From c9e41b19dd08f219835112d205126d99ad1582cb Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 28 Aug 2024 09:11:58 -0400
Subject: [PATCH 01/16] ...

---
 jobs/JGLOBAL_MARINE_BMAT                 |   8 +-
 ush/python/pygfs/task/marine_analysis.py | 118 +++++++++++++++++++++++
 ush/python/pygfs/task/marine_bmat.py     |   2 +-
 3 files changed, 123 insertions(+), 5 deletions(-)
 create mode 100644 ush/python/pygfs/task/marine_analysis.py

diff --git a/jobs/JGLOBAL_MARINE_BMAT b/jobs/JGLOBAL_MARINE_BMAT
index 3dacec9278..c9ad6cf5fb 100755
--- a/jobs/JGLOBAL_MARINE_BMAT
+++ b/jobs/JGLOBAL_MARINE_BMAT
@@ -3,11 +3,11 @@
 source "${HOMEgfs}/ush/preamble.sh"
 
 if (( 10#${ENSMEM:-0} > 0 )); then
-  export DATAjob="${DATAROOT}/${RUN}marinebmat.${PDY:-}${cyc}"
-  export DATA="${DATAjob}/${jobid}"
+  export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+  export DATA="${DATAjob}/marinebmat.${jobid}"
   # Create the directory to hold ensemble perturbations
-  export DATAenspert="${DATAjob}/enspert"
-  if [[ ! -d "${DATAenspert}" ]]; then mkdir -p "${DATAenspert}"; fi
+  export DATAens="${DATAjob}/ensdata"
+  if [[ ! -d "${DATAens}" ]]; then mkdir -p "${DATAens}"; fi
 fi
 
 # source config.base, config.ocnanal and config.marinebmat
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
new file mode 100644
index 0000000000..28be984aa5
--- /dev/null
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -0,0 +1,118 @@
+#!/usr/bin/env python3
+
+import os
+import glob
+from logging import getLogger
+import pygfs.utils.marine_da_utils as mdau
+
+from wxflow import (AttrDict,
+                    FileHandler,
+                    add_to_datetime, to_timedelta,
+                    chdir,
+                    parse_j2yaml,
+                    logit,
+                    Executable,
+                    Task)
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+class MarineAnalysis(Task):
+    """
+    Class for global marine analysis tasks
+    """
+    @logit(logger, name="MarineAnalysis")
+    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)
+
+        # 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(
+            {
+                'HOMEgdas': _home_gdas,
+                '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.",
+            }
+        )
+
+        # Extend task_config with local_dict
+        self.task_config = AttrDict(**self.task_config, **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()
+
+        # 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 backgrounds
+        # TODO(G): Check ocean backgrounds dates for consistency
+        bkg_list = parse_j2yaml(self.task_config.MARINE_DET_STAGE_BKG_YAML_TMPL, self.task_config)
+        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)
+        FileHandler(soca_utility_list).sync()
+
+        # 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)
+
+    @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_MARINEBMAT)
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('var.yaml')
+
+        mdau.run(exec_cmd)
+
+
+    @logit(logger)
+    def finalize(self: Task) -> None:
+        """Finalize the marine analysis job
+
+        This method will finalize the marine analysis job.
+        This includes:
+        -
+        - ...
+
+        """
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 4770583934..bebdb21b58 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -31,7 +31,7 @@ def __init__(self, config):
 
         # 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)
+            _enspert_relpath = os.path.relpath(self.task_config.DATAens, self.task_config.DATA)
         else:
             _enspert_relpath = None
 

From 53a4de80967b1bad34d860197b90ab830fb37f97 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@gmail.com>
Date: Wed, 4 Sep 2024 00:00:14 +0000
Subject: [PATCH 02/16] var init ok, run needs tlc

