_list.append([src, dst])
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 2be76ac028..e1b2ac2d4d 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -1,7 +1,9 @@
-import f90nml
+from datetime import datetime, timedelta
+import dateutil.parser as dparser
 import os
+from netCDF4 import Dataset
 from logging import getLogger
-import xarray as xr
+import yaml
 
 from wxflow import (FileHandler,
                     logit,
@@ -9,6 +11,7 @@
                     AttrDict,
                     parse_j2yaml,
                     Executable,
+                    save_as_yaml,
                     jinja)
 
 logger = getLogger(__name__.split('.')[-1])
@@ -23,9 +26,9 @@ def run(exec_cmd: Executable) -> None:
         logger.debug(f"Executing {exec_cmd}")
         exec_cmd()
     except OSError:
-        raise OSError(f"Failed to execute {exec_cmd}")
+        raise OSError(f"FATAL ERROR: Failed to execute {exec_cmd}")
     except Exception:
-        raise WorkflowException(f"An error occured during execution of {exec_cmd}")
+        raise WorkflowException(f"FATAL ERROR: Error occurred during execution of {exec_cmd}")
 
 
 @logit(logger)
@@ -43,22 +46,19 @@ def link_executable(task_config: AttrDict, exe_name: str) -> None:
 
 @logit(logger)
 def prep_input_nml(task_config: AttrDict) -> None:
-    """Prepare the input.nml file
-       TODO: Use jinja2 instead of f90nml
+    """Prepare the mom_input.nml file
     """
-    # stage input.nml
-    mom_input_nml_tmpl_src = os.path.join(task_config.HOMEgdas, 'parm', 'soca', 'fms', 'input.nml')
+    # stage input.nml.j2
+    mom_input_nml_tmpl_src = os.path.join(task_config.PARMsoca, 'fms', 'input.nml.j2')
     mom_input_nml_tmpl = os.path.join(task_config.DATA, 'mom_input.nml.tmpl')
     FileHandler({'copy': [[mom_input_nml_tmpl_src, mom_input_nml_tmpl]]}).sync()
 
     # swap date and stacksize
-    domain_stack_size = task_config.DOMAIN_STACK_SIZE
-    ymdhms = [int(s) for s in task_config.MARINE_WINDOW_END.strftime('%Y,%m,%d,%H,%M,%S').split(',')]
-    with open(mom_input_nml_tmpl, 'r') as nml_file:
-        nml = f90nml.read(nml_file)
-        nml['ocean_solo_nml']['date_init'] = ymdhms
-        nml['fms_nml']['domains_stack_size'] = int(domain_stack_size)
-        nml.write('mom_input.nml')
+    date_init = [int(s) for s in task_config.MARINE_WINDOW_END.strftime('%Y,%m,%d,%H,%M,%S').split(',')]
+    input_nml_config = {'domain_stack_size': task_config.DOMAIN_STACK_SIZE,
+                        'date_init': date_init}
+    jinja_input_nml = jinja.Jinja(mom_input_nml_tmpl, input_nml_config)
+    jinja_input_nml.save('mom_input.nml')
 
 
 @logit(logger)
@@ -74,3 +74,95 @@ def stage_ens_mem(task_config: AttrDict) -> None:
     letkf_stage_list = parse_j2yaml(task_config.MARINE_ENSDA_STAGE_BKG_YAML_TMPL, ensbkgconf)
     logger.info(f"{letkf_stage_list}")
     FileHandler(letkf_stage_list).sync()
+
+
+@logit(logger)
+def test_hist_date(histfile: str, ref_date: datetime) -> None:
+    """
+    Check that the date in the MOM6 history file is the expected one for the cycle.
+    TODO: Implement the same for seaice
+    """
+
+    ncf = Dataset(histfile, 'r')
+    hist_date = dparser.parse(ncf.variables['time'].units, fuzzy=True) + timedelta(hours=int(ncf.variables['time'][0]))
+    ncf.close()
+    logger.info(f"*** history file date: {hist_date} expected date: {ref_date}")
+
+    if hist_date != ref_date:
+        raise ValueError(f"FATAL ERROR: Inconsistent bkg date'")
+
+
+@logit(logger)
+def gen_bkg_list(bkg_path: str, window_begin=' ', yaml_name='bkg.yaml', ice_rst=False) -> None:
+    """
+    Generate a YAML of the list of backgrounds for the pseudo model
+    """
+
+    # Pseudo model parameters (time step, start date)
+    # TODO: make this a parameter
+    dt_pseudo = 3
+    bkg_date = window_begin
+
+    # Construct list of background file names
+    cyc = str(os.getenv('cyc')).zfill(2)
+    gcyc = str((int(cyc) - 6) % 24).zfill(2)  # previous cycle
+    fcst_hrs = list(range(6, 10, dt_pseudo))
+    files = []
+    for fcst_hr in fcst_hrs:
+        files.append(os.path.join(bkg_path, f"ocean.bkg.f{str(fcst_hr).zfill(3)}.nc"))
+
+    # Identify the ocean background that will be used for the  vertical coordinate remapping
+    ocn_filename_ic = './INPUT/MOM.res.nc'
+    test_hist_date(ocn_filename_ic, bkg_date)  # assert date of the history file is correct
+
+    # Copy/process backgrounds and generate background yaml list
+    bkg_list = []
+    for bkg in files:
+        logger.info(f"****************** bkg: {bkg}")
+        # assert validity of the ocean bkg date, remove basename
+        bkg_date = bkg_date + timedelta(hours=dt_pseudo)
+        test_hist_date(bkg, bkg_date)
+        ocn_filename = os.path.splitext(os.path.basename(bkg))[0] + '.nc'
+
+        # prepare the seaice background, aggregate if the backgrounds are CICE restarts
+        ice_filename = ocn_filename.replace("ocean", "ice")
+
+        # prepare list of ocean and ice bkg to be copied to RUNDIR
+        bkg_dict = {'date': bkg_date.strftime('%Y-%m-%dT%H:%M:%SZ'),
+                    'basename': './bkg/',
+                    'ocn_filename': ocn_filename,
+                    'ice_filename': ice_filename,
+                    'read_from_file': 1}
+
+        bkg_list.append(bkg_dict)
+
+    # save pseudo model yaml configuration
+    save_as_yaml(bkg_list, yaml_name)
+
+
+@logit(logger)
+def clean_empty_obsspaces(config, target, app='var'):
+    """
+    Remove obs spaces that point to non-existent file and save
+    """
+
+    # obs space dictionary depth is dependent on the application
+    if app == 'var':
+        obs_spaces = config['cost function']['observations']['observers']
+    else:
+        raise ValueError(f"FATAL ERROR: obs space cleaning not implemented for {app}")
+
+    # remove obs spaces that point to a non existant file
+    cleaned_obs_spaces = []
+    for obs_space in obs_spaces:
+        fname = obs_space['obs space']['obsdatain']['engine']['obsfile']
+        if os.path.isfile(fname):
+            cleaned_obs_spaces.append(obs_space)
+        else:
+            logger.info(f"WARNING: {fname} does not exist, removing obs space")
+
+    # update obs spaces
+    config['cost function']['observations']['observers'] = cleaned_obs_spaces
+
+    # save cleaned yaml
+    save_as_yaml(config, target)
diff --git a/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index 4bb473f454..19f4dd607b 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -44,10 +44,10 @@ def _get_app_configs(self):
             configs += ['anal', 'analdiag']
 
         if self.do_jediocnvar:
-            configs += ['prepoceanobs', 'ocnanalprep', 'marinebmat', 'ocnanalrun']
+            configs += ['prepoceanobs', 'marineanlinit', 'marinebmat', 'marineanlvar']
             if self.do_hybvar:
                 configs += ['ocnanalecen']
-            configs += ['ocnanalchkpt', 'ocnanalpost']
+            configs += ['marineanlchkpt', 'marineanlfinal']
             if self.do_vrfy_oceanda:
                 configs += ['ocnanalvrfy']
 
@@ -146,10 +146,10 @@ def get_task_names(self):
             gdas_gfs_common_tasks_before_fcst += ['anal']
 
         if self.do_jediocnvar:
-            gdas_gfs_common_tasks_before_fcst += ['prepoceanobs', 'ocnanalprep', 'marinebmat', 'ocnanalrun']
+            gdas_gfs_common_tasks_before_fcst += ['prepoceanobs', 'marineanlinit', 'marinebmat', 'marineanlvar']
             if self.do_hybvar:
                 gdas_gfs_common_tasks_before_fcst += ['ocnanalecen']
-            gdas_gfs_common_tasks_before_fcst += ['ocnanalchkpt', 'ocnanalpost']
+            gdas_gfs_common_tasks_before_fcst += ['marineanlchkpt', 'marineanlfinal']
             if self.do_vrfy_oceanda:
                 gdas_gfs_common_tasks_before_fcst += ['ocnanalvrfy']
 
diff --git a/workflow/hosts/awspw.yaml b/workflow/hosts/awspw.yaml
index a9c708253e..ef17d8f2f4 100644
--- a/workflow/hosts/awspw.yaml
+++ b/workflow/hosts/awspw.yaml
@@ -18,6 +18,7 @@ CHGRP_RSTPROD: 'YES'
 CHGRP_CMD: 'chgrp rstprod' # TODO: This is not yet supported.
 HPSSARCH: 'NO'
 HPSS_PROJECT: emc-global #TODO: See `ATARDIR` below.
+BASE_DATA: '/bucket/global-workflow-shared-data'
 BASE_IC: '/bucket/global-workflow-shared-data/ICSDIR'
 LOCALARCH: 'NO'
 ATARDIR: '' # TODO: This will not yet work from AWS.
diff --git a/workflow/hosts/azurepw.yaml b/workflow/hosts/azurepw.yaml
index d59736e653..1769f9ee19 100644
--- a/workflow/hosts/azurepw.yaml
+++ b/workflow/hosts/azurepw.yaml
@@ -18,6 +18,7 @@ CHGRP_RSTPROD: 'YES'
 CHGRP_CMD: 'chgrp rstprod' # TODO: This is not yet supported.
 HPSSARCH: 'NO'
 HPSS_PROJECT: emc-global #TODO: See `ATARDIR` below.
+BASE_DATA: '/bucket/global-workflow-shared-data'
 BASE_IC: '/bucket/global-workflow-shared-data/ICSDIR'
 LOCALARCH: 'NO'
 ATARDIR: '' # TODO: This will not yet work from AZURE.
diff --git a/workflow/hosts/gaea.yaml b/workflow/hosts/gaea.yaml
index 9297fed24a..5a37b5dabf 100644
--- a/workflow/hosts/gaea.yaml
+++ b/workflow/hosts/gaea.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data/git'
 DMPDIR: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data/dump'
+BASE_DATA: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data'
 BASE_IC: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data/ICSDIR'
 PACKAGEROOT: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data/nwpara'
 COMROOT: '/gpfs/f5/ufs-ard/world-shared/global/glopara/data/com'
diff --git a/workflow/hosts/googlepw.yaml b/workflow/hosts/googlepw.yaml
index 2bd9439d5f..daf6cd1eb2 100644
--- a/workflow/hosts/googlepw.yaml
+++ b/workflow/hosts/googlepw.yaml
@@ -18,6 +18,7 @@ CHGRP_RSTPROD: 'YES'
 CHGRP_CMD: 'chgrp rstprod' # TODO: This is not yet supported.
 HPSSARCH: 'NO'
 HPSS_PROJECT: emc-global #TODO: See `ATARDIR` below.
+BASE_DATA: '/bucket/global-workflow-shared-data'
 BASE_IC: '/bucket/global-workflow-shared-data/ICSDIR'
 LOCALARCH: 'NO'
 ATARDIR: '' # TODO: This will not yet work from GOOGLE.
diff --git a/workflow/hosts/hera.yaml b/workflow/hosts/hera.yaml
index 4ace199470..fa2c351aa1 100644
--- a/workflow/hosts/hera.yaml
+++ b/workflow/hosts/hera.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/scratch1/NCEPDEV/global/glopara/git'
 DMPDIR: '/scratch1/NCEPDEV/global/glopara/dump'
+BASE_DATA: '/scratch1/NCEPDEV/global/glopara/data'
 BASE_IC: '/scratch1/NCEPDEV/global/glopara/data/ICSDIR'
 PACKAGEROOT: '/scratch1/NCEPDEV/global/glopara/nwpara'
 COMINsyn: '/scratch1/NCEPDEV/global/glopara/com/gfs/prod/syndat'
diff --git a/workflow/hosts/hercules.yaml b/workflow/hosts/hercules.yaml
index 9d6339a48e..73fde6cde6 100644
--- a/workflow/hosts/hercules.yaml
+++ b/workflow/hosts/hercules.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/work/noaa/global/glopara/git_rocky9'
 DMPDIR: '/work/noaa/rstprod/dump'
+BASE_DATA: '/work/noaa/global/glopara/data'
 BASE_IC: '/work/noaa/global/glopara/data/ICSDIR'
 PACKAGEROOT: '/work/noaa/global/glopara/nwpara'
 COMINsyn: '/work/noaa/global/glopara/com/gfs/prod/syndat'
diff --git a/workflow/hosts/jet.yaml b/workflow/hosts/jet.yaml
index 21e815c9b2..80957083e0 100644
--- a/workflow/hosts/jet.yaml
+++ b/workflow/hosts/jet.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/lfs4/HFIP/hfv3gfs/glopara/git'
 DMPDIR: '/lfs4/HFIP/hfv3gfs/glopara/dump'
+BASE_DATA: '/lfs5/HFIP/hfv3gfs/glopara/data'
 BASE_IC: '/mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR'
 PACKAGEROOT: '/lfs4/HFIP/hfv3gfs/glopara/nwpara'
 COMINsyn: '/lfs4/HFIP/hfv3gfs/glopara/com/gfs/prod/syndat'
diff --git a/workflow/hosts/orion.yaml b/workflow/hosts/orion.yaml
index 4ec78fc8cc..d47b2b2bab 100644
--- a/workflow/hosts/orion.yaml
+++ b/workflow/hosts/orion.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/work/noaa/global/glopara/git_rocky9'
 DMPDIR: '/work/noaa/rstprod/dump'
+BASE_DATA: '/work/noaa/global/glopara/data'
 BASE_IC: '/work/noaa/global/glopara/data/ICSDIR'
 PACKAGEROOT: '/work/noaa/global/glopara/nwpara'
 COMINsyn: '/work/noaa/global/glopara/com/gfs/prod/syndat'
diff --git a/workflow/hosts/s4.yaml b/workflow/hosts/s4.yaml
index c2af9728f2..b93fefec39 100644
--- a/workflow/hosts/s4.yaml
+++ b/workflow/hosts/s4.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/data/prod/glopara/git'
 DMPDIR: '/data/prod/glopara/dump'
+BASE_DATA: '/data/prod/glopara'
 BASE_IC: '/data/prod/glopara/coupled_ICs'
 PACKAGEROOT: '/data/prod/glopara/nwpara'
 COMINsyn: '/data/prod/glopara/com/gfs/prod/syndat'
diff --git a/workflow/hosts/wcoss2.yaml b/workflow/hosts/wcoss2.yaml
index bf2cc41c45..15f0705f91 100644
--- a/workflow/hosts/wcoss2.yaml
+++ b/workflow/hosts/wcoss2.yaml
@@ -1,5 +1,6 @@
 BASE_GIT: '/lfs/h2/emc/global/save/emc.global/git'
 DMPDIR: '/lfs/h2/emc/dump/noscrub/dump'
+BASE_DATA: '/lfs/h2/emc/global/noscrub/emc.global/data'
 BASE_IC: '/lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR'
 PACKAGEROOT: '${PACKAGEROOT:-"/lfs/h1/ops/prod/packages"}'
 COMINsyn: '/lfs/h1/ops/prod/com/gfs/v16.3/syndat'
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 89da933d00..ab972ad08b 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -692,7 +692,7 @@ def marinebmat(self):
 
         return task
 
-    def ocnanalprep(self):
+    def marineanlinit(self):
 
         deps = []
         dep_dict = {'type': 'task', 'name': f'{self.run}prepoceanobs'}
@@ -703,14 +703,14 @@ def ocnanalprep(self):
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
-        resources = self.get_resource('ocnanalprep')
-        task_name = f'{self.run}ocnanalprep'
+        resources = self.get_resource('marineanlinit')
+        task_name = f'{self.run}marineanlinit'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.run.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanalprep.sh',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/marineanlinit.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'
@@ -720,21 +720,21 @@ def ocnanalprep(self):
 
         return task
 
-    def ocnanalrun(self):
+    def marineanlvar(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalprep'}
+        dep_dict = {'type': 'task', 'name': f'{self.run}marineanlinit'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
 
-        resources = self.get_resource('ocnanalrun')
-        task_name = f'{self.run}ocnanalrun'
+        resources = self.get_resource('marineanlvar')
+        task_name = f'{self.run}marineanlvar'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.run.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanalrun.sh',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/marineanlvar.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'
@@ -747,7 +747,7 @@ def ocnanalrun(self):
     def ocnanalecen(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalrun'}
+        dep_dict = {'type': 'task', 'name': f'{self.run}marineanlvar'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
 
@@ -768,13 +768,13 @@ def ocnanalecen(self):
 
         return task
 
-    def ocnanalchkpt(self):
+    def marineanlchkpt(self):
 
         deps = []
         if self.app_config.do_hybvar:
             dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalecen'}
         else:
-            dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalrun'}
+            dep_dict = {'type': 'task', 'name': f'{self.run}marineanlvar'}
         deps.append(rocoto.add_dependency(dep_dict))
         if self.app_config.do_mergensst:
             data = f'&ROTDIR;/{self.run}.@Y@m@d/@H/atmos/{self.run}.t@Hz.sfcanl.nc'
@@ -782,14 +782,14 @@ def ocnanalchkpt(self):
             deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
-        resources = self.get_resource('ocnanalchkpt')
-        task_name = f'{self.run}ocnanalchkpt'
+        resources = self.get_resource('marineanlchkpt')
+        task_name = f'{self.run}marineanlchkpt'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.run.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanalchkpt.sh',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/marineanlchkpt.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'
@@ -799,21 +799,21 @@ def ocnanalchkpt(self):
 
         return task
 
-    def ocnanalpost(self):
+    def marineanlfinal(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalchkpt'}
+        dep_dict = {'type': 'task', 'name': f'{self.run}marineanlchkpt'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
-        resources = self.get_resource('ocnanalpost')
-        task_name = f'{self.run}ocnanalpost'
+        resources = self.get_resource('marineanlfinal')
+        task_name = f'{self.run}marineanlfinal'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.run.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanalpost.sh',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/marineanlfinal.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'
@@ -826,7 +826,7 @@ def ocnanalpost(self):
     def ocnanalvrfy(self):
 
         deps = []
-        dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalpost'}
+        dep_dict = {'type': 'task', 'name': f'{self.run}marineanlfinal'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
@@ -932,7 +932,7 @@ def _fcst_cycled(self):
         dependencies = rocoto.create_dependency(dep=dep)
 
         if self.app_config.do_jediocnvar:
-            dep_dict = {'type': 'task', 'name': f'{self.run}ocnanalpost'}
+            dep_dict = {'type': 'task', 'name': f'{self.run}marineanlfinal'}
             dependencies.append(rocoto.add_dependency(dep_dict))
 
         if self.app_config.do_aero and self.run in self.app_config.aero_anl_runs:
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index df2b0467db..8a32827377 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -15,7 +15,7 @@ class Tasks:
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch', "cleanup",
                    'prepatmiodaobs', 'atmanlinit', 'atmanlvar', 'atmanlfv3inc', 'atmanlfinal',
                    'prepoceanobs',
-                   'ocnanalprep', 'marinebmat', 'ocnanalrun', 'ocnanalecen', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
+                   'marineanlinit', 'marinebmat', 'marineanlvar', 'ocnanalecen', 'marineanlchkpt', 'marineanlfinal', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',
                    'atmensanlinit', 'atmensanlobs', 'atmensanlsol', 'atmensanlletkf', 'atmensanlfv3inc', 'atmensanlfinal',

From a443fd183ab3b802832d5d0bc5082e84b30951d0 Mon Sep 17 00:00:00 2001
From: David Huber <69919478+DavidHuber-NOAA@users.noreply.github.com>
Date: Fri, 27 Sep 2024 00:23:48 -0400
Subject: [PATCH 16/21] Enable parallel metp jobs and fix race condition with
 the gfscleanup job (#2907)