---
 env/CONTAINER.env                             |   4 +-
 env/HERA.env                                  |   4 +-
 env/HERCULES.env                              |   4 +-
 env/JET.env                                   |   4 +-
 env/ORION.env                                 |   4 +-
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST         |   4 +-
 jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY         |   2 +-
 ...REP => JGLOBAL_MARINE_ANALYSIS_INITIALIZE} |  36 ++--
 ...UN => JGLOBAL_MARINE_ANALYSIS_VARIATIONAL} |  17 +-
 jobs/JGLOBAL_MARINE_BMAT                      |  14 +-
 .../{ocnanalprep.sh => marineanlinit.sh}      |   2 +-
 .../rocoto/{ocnanalrun.sh => marineanlvar.sh} |   4 +-
 parm/archive/gdas.yaml.j2                     |   4 +-
 parm/config/gfs/config.marineanlinit          |  10 ++
 parm/config/gfs/config.marineanlvar           |  11 ++
 parm/config/gfs/config.ocnanalprep            |  10 --
 parm/config/gfs/config.ocnanalrun             |  11 --
 parm/config/gfs/config.resources              |   6 +-
 .../exglobal_marine_analysis_initialize.py    |  24 +++
 .../exglobal_marine_analysis_variational.py   |  22 +++
 ush/python/pygfs/task/marine_analysis.py      | 160 +++++++++++++++++-
 ush/python/pygfs/task/marine_bmat.py          |  14 +-
 ush/python/pygfs/utils/marine_da_utils.py     |  95 +++++++++++
 workflow/applications/gfs_cycled.py           |   4 +-
 workflow/rocoto/gfs_tasks.py                  |  22 +--
 workflow/rocoto/tasks.py                      |   2 +-
 26 files changed, 387 insertions(+), 107 deletions(-)
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP => JGLOBAL_MARINE_ANALYSIS_INITIALIZE} (60%)
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN => JGLOBAL_MARINE_ANALYSIS_VARIATIONAL} (64%)
 rename jobs/rocoto/{ocnanalprep.sh => marineanlinit.sh} (89%)
 rename jobs/rocoto/{ocnanalrun.sh => marineanlvar.sh} (82%)
 create mode 100644 parm/config/gfs/config.marineanlinit
 create mode 100644 parm/config/gfs/config.marineanlvar
 delete mode 100644 parm/config/gfs/config.ocnanalprep
 delete mode 100644 parm/config/gfs/config.ocnanalrun
 create mode 100755 scripts/exglobal_marine_analysis_initialize.py
 create mode 100755 scripts/exglobal_marine_analysis_variational.py

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 697cf21965..da72c1f4b2 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -123,11 +123,11 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
     export APRUN_MARINEBMAT="${APRUN}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
 
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEANLVAR="${APRUN}"
 
 elif [[ "${step}" = "ocnanalchkpt" ]]; then
 
diff --git a/env/HERCULES.env b/env/HERCULES.env
index 83d934c91a..86df340855 100755
--- a/env/HERCULES.env
+++ b/env/HERCULES.env
@@ -118,10 +118,10 @@ case ${step} in
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN}"
  ;;
- "ocnanalrun")
+ "marineanlvar")
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEANLVAR="${APRUN}"
  ;;
 "ocnanalecen")
 
diff --git a/env/JET.env b/env/JET.env
index 473539ded1..019b4c1b65 100755
--- a/env/JET.env
+++ b/env/JET.env
@@ -106,10 +106,10 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
     export APRUN_MARINEBMAT="${APRUN}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEANLVAR="${APRUN}"
 
 elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
 
diff --git a/env/ORION.env b/env/ORION.env
index 65a8871cdd..e34bf8575d 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -116,11 +116,11 @@ elif [[ "${step}" = "marinebmat" ]]; then
     export NTHREADS_MARINEBMAT=${NTHREADSmax}
     export APRUN_MARINEBMAT="${APRUN}"
 
-elif [[ "${step}" = "ocnanalrun" ]]; then
+elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEANLVAR="${APRUN}"
 
 elif [[ "${step}" = "ocnanalchkpt" ]]; then
 
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
index 00597f14f8..2d28569741 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
@@ -44,6 +44,6 @@ status=$?
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || exit 1
-[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+#[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
-exit 0
+exit 1
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_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..f294841306 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 ocnanal 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/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
similarity index 64%
rename from jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
rename to jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
index 5871497223..57724aee21 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
@@ -1,14 +1,16 @@
-#!/bin/bash
+#! /usr/bin/env 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 "marineanlvar" -c "base ocnanal marineanlvar"
 