This brings in a change to EMC_verif-global that offsets the start time
of parallel instances when running metp jobs. This prevents Python from
attempting to create the same directory in multiple instances.
Simultaneously, this also fixes an issue with the `gfscleanup` job
potentially running before the `metp` jobs.
Resolves #2906
Resolves #2899
---
 parm/archive/enkf.yaml.j2        | 2 +-
 parm/config/gfs/config.resources | 4 ++--
 sorc/verif-global.fd             | 2 +-
 workflow/rocoto/gfs_tasks.py     | 8 ++++++--
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/parm/archive/enkf.yaml.j2 b/parm/archive/enkf.yaml.j2
index a95046d4d6..89fd44500b 100644
--- a/parm/archive/enkf.yaml.j2
+++ b/parm/archive/enkf.yaml.j2
@@ -27,7 +27,7 @@ enkf:
            {% else %}
               {% set steps = ["eobs", "eupd"] %}
               {% for mem in range(1, nmem_ens + 1) %}
-                 {% do steps.append("eomg_mem{{ '%03d' % mem }}") %}
+                 {% do steps.append("eomg_mem" ~ '%03d' % mem) %}
               {% endfor %}
            {% endif %}
         {% endif %}
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index d512f1f885..5024bc8873 100644
--- a/parm/config/gfs/config.resources
+++ b/parm/config/gfs/config.resources
@@ -988,8 +988,8 @@ case ${step} in
     threads_per_task=1
     walltime_gdas="03:00:00"
     walltime_gfs="06:00:00"
-    ntasks=1
-    tasks_per_node=1
+    ntasks=4
+    tasks_per_node=4
     export memory="80G"
     ;;
 
diff --git a/sorc/verif-global.fd b/sorc/verif-global.fd
index 92904d2c43..e7e6bc4358 160000
--- a/sorc/verif-global.fd
+++ b/sorc/verif-global.fd
@@ -1 +1 @@
-Subproject commit 92904d2c431969345968f74e676717057ec0042a
+Subproject commit e7e6bc43584e0b8911819b8f875cc8ee747db76d
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index ab972ad08b..6b9d6358c6 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -855,8 +855,8 @@ def fcst(self):
         try:
             task = fcst_map[self.app_config.mode]()
         except KeyError:
-            raise NotImplementedError(f'{self.app_config.mode} is not a valid type.\n' +
-                                      'Currently supported forecast types are:\n' +
+            raise NotImplementedError(f'{self.app_config.mode} is not a valid type.\n'
+                                      f'Currently supported forecast types are:\n'
                                       f'{" | ".join(fcst_map.keys())}')
 
         return task
@@ -2330,6 +2330,10 @@ def cleanup(self):
                     dep_dict = {'type': 'task', 'name': f'{self.run}npoess_pgrb2_0p5deg'}
                     deps.append(rocoto.add_dependency(dep_dict))
 
+        if self.app_config.do_metp and self.run in ['gfs']:
+            dep_dict = {'type': 'metatask', 'name': f'{self.run}metp'}
+            deps.append(rocoto.add_dependency(dep_dict))
+
         dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
 
         resources = self.get_resource('cleanup')

From 386aa6dcb8ebbe37c2efda419d5ccae46ed20cdd Mon Sep 17 00:00:00 2001
From: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
Date: Fri, 27 Sep 2024 00:46:44 -0400
Subject: [PATCH 17/21] Add GDA request template (#2948)

Add a new issue template for GDA requests
---
 .github/ISSUE_TEMPLATE/dump_request.yml | 37 +++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 .github/ISSUE_TEMPLATE/dump_request.yml

diff --git a/.github/ISSUE_TEMPLATE/dump_request.yml b/.github/ISSUE_TEMPLATE/dump_request.yml
new file mode 100644
index 0000000000..4481e7f6e0
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/dump_request.yml
@@ -0,0 +1,37 @@
+name: Global Observation Dump Request
+description: Request additional dates be added to a machine's global dump archive (GDA) or introduce experimental dump data to the GDA
+labels: ["Static Data Mgmt"]
+assignees:
+  - KateFriedman-NOAA
+  - WalterKolczynski-NOAA
+
+body:
+  - type: dropdown
+    attributes:
+      label: Machine
+      options:
+        - WCOSS2
+        - Hera/Ursa
+        - Orion/Hercules
+        - Jet
+      multiple: true
+    validations:
+      required: true
+
+  - type: input
+    attributes:
+      label: Start date
+    validations:
+      required: true
+
+  - type: input
+    attributes:
+      label: End date
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Additional information
+      placeholder: |
+        Any additional information needed (experimental obs, etc.)

From e2f56f5316e9de1ac110a53b2da3efbc24fc3643 Mon Sep 17 00:00:00 2001
From: RussTreadon-NOAA <26926959+RussTreadon-NOAA@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:39:37 -0400
Subject: [PATCH 18/21] Replace separate JEDI radiance bias correction files
 with tarball (#2875)

This PR updates g-w components which handle JEDI radiance bias
correction files. Currently, JEDI radiance bias correction files are
processed at the _satellite_sensor_. This PR replaces these multiple
files with a single radiance bias correction tarball.

Resolves #2862
---
 ci/cases/pr/C96C48_ufs_hybatmDA.yaml     |  2 +-
 env/ORION.env                            |  2 +-
 parm/archive/gdas_restarta.yaml.j2       |  2 +
 parm/config/gfs/config.resources.ORION   | 10 ++++
 parm/stage/analysis.yaml.j2              |  9 +---
 ush/python/pygfs/jedi/jedi.py            | 56 ++++++++++++++++----
 ush/python/pygfs/task/analysis.py        | 45 ----------------
 ush/python/pygfs/task/atm_analysis.py    | 66 +++++++++++++-----------
 ush/python/pygfs/task/atmens_analysis.py |  9 +++-
 9 files changed, 104 insertions(+), 97 deletions(-)

diff --git a/ci/cases/pr/C96C48_ufs_hybatmDA.yaml b/ci/cases/pr/C96C48_ufs_hybatmDA.yaml
index 0b5aa7b6ac..b1566d77a0 100644
--- a/ci/cases/pr/C96C48_ufs_hybatmDA.yaml
+++ b/ci/cases/pr/C96C48_ufs_hybatmDA.yaml
@@ -11,7 +11,7 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48/20240610
   idate: 2024022318
-  edate: 2024022400
+  edate: 2024022406
   nens: 2
   gfs_cyc: 1
   start: warm
diff --git a/env/ORION.env b/env/ORION.env
index 1bc7eb60d4..3b8053d060 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -142,7 +142,7 @@ elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
 
-    export APRUN_MARINEANLCHKPT="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEANLCHKPT="${APRUN_default} --cpus-per-task=${NTHREADS_OCNANAL}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 
diff --git a/parm/archive/gdas_restarta.yaml.j2 b/parm/archive/gdas_restarta.yaml.j2
index 9d86292065..fc5ce9478d 100644
--- a/parm/archive/gdas_restarta.yaml.j2
+++ b/parm/archive/gdas_restarta.yaml.j2
@@ -32,6 +32,8 @@ gdas_restarta:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}abias_int"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}dtfanl.nc"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}loginc.txt"
+        {% else %}
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}rad_varbc_params.tar"
         {% endif %}
 
         # Snow surface data
diff --git a/parm/config/gfs/config.resources.ORION b/parm/config/gfs/config.resources.ORION
index d761df7b73..461b6f14f7 100644
--- a/parm/config/gfs/config.resources.ORION
+++ b/parm/config/gfs/config.resources.ORION
@@ -23,6 +23,16 @@ case ${step} in
     # Remove this block once the GSI issue is resolved.
     export walltime="00:45:00"
   ;;
+  "atmanlvar")
+    # Run on 8 nodes for memory requirement
+    export tasks_per_node=8
+    export walltime="00:45:00"
+  ;;
+  "atmensanlobs")
+    # Run on 8 nodes for memory requirement
+    export tasks_per_node=8
+    export walltime="00:45:00"
+  ;;
   *)
   ;;
 esac
diff --git a/parm/stage/analysis.yaml.j2 b/parm/stage/analysis.yaml.j2
index 9a2ec5bbdf..424bf2b5fe 100644
--- a/parm/stage/analysis.yaml.j2
+++ b/parm/stage/analysis.yaml.j2
@@ -10,17 +10,10 @@ analysis:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
-        {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "atmi009.nc", "atmi003.nc", "radstat", "ratminc.nc", "ratmi009.nc", "ratmi003.nc"] %}
+        {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "atmi009.nc", "atmi003.nc", "radstat", "ratminc.nc", "ratmi009.nc", "ratmi003.nc", "rad_varbc_params.tar"] %}
         {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z." ~ ftype) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.{{ ftype }}", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"]
         {% endif %}
         {% endfor %}
-        {% if DO_JEDIATMVAR %}
-        {% for ftype in ["satbias.nc", "satbias_cov.nc", "tlapse.txt"] %}
-        {% for file in glob(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z.atms_*." ~ ftype) %}
-        - ["{{ file }}", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"]
-        {% endfor %}
-        {% endfor %}
-        {% endif %}
         {% endfor %} # mem loop
 {% endif %}
diff --git a/ush/python/pygfs/jedi/jedi.py b/ush/python/pygfs/jedi/jedi.py
index 62dcb517ca..415a0a3c08 100644
--- a/ush/python/pygfs/jedi/jedi.py
+++ b/ush/python/pygfs/jedi/jedi.py
@@ -1,10 +1,12 @@
 #!/usr/bin/env python3
 
 import os
+import tarfile
 from logging import getLogger
 from typing import List, Dict, Any, Optional
 from jcb import render
 from wxflow import (AttrDict,
+                    FileHandler,
                     chdir, rm_p,
                     parse_j2yaml,
                     logit,
@@ -188,19 +190,19 @@ def get_obs_dict(self, task_config: AttrDict) -> Dict[str, Any]:
         return obs_dict
 
     @logit(logger)
-    def get_bias_dict(self, task_config: AttrDict) -> Dict[str, Any]:
+    def get_bias_dict(self, task_config: AttrDict, bias_file) -> Dict[str, Any]:
         """Compile a dictionary of observation files to copy
 
-        This method extracts 'observers' from the JEDI yaml and from that list, extracts a list of
-        observation bias correction files that are to be copied to the run directory
+        This method extracts 'observers' from the JEDI yaml and determines from that list
+        if bias correction tar files are to be copied to the run directory
         from the component directory.
-        TODO: COM_ATMOS_ANALYSIS_PREV is hardwired here and this method is not appropriate in
-        `analysis.py` and should be implemented in the component where this is applicable.
 
         Parameters
         ----------
         task_config: AttrDict
             Attribute-dictionary of all configuration variables associated with a GDAS task.
+        bias_file
+            name of bias correction tar file
 
         Returns
         ----------
@@ -216,18 +218,52 @@ def get_bias_dict(self, task_config: AttrDict) -> Dict[str, Any]:
                 obfile = ob['obs bias']['input file']
                 obdir = os.path.dirname(obfile)
                 basename = os.path.basename(obfile)
-                prefix = '.'.join(basename.split('.')[:-2])
-                for file in ['satbias.nc', 'satbias_cov.nc', 'tlapse.txt']:
-                    bfile = f"{prefix}.{file}"
-                    copylist.append([os.path.join(task_config.COM_ATMOS_ANALYSIS_PREV, bfile), os.path.join(obdir, bfile)])
-                    # TODO: Why is this specific to ATMOS?
+                prefix = '.'.join(basename.split('.')[:-3])
+                bfile = f"{prefix}.{bias_file}"
+                tar_file = os.path.join(obdir, bfile)
+                copylist.append([os.path.join(task_config.VarBcDir, bfile), tar_file])
+                break
 
         bias_dict = {
             'mkdir': [os.path.join(task_config.DATA, 'bc')],
             'copy': copylist
         }
+
         return bias_dict
 
+    @staticmethod
+    @logit(logger)
+    def extract_tar(tar_file: str) -> None:
+        """Extract files from a tarball
+
+        This method extract files from a tarball
+
+        Parameters
+        ----------
+        tar_file
+            path/name of tarball
+
+        Returns
+        ----------
+        None
+        """
+
+        # extract files from tar file
+        tar_path = os.path.dirname(tar_file)
+        try:
+            with tarfile.open(tar_file, "r") as tarball:
+                tarball.extractall(path=tar_path)
+                logger.info(f"Extract {tarball.getnames()}")
+        except tarfile.ReadError as err:
+            if tarfile.is_tarfile(tar_file):
+                logger.error(f"FATAL ERROR: {tar_file} could not be read")
+                raise tarfile.ReadError(f"FATAL ERROR: unable to read {tar_file}")
+            else:
+                logger.info()
+        except tarfile.ExtractError as err:
+            logger.exception(f"FATAL ERROR: unable to extract from {tar_file}")
+            raise tarfile.ExtractError("FATAL ERROR: unable to extract from {tar_file}")
+
 
 @logit(logger)
 def find_value_in_nested_dict(nested_dict: Dict, target_key: str) -> Any:
diff --git a/ush/python/pygfs/task/analysis.py b/ush/python/pygfs/task/analysis.py
index 6f7d3dfc68..1d8b38483b 100644
--- a/ush/python/pygfs/task/analysis.py
+++ b/ush/python/pygfs/task/analysis.py
@@ -41,10 +41,6 @@ def initialize(self) -> None:
         obs_dict = self.get_obs_dict()
         FileHandler(obs_dict).sync()
 
-        # some analyses need to stage bias corrections
-        bias_dict = self.get_bias_dict()
-        FileHandler(bias_dict).sync()
-
         # link jedi executable to run directory
         self.link_jediexe()
 
@@ -127,47 +123,6 @@ def get_obs_dict(self) -> Dict[str, Any]:
         }
         return obs_dict
 
-    @logit(logger)
-    def get_bias_dict(self) -> Dict[str, Any]:
-        """Compile a dictionary of observation files to copy
-
-        This method extracts 'observers' from the JEDI yaml and from that list, extracts a list of
-        observation bias correction files that are to be copied to the run directory
-        from the component directory.
-        TODO: COM_ATMOS_ANALYSIS_PREV is hardwired here and this method is not appropriate in
-        `analysis.py` and should be implemented in the component where this is applicable.
-
-        Parameters
-        ----------
-
-        Returns
-        ----------
-        bias_dict: Dict
-            a dictionary containing the list of observation bias files to copy for FileHandler
-        """
-
-        logger.info(f"Extracting a list of bias correction files from Jedi config file")
-        observations = find_value_in_nested_dict(self.task_config.jedi_config, 'observations')
-        logger.debug(f"observations:\n{pformat(observations)}")
-
-        copylist = []
-        for ob in observations['observers']:
-            if 'obs bias' in ob.keys():
-                obfile = ob['obs bias']['input file']
-                obdir = os.path.dirname(obfile)
-                basename = os.path.basename(obfile)
-                prefix = '.'.join(basename.split('.')[:-2])
-                for file in ['satbias.nc', 'satbias_cov.nc', 'tlapse.txt']:
-                    bfile = f"{prefix}.{file}"
-                    copylist.append([os.path.join(self.task_config.COM_ATMOS_ANALYSIS_PREV, bfile), os.path.join(obdir, bfile)])
-                    # TODO: Why is this specific to ATMOS?
-
-        bias_dict = {
-            'mkdir': [os.path.join(self.task_config.DATA, 'bc')],
-            'copy': copylist
-        }
-        return bias_dict
-
     @logit(logger)
     def add_fv3_increments(self, inc_file_tmpl: str, bkg_file_tmpl: str, incvars: List) -> None:
         """Add cubed-sphere increments to cubed-sphere backgrounds
diff --git a/ush/python/pygfs/task/atm_analysis.py b/ush/python/pygfs/task/atm_analysis.py
index 8d340a5b73..5f67ea9d72 100644
--- a/ush/python/pygfs/task/atm_analysis.py
+++ b/ush/python/pygfs/task/atm_analysis.py
@@ -139,10 +139,17 @@ def initialize_analysis(self) -> None:
 
         # stage bias corrections
         logger.info(f"Staging list of bias correction files generated from JEDI config")
-        bias_dict = self.jedi.get_bias_dict(self.task_config)
+        self.task_config.VarBcDir = f"{self.task_config.COM_ATMOS_ANALYSIS_PREV}"
+        bias_file = f"rad_varbc_params.tar"
+        bias_dict = self.jedi.get_bias_dict(self.task_config, bias_file)
         FileHandler(bias_dict).sync()
         logger.debug(f"Bias correction files:\n{pformat(bias_dict)}")
 
+        # extract bias corrections
+        tar_file = os.path.join(self.task_config.DATA, 'obs', f"{self.task_config.GPREFIX}{bias_file}")
+        logger.info(f"Extract bias correction files from {tar_file}")
+        self.jedi.extract_tar(tar_file)
+
         # stage CRTM fix files
         logger.info(f"Staging CRTM fix files from {self.task_config.CRTM_FIX_YAML}")
         crtm_fix_dict = parse_j2yaml(self.task_config.CRTM_FIX_YAML, self.task_config)
@@ -265,37 +272,34 @@ def finalize(self) -> None:
             }
             FileHandler(yaml_copy).sync()
 
-        # copy bias correction files to ROTDIR
-        logger.info("Copy bias correction files from DATA/ to COM/")
-        biasdir = os.path.join(self.task_config.DATA, 'bc')
-        biasls = os.listdir(biasdir)
-        biaslist = []
-        for bfile in biasls:
-            src = os.path.join(biasdir, bfile)
-            dest = os.path.join(self.task_config.COM_ATMOS_ANALYSIS, bfile)
-            biaslist.append([src, dest])
-
-        gprefix = f"{self.task_config.GPREFIX}"
-        gsuffix = f"{to_YMDH(self.task_config.previous_cycle)}" + ".txt"
-        aprefix = f"{self.task_config.APREFIX}"
-        asuffix = f"{to_YMDH(self.task_config.current_cycle)}" + ".txt"
-
-        logger.info(f"Copying {gprefix}*{gsuffix} from DATA/ to COM/ as {aprefix}*{asuffix}")
-        obsdir = os.path.join(self.task_config.DATA, 'obs')
-        obsls = os.listdir(obsdir)
-        for ofile in obsls:
-            if ofile.endswith(".txt"):
-                src = os.path.join(obsdir, ofile)
-                tfile = ofile.replace(gprefix, aprefix)
-                tfile = tfile.replace(gsuffix, asuffix)
-                dest = os.path.join(self.task_config.COM_ATMOS_ANALYSIS, tfile)
-                biaslist.append([src, dest])
-
-        bias_copy = {
-            'mkdir': [self.task_config.COM_ATMOS_ANALYSIS],
-            'copy': biaslist,
+        # path of output radiance bias correction tarfile
+        bfile = f"{self.task_config.APREFIX}rad_varbc_params.tar"
+        radtar = os.path.join(self.task_config.COM_ATMOS_ANALYSIS, bfile)
+
+        # rename and copy tlapse radiance bias correction files from obs to bc
+        tlapobs = glob.glob(os.path.join(self.task_config.DATA, 'obs', '*tlapse.txt'))
+        copylist = []
+        for tlapfile in tlapobs:
+            obsfile = os.path.basename(tlapfile).split('.', 2)
+            newfile = f"{self.task_config.APREFIX}{obsfile[2]}"
+            copylist.append([tlapfile, os.path.join(self.task_config.DATA, 'bc', newfile)])
+        tlapse_dict = {
+            'copy': copylist
         }
-        FileHandler(bias_copy).sync()
+        FileHandler(tlapse_dict).sync()
+
+        # get lists of radiance bias correction files to add to tarball
+        satlist = glob.glob(os.path.join(self.task_config.DATA, 'bc', '*satbias*nc'))
+        tlaplist = glob.glob(os.path.join(self.task_config.DATA, 'bc', '*tlapse.txt'))
+
+        # tar radiance bias correction files to ROTDIR
+        logger.info(f"Creating radiance bias correction tar file {radtar}")
+        with tarfile.open(radtar, 'w') as radbcor:
+            for satfile in satlist:
+                radbcor.add(satfile, arcname=os.path.basename(satfile))
+            for tlapfile in tlaplist:
+                radbcor.add(tlapfile, arcname=os.path.basename(tlapfile))
+            logger.info(f"Add {radbcor.getnames()}")
 
         # Copy FV3 atm increment to comrot directory
         logger.info("Copy UFS model readable atm increment file")
diff --git a/ush/python/pygfs/task/atmens_analysis.py b/ush/python/pygfs/task/atmens_analysis.py
index 55e72702b1..4b2f8ebbf4 100644
--- a/ush/python/pygfs/task/atmens_analysis.py
+++ b/ush/python/pygfs/task/atmens_analysis.py
@@ -138,10 +138,17 @@ def initialize_analysis(self) -> None:
 