 ##############################################
 # Set variables used in the script
 ##############################################
 
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
@@ -17,7 +19,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalr
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNRUNSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_run.sh}
+EXSCRIPT=${GDASMARINERUNSH:-${SCRgfs}/exglobal_marine_analysis_variational.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -33,9 +35,4 @@ 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_BMAT b/jobs/JGLOBAL_MARINE_BMAT
index c9ad6cf5fb..5dec9b153c 100755
--- a/jobs/JGLOBAL_MARINE_BMAT
+++ b/jobs/JGLOBAL_MARINE_BMAT
@@ -2,13 +2,13 @@
 
 source "${HOMEgfs}/ush/preamble.sh"
 
-if (( 10#${ENSMEM:-0} > 0 )); then
-  export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
-  export DATA="${DATAjob}/marinebmat.${jobid}"
-  # Create the directory to hold ensemble perturbations
-  export DATAens="${DATAjob}/ensdata"
-  if [[ ! -d "${DATAens}" ]]; then mkdir -p "${DATAens}"; 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 ${machine}.env
diff --git a/jobs/rocoto/ocnanalprep.sh b/jobs/rocoto/marineanlinit.sh
similarity index 89%
rename from jobs/rocoto/ocnanalprep.sh
rename to jobs/rocoto/marineanlinit.sh
index 3830fe1c39..953fc0dcfd 100755
--- a/jobs/rocoto/ocnanalprep.sh
+++ b/jobs/rocoto/marineanlinit.sh
@@ -14,6 +14,6 @@ export jobid="${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/ocnanalrun.sh b/jobs/rocoto/marineanlvar.sh
similarity index 82%
rename from jobs/rocoto/ocnanalrun.sh
rename to jobs/rocoto/marineanlvar.sh
index 5f998af989..35a21a2bcb 100755
--- a/jobs/rocoto/ocnanalrun.sh
+++ b/jobs/rocoto/marineanlvar.sh
@@ -8,11 +8,11 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalrun"
+export job="marineanlvar"
 export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
+"${HOMEgfs}/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL"
 status=$?
 exit "${status}"
diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
index db92141ede..3bc4a4125e 100644
--- a/parm/archive/gdas.yaml.j2
+++ b/parm/archive/gdas.yaml.j2
@@ -21,9 +21,9 @@ 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 }}marineanlvar.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalpost.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalchkpt.log"
                 {% if DOHYBVAR %}
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.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.resources b/parm/config/gfs/config.resources
index 978dca6d51..a279878c6f 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 ocnanalchkpt ocnanalpost ocnanalvrfy"
     exit 1
 
 fi
@@ -469,7 +469,7 @@ case ${step} in
     memory="3072M"
     ;;
 
-  "ocnanalprep")
+  "marineanlinit")
     walltime="00:10:00"
     ntasks=1
     threads_per_task=1
@@ -503,7 +503,7 @@ case ${step} in
     tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
     ;;
 
-  "ocnanalrun")
+  "marineanlvar")
     ntasks=16
     case ${OCNRES} in
       "025")
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..5e15f410c6
--- /dev/null
+++ b/scripts/exglobal_marine_analysis_variational.py
@@ -0,0 +1,22 @@
+#!/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)
+    MarineAnl.variational()
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 28be984aa5..6065481419 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -1,22 +1,42 @@
 #!/usr/bin/env python3
 
+import copy
 import os
 import glob
 from logging import getLogger
 import pygfs.utils.marine_da_utils as mdau
+import re
+import yaml
+from jcb import render
 
 from wxflow import (AttrDict,
                     FileHandler,
-                    add_to_datetime, to_timedelta,
-                    chdir,
+                    add_to_datetime, to_timedelta, to_YMD,
                     parse_j2yaml,
                     logit,
                     Executable,
-                    Task)
+                    Task,
+                    Template, TemplateConstants, YAMLFile)
 
 logger = getLogger(__name__.split('.')[-1])
 