         # stage bias corrections
         logger.info(f"Staging list of bias correction files generated from JEDI config")
-        bias_dict = self.jedi.get_bias_dict(self.task_config)
+        self.task_config.VarBcDir = f"{self.task_config.COM_ATMOS_ANALYSIS_PREV}"
+        bias_file = f"rad_varbc_params.tar"
+        bias_dict = self.jedi.get_bias_dict(self.task_config, bias_file)
         FileHandler(bias_dict).sync()
         logger.debug(f"Bias correction files:\n{pformat(bias_dict)}")
 
+        # extract bias corrections
+        tar_file = os.path.join(self.task_config.DATA, 'obs', f"{self.task_config.GPREFIX}{bias_file}")
+        logger.info(f"Extract bias correction files from {tar_file}")
+        self.jedi.extract_tar(tar_file)
+
         # stage CRTM fix files
         logger.info(f"Staging CRTM fix files from {self.task_config.CRTM_FIX_YAML}")
         crtm_fix_dict = parse_j2yaml(self.task_config.CRTM_FIX_YAML, self.task_config)

From 8f0541cd61755e74e1f3116dedcc3afc8fa9cda1 Mon Sep 17 00:00:00 2001
From: Innocent Souopgui
 <162634017+InnocentSouopgui-NOAA@users.noreply.github.com>
Date: Mon, 30 Sep 2024 11:41:46 -0500
Subject: [PATCH 19/21] Move to contrib installation of spack-stack on Jet
 (#2878)

Migrates Global Workflow to use contrib installation of spack-stack on
Jet.
Following the failure of the storage /lfs4 on Jet, the installation of
spack spack moved to /contrib.
All softwares relying on spack-stack on Jet needs update.

Resolves #2841
Refs NOAA-EMC/gfs-utils#78
Refs NOAA-EMC/GSI#786
Refs NOAA-EMC/GSI-Monitor#143
Refs NOAA-EMC/GSI-utils#51
Refs ufs-community/UFS_UTILS#977
---
 docs/note_fixfield.txt             |  2 +-
 docs/source/components.rst         |  2 +-
 docs/source/init.rst               |  4 ++--
 modulefiles/module_base.jet.lua    |  2 +-
 modulefiles/module_gwsetup.jet.lua |  2 +-
 parm/config/gfs/config.aero        |  2 +-
 sorc/gfs_utils.fd                  |  2 +-
 sorc/gsi_enkf.fd                   |  2 +-
 sorc/gsi_monitor.fd                |  2 +-
 sorc/link_workflow.sh              |  2 +-
 sorc/ufs_model.fd                  |  2 +-
 sorc/ufs_utils.fd                  |  2 +-
 ush/detect_machine.sh              |  2 +-
 ush/forecast_predet.sh             |  1 -
 versions/build.jet.ver             |  4 ++--
 versions/run.jet.ver               |  8 ++++++--
 workflow/hosts.py                  |  2 +-
 workflow/hosts/jet.yaml            | 22 +++++++++++-----------
 18 files changed, 34 insertions(+), 31 deletions(-)

diff --git a/docs/note_fixfield.txt b/docs/note_fixfield.txt
index a7a4001561..32e44b9d98 100644
--- a/docs/note_fixfield.txt
+++ b/docs/note_fixfield.txt
@@ -4,7 +4,7 @@ They are saved locally on all platforms
 
 Hera: /scratch1/NCEPDEV/global/glopara/fix
 Orion/Hercules: /work/noaa/global/glopara/fix
-Jet: /mnt/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix
+Jet: /mnt/lfs5/HFIP/hfv3gfs/glopara/FIX/fix
 S4: /data/prod/glopara/fix
 
 ------------------------------------------------------------------------------
diff --git a/docs/source/components.rst b/docs/source/components.rst
index 869ef89bab..f5a60a96af 100644
--- a/docs/source/components.rst
+++ b/docs/source/components.rst
@@ -59,7 +59,7 @@ Observation data, also known as dump data, is prepared in production and then ar
 
 * Hera: ``/scratch1/NCEPDEV/global/glopara/dump``
 * Orion/Hercules: ``/work/noaa/rstprod/dump``
-* Jet: ``/mnt/lfs4/HFIP/hfv3gfs/glopara/dump``
+* Jet: ``/mnt/lfs5/HFIP/hfv3gfs/glopara/dump``
 * WCOSS2: ``/lfs/h2/emc/global/noscrub/emc.global/dump``
 * S4: ``/data/prod/glopara/dump``
 
diff --git a/docs/source/init.rst b/docs/source/init.rst
index e1cabdc8e0..aa71e4e294 100644
--- a/docs/source/init.rst
+++ b/docs/source/init.rst
@@ -111,7 +111,7 @@ Warm-start cycled w/ coupled (S2S) model C48 atmosphere C48 enkf (80 members) 5
    Hera: /scratch1/NCEPDEV/global/glopara/data/ICSDIR/C48C48mx500
    Orion/Hercules: /work/noaa/global/glopara/data/ICSDIR/C48C48mx500
    WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/data/ICSDIR/C48C48mx500
-   Jet: /lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/C48C48mx500
+   Jet: /lfs5/HFIP/hfv3gfs/glopara/data/ICSDIR/C48C48mx500
    AWS: https://noaa-nws-global-pds.s3.amazonaws.com/index.html#data/ICSDIR/C48C48mx500
 
 Start date = 2021032312
@@ -227,7 +227,7 @@ Forecast-only P8 prototype initial conditions are made available to users on sup
     WCOSS2: /lfs/h2/emc/global/noscrub/emc.global/IC/COUPLED
     HERA: /scratch1/NCEPDEV/climate/role.ufscpara/IC
     ORION/Hercules: /work/noaa/global/glopara/data/ICSDIR/prototype_ICs
-    JET: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs
+    JET: /mnt/lfs5/HFIP/hfv3gfs/glopara/data/ICSDIR/prototype_ICs
     S4: /data/prod/glopara/coupled_ICs
 
 These locations are known within the workflow via paths set in ``parm/config/config.coupled_ic``.
diff --git a/modulefiles/module_base.jet.lua b/modulefiles/module_base.jet.lua
index 2f00c301df..56735a2057 100644
--- a/modulefiles/module_base.jet.lua
+++ b/modulefiles/module_base.jet.lua
@@ -52,7 +52,7 @@ setenv("UTILROOT",(os.getenv("prod_util_ROOT") or "None"))
 prepend_path("MODULEPATH", pathJoin("/lfs5/HFIP/hfv3gfs/glopara/git/prepobs/v" .. (os.getenv("prepobs_run_ver") or "None"), "modulefiles"))
 load(pathJoin("prepobs", (os.getenv("prepobs_run_ver") or "None")))
 
-prepend_path("MODULEPATH", pathJoin("/lfs4/HFIP/hfv3gfs/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
+prepend_path("MODULEPATH", pathJoin("/lfs5/HFIP/hfv3gfs/glopara/git/Fit2Obs/v" .. (os.getenv("fit2obs_ver") or "None"), "modulefiles"))
 load(pathJoin("fit2obs", (os.getenv("fit2obs_ver") or "None")))
 
 whatis("Description: GFS run environment")
diff --git a/modulefiles/module_gwsetup.jet.lua b/modulefiles/module_gwsetup.jet.lua
index bc14b19a79..a722c812a5 100644
--- a/modulefiles/module_gwsetup.jet.lua
+++ b/modulefiles/module_gwsetup.jet.lua
@@ -4,7 +4,7 @@ Load environment to run GFS workflow setup scripts on Jet
 
 load(pathJoin("rocoto"))
 
-prepend_path("MODULEPATH", "/mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.6.0/envs/gsi-addon-dev-rocky8/install/modulefiles/Core")
+prepend_path("MODULEPATH", "/contrib/spack-stack/spack-stack-1.6.0/envs/gsi-addon-intel/install/modulefiles/Core")
 
 local stack_intel_ver=os.getenv("stack_intel_ver") or "2021.5.0"
 local python_ver=os.getenv("python_ver") or "3.11.6"
diff --git a/parm/config/gfs/config.aero b/parm/config/gfs/config.aero
index 2fae019574..f49593a439 100644
--- a/parm/config/gfs/config.aero
+++ b/parm/config/gfs/config.aero
@@ -24,7 +24,7 @@ case ${machine} in
     AERO_INPUTS_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/gocart_emissions"
     ;;
   "JET")
-    AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
+    AERO_INPUTS_DIR="/lfs5/HFIP/hfv3gfs/glopara/data/gocart_emissions"
     ;;
   *)
     echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
diff --git a/sorc/gfs_utils.fd b/sorc/gfs_utils.fd
index bd8f13d867..a00cc0949e 160000
--- a/sorc/gfs_utils.fd
+++ b/sorc/gfs_utils.fd
@@ -1 +1 @@
-Subproject commit bd8f13d867721e4ee28de4af437a0de4283609c3
+Subproject commit a00cc0949e2f901e73b58d54834517743916c69a
diff --git a/sorc/gsi_enkf.fd b/sorc/gsi_enkf.fd
index 529bb796be..9f44c8798c 160000
--- a/sorc/gsi_enkf.fd
+++ b/sorc/gsi_enkf.fd
@@ -1 +1 @@
-Subproject commit 529bb796bea0e490f186729cd168a91c034bb12d
+Subproject commit 9f44c8798c2087aca06df8f629699632e57df431
diff --git a/sorc/gsi_monitor.fd b/sorc/gsi_monitor.fd
index e1f9f21af1..278ee629e8 160000
--- a/sorc/gsi_monitor.fd
+++ b/sorc/gsi_monitor.fd
@@ -1 +1 @@
-Subproject commit e1f9f21af16ce912fdc2cd75c5b27094a550a0c5
+Subproject commit 278ee629e87558822e8d13b3fb3b0e16006aa856
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 9426a09ce9..870ddc5eba 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -73,7 +73,7 @@ case "${machine}" in
   "hera")     FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix" ;;
   "orion")    FIX_DIR="/work/noaa/global/glopara/fix" ;;
   "hercules") FIX_DIR="/work/noaa/global/glopara/fix" ;;
-  "jet")      FIX_DIR="/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix" ;;
+  "jet")      FIX_DIR="/lfs5/HFIP/hfv3gfs/glopara/FIX/fix" ;;
   "s4")       FIX_DIR="/data/prod/glopara/fix" ;;
   "gaea")     FIX_DIR="/gpfs/f5/ufs-ard/world-shared/global/glopara/data/fix" ;;
   "noaacloud") FIX_DIR="/contrib/global-workflow-shared-data/fix" ;;
diff --git a/sorc/ufs_model.fd b/sorc/ufs_model.fd
index fcc9f8461d..6a4e09e947 160000
--- a/sorc/ufs_model.fd
+++ b/sorc/ufs_model.fd
@@ -1 +1 @@
-Subproject commit fcc9f8461db5eafbfd1f080da61ea79156ca0145
+Subproject commit 6a4e09e94773ffa39ce7ab6a54a885efada91f21
diff --git a/sorc/ufs_utils.fd b/sorc/ufs_utils.fd
index 3ef2e6bd72..06eec5b6f6 160000
--- a/sorc/ufs_utils.fd
+++ b/sorc/ufs_utils.fd
@@ -1 +1 @@
-Subproject commit 3ef2e6bd725d2662fd6ee95897cb7bac222e5144
+Subproject commit 06eec5b6f636123835e2dfd9fc5229980c006735
diff --git a/ush/detect_machine.sh b/ush/detect_machine.sh
index b049a6040e..8ad217140a 100755
--- a/ush/detect_machine.sh
+++ b/ush/detect_machine.sh
@@ -67,7 +67,7 @@ if [[ -d /lfs/h3 ]]; then
 elif [[ -d /lfs/h1 && ! -d /lfs/h3 ]]; then
   # We are on NOAA TDS Acorn
   MACHINE_ID=acorn
-elif [[ -d /mnt/lfs1 ]]; then
+elif [[ -d /mnt/lfs5 ]]; then
   # We are on NOAA Jet
   MACHINE_ID=jet
 elif [[ -d /scratch1 ]]; then
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index d7c04ea699..5aa9dc9ac7 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -548,7 +548,6 @@ FV3_predet(){
       ${NCP} "${PARMgfs}/post/gefs/postxconfig-NT-gefs-f00.txt"   "${DATA}/postxconfig-NT_FH00.txt"
     fi
   fi
-
 }
 
 # Disable variable not used warnings
diff --git a/versions/build.jet.ver b/versions/build.jet.ver
index e103725d41..319a8fa0a6 100644
--- a/versions/build.jet.ver
+++ b/versions/build.jet.ver
@@ -1,5 +1,5 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
-export spack_env=gsi-addon-dev
+export spack_env=gsi-addon-intel
 source "${HOMEgfs:-}/versions/spack.ver"
-export spack_mod_path="/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
+export spack_mod_path="/contrib/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
diff --git a/versions/run.jet.ver b/versions/run.jet.ver
index 1e41fd0036..90553fb277 100644
--- a/versions/run.jet.ver
+++ b/versions/run.jet.ver
@@ -1,6 +1,6 @@
 export stack_intel_ver=2021.5.0
 export stack_impi_ver=2021.5.1
-export spack_env=gsi-addon-dev-rocky8
+export spack_env=gsi-addon-intel
 
 export hpss_ver=
 export ncl_ver=6.6.2
@@ -11,4 +11,8 @@ export gempak_ver=7.4.2
 export perl_ver=5.38.0
 
 source "${HOMEgfs:-}/versions/spack.ver"
-export spack_mod_path="/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
+export spack_mod_path="/contrib/spack-stack/spack-stack-${spack_stack_ver}/envs/${spack_env}/install/modulefiles/Core"
+
+# Local version of TC_tracker
+export ens_tracker_ver=v1.1.15.7
+
diff --git a/workflow/hosts.py b/workflow/hosts.py
index 34ea067ade..7bde58f95f 100644
--- a/workflow/hosts.py
+++ b/workflow/hosts.py
@@ -42,7 +42,7 @@ def detect(cls):
             machine = 'HERA'
         elif os.path.exists('/work/noaa'):
             machine = socket.gethostname().split("-", 1)[0].upper()
-        elif os.path.exists('/lfs4/HFIP'):
+        elif os.path.exists('/lfs5/HFIP'):
             machine = 'JET'
         elif os.path.exists('/lfs/f1'):
             machine = 'WCOSS2'
diff --git a/workflow/hosts/jet.yaml b/workflow/hosts/jet.yaml
index 80957083e0..a53224fe52 100644
--- a/workflow/hosts/jet.yaml
+++ b/workflow/hosts/jet.yaml
@@ -1,12 +1,12 @@
-BASE_GIT: '/lfs4/HFIP/hfv3gfs/glopara/git'
-DMPDIR: '/lfs4/HFIP/hfv3gfs/glopara/dump'
+BASE_GIT: '/lfs5/HFIP/hfv3gfs/glopara/git'
+DMPDIR: '/lfs5/HFIP/hfv3gfs/glopara/dump'
 BASE_DATA: '/lfs5/HFIP/hfv3gfs/glopara/data'
-BASE_IC: '/mnt/lfs4/HFIP/hfv3gfs/glopara/data/ICSDIR'
-PACKAGEROOT: '/lfs4/HFIP/hfv3gfs/glopara/nwpara'
-COMINsyn: '/lfs4/HFIP/hfv3gfs/glopara/com/gfs/prod/syndat'
-HOMEDIR: '/lfs4/HFIP/hfv3gfs/${USER}'
-STMP: '/lfs4/HFIP/hfv3gfs/${USER}/stmp'
-PTMP: '/lfs4/HFIP/hfv3gfs/${USER}/ptmp'
+BASE_IC: '/mnt/lfs5/HFIP/hfv3gfs/glopara/data/ICSDIR'
+PACKAGEROOT: '/lfs5/HFIP/hfv3gfs/glopara/nwpara'
+COMINsyn: '/lfs5/HFIP/hfv3gfs/glopara/com/gfs/prod/syndat'
+HOMEDIR: '/lfs5/HFIP/hfv3gfs/${USER}'
+STMP: '/lfs5/HFIP/hfv3gfs/${USER}/stmp'
+PTMP: '/lfs5/HFIP/hfv3gfs/${USER}/ptmp'
 NOSCRUB: $HOMEDIR
 ACCOUNT: hfv3gfs
 SCHEDULER: slurm
@@ -25,6 +25,6 @@ ATARDIR: '/NCEPDEV/${HPSS_PROJECT}/1year/${USER}/${machine}/scratch/${PSLOT}'
 MAKE_NSSTBUFR: 'NO'
 MAKE_ACFTBUFR: 'NO'
 SUPPORTED_RESOLUTIONS: ['C384', 'C192', 'C96', 'C48']
-COMINecmwf: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/external_gempak/ecmwf
-COMINnam: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/external_gempak/nam
-COMINukmet: /mnt/lfs4/HFIP/hfv3gfs/glopara/data/external_gempak/ukmet
+COMINecmwf: /mnt/lfs5/HFIP/hfv3gfs/glopara/data/external_gempak/ecmwf
+COMINnam: /mnt/lfs5/HFIP/hfv3gfs/glopara/data/external_gempak/nam
+COMINukmet: /mnt/lfs5/HFIP/hfv3gfs/glopara/data/external_gempak/ukmet

From 330e74b84da5446c80bf55e896a8952f17de68b4 Mon Sep 17 00:00:00 2001
From: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Date: Mon, 7 Oct 2024 12:29:21 -0400
Subject: [PATCH 20/21] Add corrections to the variable names for GEFS (#2969)

# Description
Corrections were made to the GEFS variable names in the parm files so
that they can be successfully extracted from the atmos master files in
the atmos_prod task.

Resolves #2967
---
 parm/product/gefs.0p25.fFFF.paramlist.b.txt | 58 ++++++++++-----------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
index f7fdb73ddf..85f5e6f711 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.b.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -33,32 +33,32 @@
 :CAPE:255-0 mb above ground:
 :CDUVB:surface:
 :CIN:255-0 mb above ground:
-:CLWMR:1000 mb:
-:CLWMR:100 mb:
-:CLWMR:10 mb:
-:CLWMR:150 mb:
-:CLWMR:200 mb:
-:CLWMR:20 mb:
-:CLWMR:250 mb:
-:CLWMR:300 mb:
-:CLWMR:30 mb:
-:CLWMR:350 mb:
-:CLWMR:400 mb:
-:CLWMR:450 mb:
-:CLWMR:500 mb:
-:CLWMR:50 mb:
-:CLWMR:550 mb:
-:CLWMR:600 mb:
-:CLWMR:650 mb:
-:CLWMR:700 mb:
-:CLWMR:70 mb:
-:CLWMR:750 mb:
-:CLWMR:800 mb:
-:CLWMR:850 mb:
-:CLWMR:900 mb:
-:CLWMR:925 mb:
-:CLWMR:950 mb:
-:CLWMR:975 mb:
+:CLMR:1000 mb:
+:CLMR:100 mb:
+:CLMR:10 mb:
+:CLMR:150 mb:
+:CLMR:200 mb:
+:CLMR:20 mb:
+:CLMR:250 mb:
+:CLMR:300 mb:
+:CLMR:30 mb:
+:CLMR:350 mb:
+:CLMR:400 mb:
+:CLMR:450 mb:
+:CLMR:500 mb:
+:CLMR:50 mb:
+:CLMR:550 mb:
+:CLMR:600 mb:
+:CLMR:650 mb:
+:CLMR:700 mb:
+:CLMR:70 mb:
+:CLMR:750 mb:
+:CLMR:800 mb:
+:CLMR:850 mb:
+:CLMR:900 mb:
+:CLMR:925 mb:
+:CLMR:950 mb:
+:CLMR:975 mb:
 :CNWAT:surface:
 :CPRAT:surface:
 :CWAT:entire atmosphere (considered as a single layer):
@@ -276,9 +276,9 @@
 :TCDC:475 mb:
 :TCDC:boundary layer cloud layer:
 :TCDC:convective cloud layer:
-:TCDC:high cloud layer:
-:TCDC:low cloud layer:
-:TCDC:middle cloud layer:
+:HCDC:high cloud layer:
+:LCDC:low cloud layer:
+:MCDC:middle cloud layer:
 :TMP:0.995 sigma level:
 :TMP:1000 mb:
 :TMP:100 m above ground:

From a42c833abe81df112e80da35843d698677d58bd7 Mon Sep 17 00:00:00 2001
From: Neil Barton <103681022+NeilBarton-NOAA@users.noreply.github.com>
Date: Tue, 8 Oct 2024 16:53:39 -0400
Subject: [PATCH 21/21] Adding a CI for using Replay ICs with an offset hour of
 3 (#2788)

This PR adds a CI testing using C96mx100 resolution and the S2SWA app. 2
perturb members are included with the control member.