 
+def parse_obs_list_file(gdas_home):
+    # Get the list of observation types from the obs_list.yaml
+    obs_list_path = os.path.join(gdas_home, 'parm', 'soca', 'obs', 'obs_list.yaml')
+    obs_types = []
+    with open(obs_list_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'\$\{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
@@ -27,6 +47,7 @@ def __init__(self, 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_begin_iso = _window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')
         _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
@@ -40,15 +61,19 @@ def __init__(self, config):
             {
                 'HOMEgdas': _home_gdas,
                 'MARINE_WINDOW_BEGIN': _window_begin,
+                'MARINE_WINDOW_BEGIN_ISO': _window_begin_iso,
                 'MARINE_WINDOW_END': _window_end,
+                'MARINE_WINDOW_LENGTH': f"PT{self.task_config['assim_freq']}H",
                 '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'),
+                'MARINE_OBS_LIST_YAML': os.path.join(_home_gdas, 'parm', 'soca', 'obs', 'obs_list.yaml'),
                 'ENSPERT_RELPATH': _enspert_relpath,
                 'CALC_SCALE_EXEC': _calc_scale_exec,
                 'APREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",
+                'OPREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z."
             }
         )
 
@@ -70,6 +95,13 @@ def initialize(self: Task) -> None:
         """
         super().initialize()
 
+        # prepare the directory structure to run SOCA
+        self._prep_scratch_dir()
+
+        # fetch observations from COMROOT
+        # TODO(GV or AE): Keep a copy of the obs in the scratch fs after the obs prep job
+        self._fetch_observations()
+
         # 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)
@@ -88,19 +120,139 @@ def initialize(self: Task) -> None:
         soca_utility_list = parse_j2yaml(self.task_config.UTILITY_YAML_TMPL, self.task_config)
         FileHandler(soca_utility_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 static B resources
+        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()
+
+    @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.APREFIX}{ob['obs space']['name'].lower()}.{to_YMD(self.task_config.PDY)}{self.task_config.cyc}.nc4")
+            obs_files.append(f"{self.task_config.APREFIX}{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 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()
+
+    @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
+        with open('obs_list_short.yaml', 'w') as file:
+            yaml.dump(parse_obs_list_file(self.task_config.HOMEgdas), file, default_flow_style=False)
+        os.environ['OBS_LIST_SHORT'] = 'obs_list_short.yaml'
+
+        # Render the JCB configuration files
+        jcb_base_yaml = os.path.join(self.task_config.HOMEgdas, 'parm', 'soca', 'marine-jcb-base.yaml')
+        jcb_algo_yaml = os.path.join(self.task_config.HOMEgdas, 'parm', 'soca', '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')
+
+
     @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_MARINEBMAT)
+        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)
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index bebdb21b58..8fccb91ee7 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -30,10 +30,7 @@ def __init__(self, config):
         _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.DATAens, 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(
@@ -137,9 +134,12 @@ def initialize(self: Task) -> None:
                                                 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.DATA, '..', 'staticb')
+        link_name = os.path.join(self.task_config.DATA, 'diagb')
+        if os.path.exists(link_name):
+            os.remove(link_name)
+        os.symlink(link_target, link_name)
 
     @logit(logger)
     def gridgen(self: Task) -> None:
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 2be76ac028..450678b2fc 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -1,7 +1,11 @@
+from netCDF4 import Dataset
+from datetime import datetime, timedelta
+import dateutil.parser as dparser
 import f90nml
 import os
 from logging import getLogger
 import xarray as xr
+import yaml
 
 from wxflow import (FileHandler,
                     logit,
@@ -9,6 +13,7 @@
                     AttrDict,
                     parse_j2yaml,
                     Executable,
+                    save_as_yaml,
                     jinja)
 
 logger = getLogger(__name__.split('.')[-1])
@@ -74,3 +79,93 @@ 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}")
+    assert hist_date == ref_date, '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
+    f = open(yaml_name, 'w')
+    yaml.dump(bkg_list, f, sort_keys=False, default_flow_style=False)
+
+@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:
+        logger.error(f"Error: {app} case not implemented yet!")
+
+    # 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"{fname} does not exist, removing obs space")
+            print("File does not exist")
+
+    # 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 f534764245..5b9aebc8ae 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -43,7 +43,7 @@ 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']
@@ -145,7 +145,7 @@ 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']
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index f60ac9a549..11ab810dc3 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -657,7 +657,7 @@ def marinebmat(self):
 