---------

Co-authored-by: Eric.Sinsky <eric.sinsky@noaa.gov>
Co-authored-by: Eric Sinsky - NOAA <48259628+EricSinsky-NOAA@users.noreply.github.com>
Co-authored-by: Walter Kolczynski - NOAA <Walter.Kolczynski@noaa.gov>
---
 ci/cases/pr/C48_S2SWA_gefs.yaml               |  2 +-
 ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml    | 19 +++++++++++
 ...ci_defaults.yaml => gefs_defaults_ci.yaml} |  0
 ci/cases/yamls/gefs_replay_ci.yaml            | 14 ++++++++
 jobs/JGLOBAL_WAVE_POST_PNT                    |  2 +-
 parm/archive/gefs_arcdir.yaml.j2              |  8 ++++-
 parm/config/gefs/config.atmos_products        |  7 +++-
 parm/config/gefs/config.base                  | 32 +++++++++----------
 parm/config/gefs/config.efcs                  |  4 ---
 parm/config/gefs/config.extractvars           |  2 +-
 parm/config/gefs/yaml/defaults.yaml           |  4 +++
 parm/product/gefs.0p25.fFFF.paramlist.a.txt   |  3 +-
 parm/product/gefs.0p25.fFFF.paramlist.b.txt   |  1 +
 ...2 => atmosphere_ens_perturbations.yaml.j2} |  6 ++--
 parm/stage/master_gefs.yaml.j2                |  4 +--
 ...aml.j2 => ocean_ens_perturbations.yaml.j2} |  6 ++--
 scripts/exgfs_wave_post_pnt.sh                |  4 ++-
 ush/extractvars_tools.sh                      |  3 +-
 ush/ocnice_extractvars.sh                     | 14 ++++++--
 ush/parsing_namelists_MOM6.sh                 |  6 ++++
 workflow/rocoto/gefs_tasks.py                 |  1 +
 21 files changed, 102 insertions(+), 40 deletions(-)
 create mode 100644 ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml
 rename ci/cases/yamls/{gefs_ci_defaults.yaml => gefs_defaults_ci.yaml} (100%)
 create mode 100644 ci/cases/yamls/gefs_replay_ci.yaml
 rename parm/stage/{atmosphere_perturbation.yaml.j2 => atmosphere_ens_perturbations.yaml.j2} (79%)
 rename parm/stage/{ocean_replay.yaml.j2 => ocean_ens_perturbations.yaml.j2} (79%)

diff --git a/ci/cases/pr/C48_S2SWA_gefs.yaml b/ci/cases/pr/C48_S2SWA_gefs.yaml
index a924b416c3..98f0fcfadb 100644
--- a/ci/cases/pr/C48_S2SWA_gefs.yaml
+++ b/ci/cases/pr/C48_S2SWA_gefs.yaml
@@ -15,7 +15,7 @@ arguments:
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2021032312
   edate: 2021032312
-  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_ci_defaults.yaml
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_defaults_ci.yaml
 
 skip_ci_on_hosts:
   - wcoss2
diff --git a/ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml b/ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml
new file mode 100644
index 0000000000..1475e81ea0
--- /dev/null
+++ b/ci/cases/pr/C96_S2SWA_gefs_replay_ics.yaml
@@ -0,0 +1,19 @@
+experiment:
+  system: gefs
+  mode: forecast-only
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: S2SWA
+  resdetatmos: 96
+  resdetocean: 1.0
+  resensatmos: 96
+  nens: 2
+  gfs_cyc: 1
+  start: warm
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  idate: 2020110100
+  edate: 2020110100
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gefs_replay_ci.yaml
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96mx100/20240610
diff --git a/ci/cases/yamls/gefs_ci_defaults.yaml b/ci/cases/yamls/gefs_defaults_ci.yaml
similarity index 100%
rename from ci/cases/yamls/gefs_ci_defaults.yaml
rename to ci/cases/yamls/gefs_defaults_ci.yaml
diff --git a/ci/cases/yamls/gefs_replay_ci.yaml b/ci/cases/yamls/gefs_replay_ci.yaml
new file mode 100644
index 0000000000..dfbd9ae065
--- /dev/null
+++ b/ci/cases/yamls/gefs_replay_ci.yaml
@@ -0,0 +1,14 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
+base:
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  REPLAY_ICS: "YES"
+  FCST_BREAKPOINTS: ""
+  FHMAX_GFS: 48
+  FHMAX_HF_GFS: 24
+  DO_EXTRACTVARS: "YES"
+  FHOUT_HF_GFS: 3
+  FHOUT_OCN_GFS: 24
+  FHOUT_ICE_GFS: 24
+  HOMEDIR: {{ 'RUNTESTS' | getenv }}/GLOBAL
+
diff --git a/jobs/JGLOBAL_WAVE_POST_PNT b/jobs/JGLOBAL_WAVE_POST_PNT
index 769159be61..6be2d88906 100755
--- a/jobs/JGLOBAL_WAVE_POST_PNT
+++ b/jobs/JGLOBAL_WAVE_POST_PNT
@@ -25,7 +25,7 @@ export WAV_MOD_TAG=${RUN}wave${waveMEMB}
 
 export CFP_VERBOSE=1
 
-export FHMAX_WAV_PNT=${FHMAX_WAV}
+export FHMAX_WAV_PNT=$(( FHMAX_WAV - OFFSET_START_HOUR ))
 export DOSPC_WAV='YES' # Spectral post
 export DOBLL_WAV='YES' # Bulletin post
 export DOBNDPNT_WAV='NO'  #not boundary points
diff --git a/parm/archive/gefs_arcdir.yaml.j2 b/parm/archive/gefs_arcdir.yaml.j2
index a59a0e1a8f..d1008bc5c4 100644
--- a/parm/archive/gefs_arcdir.yaml.j2
+++ b/parm/archive/gefs_arcdir.yaml.j2
@@ -17,11 +17,17 @@
 
 {% set COMIN_ATMOS_ENSSTAT_1p00 = COM_ATMOS_GRIB_GRID_TMPL | replace_tmpl(tmpl_dict) %}
 
+{% if REPLAY_ICS %}
+    {% set ofst_hr = FHOUT_GFS %}
+{% else %}
+    {% set ofst_hr = FHMIN_GFS %}
+{% endif %}
+
 # Select ensstat files to copy to the arcdir
 {% if RUN == "gefs" %}
     {% set ensstat_files = [] %}
     {% if path_exists(COMIN_ATMOS_ENSSTAT_1p00) %}
-        {% for fhr in range(FHMIN_GFS, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
+        {% for fhr in range(ofst_hr, FHMAX_GFS + FHOUT_GFS, FHOUT_GFS) %}
             {% do ensstat_files.append([COMIN_ATMOS_ENSSTAT_1p00 ~ "/" ~ head ~ "mean.pres_." ~
                                         "1p00" ~ ".f" ~ '%03d'|format(fhr) ~ ".grib2",
                                         GEFS_ARCH]) %}
diff --git a/parm/config/gefs/config.atmos_products b/parm/config/gefs/config.atmos_products
index 4a0fb8b49f..73614ba08e 100644
--- a/parm/config/gefs/config.atmos_products
+++ b/parm/config/gefs/config.atmos_products
@@ -16,7 +16,12 @@ export INTERP_ATMOS_MASTERSH="${USHgfs}/interp_atmos_master.sh"
 export INTERP_ATMOS_SFLUXSH="${USHgfs}/interp_atmos_sflux.sh"
 
 export downset=2
-export FHOUT_PGBS=${FHOUT_GFS:-3}  # Output frequency of supplemental gfs pgb file at 1.0 and 0.5 deg
+
+if [[ "${FHMAX_HF_GFS:-0}" == "0" ]]; then
+    export FHOUT_PGBS=${FHOUT_GFS:-3}  # Output frequency of supplemental gfs pgb file at 1.0 and 0.5 deg
+else
+    export FHOUT_PGBS=${FHOUT_HF_GFS:-1}
+fi
 export FLXGF="NO"  # Create interpolated sflux.1p00 file
 
 # paramlist files for the different forecast hours and downsets
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index a0bd8b3bd1..6cf8488f91 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -229,6 +229,15 @@ export FHOUT_ICE=3
 # GFS cycle info
 export gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4: all 4 cycles.
 
+# set variables needed for use with REPLAY ICs
+export REPLAY_ICS=@REPLAY_ICS@
+if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+    export OFFSET_START_HOUR=$(( assim_freq / 2 ))
+else
+    export OFFSET_START_HOUR=0
+fi
+
+
 # GFS output and frequency
 export FHMIN_GFS=0
 export FHMAX_GFS="@FHMAX_GFS@"
@@ -238,10 +247,10 @@ export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
 
 export FHOUT_GFS=6
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
-export FHOUT_HF_GFS=1
-export FHOUT_OCN_GFS=6
-export FHOUT_ICE_GFS=6
-export FHMIN_WAV=0
+export FHOUT_HF_GFS=@FHOUT_HF_GFS@
+export FHOUT_OCN_GFS=@FHOUT_OCN_GFS@
+export FHOUT_ICE_GFS=@FHOUT_ICE_GFS@
+export FHMIN_WAV=${OFFSET_START_HOUR:-0}
 export FHOUT_WAV=3
 export FHMAX_HF_WAV=120
 export FHOUT_HF_WAV=1
@@ -290,20 +299,9 @@ export NMEM_ENS=@NMEM_ENS@
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
-# initialize ocean ensemble members with perturbations
-#   if true, only occurs for members greater than zero
-export REPLAY_ICS=@REPLAY_ICS@
-if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
-    export OFFSET_START_HOUR=$(( assim_freq / 2 ))
-else
-    export OFFSET_START_HOUR=0
-fi
-
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
-# Check if cycle is cold starting
-if [[ "${EXP_WARM_START}" = ".false." ]]; then
-  export IAU_FHROT=${OFFSET_START_HOUR}
-else
+# Check if cycle is warm starting with IAU
+if [[ "${EXP_WARM_START}" = ".true." ]]; then
   if [[ "${DOIAU}" = "YES" ]]; then
     export IAU_FHROT=3
   else
diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
index 807ed66d48..9bd55afa54 100644
--- a/parm/config/gefs/config.efcs
+++ b/parm/config/gefs/config.efcs
@@ -46,10 +46,6 @@ export SKEB_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 export SKEBNORM=1
 export SKEB_NPASS=30
 export SKEB_VDOF=5
-export DO_SHUM="YES"
-export SHUM=0.005
-export SHUM_TAU=21600.
-export SHUM_LSCALE=500000.
 export DO_SPPT="YES"
 export SPPT="0.56,0.28,0.14,0.056,0.028"
 export SPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
diff --git a/parm/config/gefs/config.extractvars b/parm/config/gefs/config.extractvars
index cc93fcf5e0..7f1166a869 100644
--- a/parm/config/gefs/config.extractvars
+++ b/parm/config/gefs/config.extractvars
@@ -14,7 +14,7 @@ export compress_ice=1 #1: Compress extracted ice product, 0: Do not compress ext
 
 export ocnres="1p00" # Resolution of ocean products
 export iceres="native" # Resolution of ice products
-export wavres="0p25" # Resolution of wave products
+export wavres="${waveGRD:4:1}p${waveGRD:5:2}"  # Resolution of wave products
 
 export depthvar_name="z_l" # Name of depth variable in NetCDF ocean products
 export zmin="0." # Minimum depth to extract from NetCDF ocean products
diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
index 382e60ee12..b5870b3e7e 100644
--- a/parm/config/gefs/yaml/defaults.yaml
+++ b/parm/config/gefs/yaml/defaults.yaml
@@ -11,7 +11,11 @@ base:
   DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
+  FHOUT_HF_GFS: 1
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"
+  FHOUT_OCN_GFS: 6
+  FHOUT_ICE_GFS: 6
+  HPSSARCH: "NO"
   LOCALARCH: "NO"
diff --git a/parm/product/gefs.0p25.fFFF.paramlist.a.txt b/parm/product/gefs.0p25.fFFF.paramlist.a.txt
index a4a3ace385..303752ac17 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.a.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.a.txt
@@ -12,13 +12,14 @@
 :CSNOW:surface:
 :CFRZR:surface:
 :CICEP:surface:
+:FDNSSTMP:surface:
 :PWAT:entire atmosphere (considered as a single layer):
 :CAPE:180-0 mb above ground:
 :CAPE:surface:
 :CIN:180-0 mb above ground:
 :CIN:surface:
 :HLCY:3000-0 m above ground:
-:TCDC:entire atmosphere:
+:TCDC:entire atmosphere (considered as a single layer):
 :WEASD:surface:
 :SNOD:surface:
 :ULWRF:top of atmosphere:
diff --git a/parm/product/gefs.0p25.fFFF.paramlist.b.txt b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
index 85f5e6f711..ccad9da4d0 100644
--- a/parm/product/gefs.0p25.fFFF.paramlist.b.txt
+++ b/parm/product/gefs.0p25.fFFF.paramlist.b.txt
@@ -346,6 +346,7 @@
 :TMP:surface:
 :TMP:tropopause:
 :TOZNE:entire atmosphere (considered as a single layer):
+:TSNOWP:surface:
 :TSOIL:0.1-0.4 m below ground:
 :TSOIL:0.4-1 m below ground:
 :TSOIL:1-2 m below ground:
diff --git a/parm/stage/atmosphere_perturbation.yaml.j2 b/parm/stage/atmosphere_ens_perturbations.yaml.j2
similarity index 79%
rename from parm/stage/atmosphere_perturbation.yaml.j2
rename to parm/stage/atmosphere_ens_perturbations.yaml.j2
index 0e097b71dc..d9caf58b72 100644
--- a/parm/stage/atmosphere_perturbation.yaml.j2
+++ b/parm/stage/atmosphere_ens_perturbations.yaml.j2
@@ -1,12 +1,12 @@
-atmosphere_perturbation:
+atmosphere_ens_perturbation:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
     copy:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}/{{ RUN }}.t{{ current_cycle_HH }}z.atminc.nc"]
diff --git a/parm/stage/master_gefs.yaml.j2 b/parm/stage/master_gefs.yaml.j2
index bdd4c8de5f..2bfe3a9d58 100644
--- a/parm/stage/master_gefs.yaml.j2
+++ b/parm/stage/master_gefs.yaml.j2
@@ -116,7 +116,7 @@
 
 {% if REPLAY_ICS %}
 {% filter indent(width=4) %}
-{% include "atmosphere_perturbation.yaml.j2" %}
+{% include "atmosphere_ens_perturbations.yaml.j2" %}
 {% endfilter %}
 {% endif %}
 
@@ -137,7 +137,7 @@
 {% endif %}
 {% if REPLAY_ICS %}
 {% filter indent(width=4) %}
-{% include "ocean_replay.yaml.j2" %}
+{% include "ocean_ens_perturbations.yaml.j2" %}
 {% endfilter %}
 {% endif %}
 {% if EXP_WARM_START %}
diff --git a/parm/stage/ocean_replay.yaml.j2 b/parm/stage/ocean_ens_perturbations.yaml.j2
similarity index 79%
rename from parm/stage/ocean_replay.yaml.j2
rename to parm/stage/ocean_ens_perturbations.yaml.j2
index 8b52108bec..fede3816a7 100644
--- a/parm/stage/ocean_replay.yaml.j2
+++ b/parm/stage/ocean_ens_perturbations.yaml.j2
@@ -1,12 +1,12 @@
-ocean_replay:
+ocean_ens_perturbation:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_OCEAN_ANALYSIS_MEM }}"
         {% endfor %} # mem loop
     copy:
-        {% for mem in range(first_mem, last_mem + 1) %}
+        {% for mem in range(first_mem + 1, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_OCEAN_ANALYSIS_MEM = COMOUT_OCEAN_ANALYSIS_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_OCEAN_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.mom6_perturbation.nc", "{{ COMOUT_OCEAN_ANALYSIS_MEM }}/mom6_increment.nc"]
diff --git a/scripts/exgfs_wave_post_pnt.sh b/scripts/exgfs_wave_post_pnt.sh
index 0b8874f3fb..06769303a1 100755
--- a/scripts/exgfs_wave_post_pnt.sh
+++ b/scripts/exgfs_wave_post_pnt.sh
@@ -252,7 +252,9 @@ source "${USHgfs}/preamble.sh"
                                ww3_outp_spec.inp.tmpl > ww3_outp.inp
 
     ${NLN} mod_def.$waveuoutpGRD mod_def.ww3
-    HMS="${cyc}0000"
+    #export OFFSET_START_HOUR=$( printf "%02d" ${half_assim} )
+    hh=$( printf "%02d" $(( cyc + OFFSET_START_HOUR )) )
+    HMS="${hh}0000"
     if [[ -f "${COMIN_WAVE_HISTORY}/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${PDY}.${HMS}" ]]; then
       ${NLN} "${COMIN_WAVE_HISTORY}/${WAV_MOD_TAG}.out_pnt.${waveuoutpGRD}.${PDY}.${HMS}" \
         "./out_pnt.${waveuoutpGRD}"
diff --git a/ush/extractvars_tools.sh b/ush/extractvars_tools.sh
index daf61a3d2e..51c2586cb5 100644
--- a/ush/extractvars_tools.sh
+++ b/ush/extractvars_tools.sh
@@ -17,7 +17,8 @@ check_atmos() {
   done
   mapfile -t requestedvar_in_allgrb2file_arr < "${requestedvar_in_allgrb2file}"
   while read -r vari; do
-    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ ${vari} ]] ;then
+    # shellcheck disable=SC2076
+    if [[ ! ${requestedvar_in_allgrb2file_arr[*]} =~ "${vari}" ]] ;then
       echo "WARNING: PARM VARIABLE (${vari}) is not available in pgrb and pgrb2b for f${fnhl}."
     fi
   done <"${varlistl}"
diff --git a/ush/ocnice_extractvars.sh b/ush/ocnice_extractvars.sh
index 51276172b9..78c4cbd91e 100755
--- a/ush/ocnice_extractvars.sh
+++ b/ush/ocnice_extractvars.sh
@@ -21,15 +21,23 @@ comout_rfcst_prod_ocnice=${6}
 
 [[ -d "${subdata}" ]] || mkdir -p "${subdata}"
 
-for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
+for (( nh = FHMIN_GFS + fhout_ocnice; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
   fnh=$(printf "%3.3d" "${nh}")
 
   if [[ ${component_name} == "ocn" ]]; then
-    infile=${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
+    if [[ "${datares}" == "native" ]]; then
+      infile="${COMIN_OCEAN_HISTORY}/${RUN}.ocean.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+    else
+      infile="${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc"
+    fi
     # For ocean products, add an argument to extract a subset of levels
     otherargs=(-d "${depthvar_name},""${zmin},""${zmax}")
   elif [[ ${component_name} == "ice" ]]; then
-    infile=${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
+    if [[ "${datares}" == "native" ]]; then
+      infile="${COMIN_ICE_HISTORY}/${RUN}.ice.t${cyc}z.${fhout_ocnice}hr_avg.f${fnh}.nc"
+    else
+      infile="${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc"
+    fi
     otherargs=()
   fi
   outfile=${subdata}/${RUN}.${component_name}.t${cyc}z.${datares}.f${fnh}.nc
diff --git a/ush/parsing_namelists_MOM6.sh b/ush/parsing_namelists_MOM6.sh
index 9010851806..3ac2cb465e 100755
--- a/ush/parsing_namelists_MOM6.sh
+++ b/ush/parsing_namelists_MOM6.sh
@@ -41,6 +41,12 @@ cat input.nml
 # ---------
 # Prepare local variables for use in MOM_input.IN from UFSWM
 # The ones already defined are left commented as a reminder
+# == MOM options to start from coarsed grained restarts, set to off by default
+#       options only available for 05 and 1 degree grids
+#       as restarts are coarsed grained/interpolated from the 0.25 degrees grid
+local MOM6_INIT_FROM_Z=${MOM6_INIT_FROM_Z:-True}
+local MOM6_WARMSTART_FILE=${MOM6_WARMSTART_FILE:-"none"}
+local MOM6_INIT_UV=${MOM6_INIT_UV:-"zero"}
 # == MOM_domains section ==
 # NX_GLB
 # NY_GLB
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index e214bb8c19..4ed6b3d038 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -314,6 +314,7 @@ def atmos_ensstat(self):
 
     def wavepostsbs(self):
         deps = []
+
         dep_dict = {'type': 'metatask', 'name': f'fcst_mem#member#'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)