         return task
 
-    def ocnanalprep(self):
+    def marineanlinit(self):
 
         deps = []
         dep_dict = {'type': 'task', 'name': f'{self.run}prepoceanobs'}
@@ -668,14 +668,14 @@ 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;'
@@ -685,21 +685,21 @@ 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;'
@@ -712,7 +712,7 @@ 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)
 
@@ -739,7 +739,7 @@ def ocnanalchkpt(self):
         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'
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index ab89247fbb..4f6b8df391 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -16,7 +16,7 @@ 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', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',
                    'atmensanlinit', 'atmensanlletkf', 'atmensanlfv3inc', 'atmensanlfinal',

From ba78b003ccc8f6dc2433c42feac4210bb5c67510 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Sun, 8 Sep 2024 22:08:43 -0500
Subject: [PATCH 03/16] updated checkpoint task

---
 ci/cases/gfsv17/ocnanal.yaml                  |   2 +-
 env/HERA.env                                  |   4 +-
 env/HERCULES.env                              |   4 +-
 env/ORION.env                                 |   4 +-
 ...KPT => JGLOBAL_MARINE_ANALYSIS_CHECKPOINT} |  28 +--
 jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE       |   2 +-
 jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL      |   2 +-
 jobs/JGLOBAL_MARINE_BMAT                      |   2 +-
 .../{ocnanalchkpt.sh => marineanlchkpt.sh}    |   5 +-
 parm/archive/gdas.yaml.j2                     |   2 +-
 .../gfs/{config.ocnanal => config.marineanl}  |   6 +-
 parm/config/gfs/config.marineanlchkpt         |  11 ++
 parm/config/gfs/config.ocnanalchkpt           |  11 --
 parm/config/gfs/config.resources              |   4 +-
 parm/config/gfs/yaml/defaults.yaml            |   4 +-
 .../exglobal_marine_analysis_checkpoint.py    |  29 +++
 sorc/link_workflow.sh                         |  20 ++
 ush/python/pygfs/task/marine_analysis.py      | 184 +++++++++++++++---
 ush/python/pygfs/task/marine_bmat.py          |  18 +-
 workflow/applications/gfs_cycled.py           |   4 +-
 workflow/rocoto/gfs_tasks.py                  |  10 +-
 workflow/rocoto/tasks.py                      |   2 +-
 22 files changed, 267 insertions(+), 91 deletions(-)
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT => JGLOBAL_MARINE_ANALYSIS_CHECKPOINT} (53%)
 rename jobs/rocoto/{ocnanalchkpt.sh => marineanlchkpt.sh} (77%)
 rename parm/config/gfs/{config.ocnanal => config.marineanl} (89%)
 create mode 100644 parm/config/gfs/config.marineanlchkpt
 delete mode 100644 parm/config/gfs/config.ocnanalchkpt
 create mode 100755 scripts/exglobal_marine_analysis_checkpoint.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/HERA.env b/env/HERA.env
index da72c1f4b2..2c2a0bf751 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -129,11 +129,11 @@ elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUN_MARINEANLVAR="${APRUN}"
 
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
 
-    export APRUN_OCNANAL="${APRUN}"
+    export APRUN_MARINEANLCHKPT="${APRUN}"
 
 elif [[ "${step}" = "ocnanalecen" ]]; then
 
diff --git a/env/HERCULES.env b/env/HERCULES.env
index 86df340855..affcae7b5d 100755
--- a/env/HERCULES.env
+++ b/env/HERCULES.env
@@ -133,12 +133,12 @@ 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} --cpus-per-task=${NTHREADS_OCNANAL}"
+    export APRUN_MARINEANLCHKPT="${APRUN} --cpus-per-task=${NTHREADS_OCNANAL}"
  ;;
  "anal" | "analcalc")
 
diff --git a/env/ORION.env b/env/ORION.env
index e34bf8575d..5c86926e69 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -122,12 +122,12 @@ elif [[ "${step}" = "marineanlvar" ]]; then
 
     export APRUN_MARINEANLVAR="${APRUN}"
 
-elif [[ "${step}" = "ocnanalchkpt" ]]; then
+elif [[ "${step}" = "marineanlchkpt" ]]; then
 
     export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"
 
     export NTHREADS_OCNANAL=${NTHREADSmax}
-    export APRUN_OCNANAL="${APRUN} --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/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
similarity index 53%
rename from jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
rename to jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
index 875fe9d0ee..12e19564d8 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+++ 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 "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnanalchkpt"
+export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
+export DATA="${DATAjob}/marinevariational"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl marineanlchkpt"
 
 
 ##############################################
@@ -11,22 +12,10 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnana
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(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 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=${gcyc} declare_from_tmpl -rx COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
-
-
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
@@ -34,7 +23,7 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx COM_ATMOS_HISTORY_PREV
 ###############################################################
 # Run relevant script
 
-EXSCRIPT=${GDASOCNCHKPTSH:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_chkpt.sh}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_checkpoint.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -50,9 +39,4 @@ if [[ -e "${pgmout}" ]] ; then
   cat "${pgmout}"
 fi
 
-##########################################
-# Do not remove the Temporary working directory (do this in POST)
-##########################################
-cd "${DATAROOT}" || exit 1
-
 exit 0
diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE b/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
index f294841306..eb167af94d 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_INITIALIZE
@@ -3,7 +3,7 @@
 source "${HOMEgfs}/ush/preamble.sh"
 export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
 export DATA="${DATAjob}/marinevariational"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base ocnanal marineanlinit"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlinit" -c "base marineanl marineanlinit"
 
 
 ##############################################
diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
index 57724aee21..7780353294 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_VARIATIONAL
@@ -4,7 +4,7 @@ source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
 export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
 export DATA="${DATAjob}/marinevariational"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlvar" -c "base ocnanal marineanlvar"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlvar" -c "base marineanl marineanlvar"
 
 ##############################################
 # Set variables used in the script
diff --git a/jobs/JGLOBAL_MARINE_BMAT b/jobs/JGLOBAL_MARINE_BMAT
index 5dec9b153c..3189df0463 100755
--- a/jobs/JGLOBAL_MARINE_BMAT
+++ b/jobs/JGLOBAL_MARINE_BMAT
@@ -12,7 +12,7 @@ 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/ocnanalchkpt.sh b/jobs/rocoto/marineanlchkpt.sh
similarity index 77%
rename from jobs/rocoto/ocnanalchkpt.sh
rename to jobs/rocoto/marineanlchkpt.sh
index ae98bc8e88..b004be28e2 100755
--- a/jobs/rocoto/ocnanalchkpt.sh
+++ b/jobs/rocoto/marineanlchkpt.sh
@@ -8,11 +8,10 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalchkpt"
-export jobid="${job}.$$"
+export job="marineanlchkpt"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
 status=$?
 exit "${status}"
diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
index 3bc4a4125e..066152368b 100644
--- a/parm/archive/gdas.yaml.j2
+++ b/parm/archive/gdas.yaml.j2
@@ -25,7 +25,7 @@ gdas:
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marinebmat.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlvar.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalpost.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalchkpt.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlchkpt.log"
                 {% if DOHYBVAR %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalecen.log"
                 {% endif %}
diff --git a/parm/config/gfs/config.ocnanal b/parm/config/gfs/config.marineanl
similarity index 89%
rename from parm/config/gfs/config.ocnanal
rename to parm/config/gfs/config.marineanl
index 4d58f2dedf..86ffe80f85 100644
--- a/parm/config/gfs/config.ocnanal
+++ b/parm/config/gfs/config.marineanl
@@ -1,9 +1,9 @@
 #!/bin/bash
 
-########## config.ocnanal ##########
+########## config.marineanl ##########
 # configuration common to all ocean analysis tasks
 
-echo "BEGIN: config.ocnanal"
+echo "BEGIN: config.marineanl"
 
 export OBS_YAML_DIR="${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config"
 export OBS_LIST=@SOCA_OBS_LIST@  # TODO(GA): doesn't look necessary as is to have
@@ -17,4 +17,4 @@ export SOCA_FIX_YAML_TMPL="${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"
+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
+. "${EXPDIR}/config.resources" marineanlchkpt
+
+echo "END: config.marineanlchkpt"
diff --git a/parm/config/gfs/config.ocnanalchkpt b/parm/config/gfs/config.ocnanalchkpt
deleted file mode 100644
index c059fdba42..0000000000
--- a/parm/config/gfs/config.ocnanalchkpt
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalchkpt ##########
-# Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalchkpt"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalchkpt
-
-echo "END: config.ocnanalchkpt"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index a279878c6f..14228d335c 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 "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf ocnanalchkpt ocnanalpost ocnanalvrfy"
+    echo "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt ocnanalpost ocnanalvrfy"
     exit 1
 
 fi
@@ -582,7 +582,7 @@ case ${step} in
     ;;
 
 
-  "ocnanalchkpt")
+  "marineanlchkpt")
     walltime="00:10:00"
     ntasks=1
     threads_per_task=1
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index 24729ac43e..bd424d7b28 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -45,7 +45,7 @@ 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
@@ -54,4 +54,4 @@ 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: "${PARMgfs}/gdas/soca/obsprep/obsprep_config.yaml"
-  DMPDIR: "/scratch1/NCEPDEV/global/glopara/data/experimental_obs"
+  DMPDIR: "${PARMgfs}/gdas/experimental_obs"
diff --git a/scripts/exglobal_marine_analysis_checkpoint.py b/scripts/exglobal_marine_analysis_checkpoint.py
new file mode 100755
index 0000000000..233b267186
--- /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/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 92cc1d50b1..953b48c097 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -281,6 +281,26 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   done
 fi
 
+#------------------------------
+#-- Link the JEDI/SOCA experimental observations
+#------------------------------
+case "${machine}" in
+  "wcoss2")   EXPOBS_DIR="" ;;
+  "hera")     EXPOBS_DIR="/scratch1/NCEPDEV/global/glopara/data/experimental_obs" ;;
+  "orion")    EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs/" ;;
+  "hercules") EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs/" ;;
+  "jet")      EXPOBS_DIR="" ;;
+  "s4")       EXPOBS_DIR="" ;;
+  "gaea")     EXPOBS_DIR="" ;;
+  "noaacloud") EXPOBS_DIR="" ;;
+  *)
+    echo "FATAL: Unknown target machine ${machine}, couldn't set EXPOBS_DIR"
+    exit 1
+    ;;
+esac
+if [[ -d "${EXPOBS_DIR}" ]]; then
+  ${LINK_OR_COPY} "${EXPOBS_DIR}" "${HOMEgfs}/parm/gdas/experimental_obs"
+fi
 
 #------------------------------
 #--add DA Monitor file (NOTE: ensure to use correct version)
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 6065481419..3428da15ab 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -2,7 +2,6 @@
 
 import copy
 import os
-import glob
 from logging import getLogger
 import pygfs.utils.marine_da_utils as mdau
 import re
@@ -47,7 +46,6 @@ def __init__(self, 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_begin_iso = _window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')
         _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
@@ -61,12 +59,14 @@ def __init__(self, config):
             {
                 'HOMEgdas': _home_gdas,
                 'MARINE_WINDOW_BEGIN': _window_begin,
-                'MARINE_WINDOW_BEGIN_ISO': _window_begin_iso,
+                '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'),
                 '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'),
+                'JCB_GDAS_ALGO': os.path.join(_home_gdas, 'parm', 'jcb-gdas', 'algorithm', 'marine'),
                 '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'),
                 'MARINE_OBS_LIST_YAML': os.path.join(_home_gdas, 'parm', 'soca', 'obs', 'obs_list.yaml'),
@@ -78,7 +78,8 @@ def __init__(self, config):
         )
 
         # Extend task_config with local_dict
-        self.task_config = AttrDict(**self.task_config, **local_dict)
+        self.task_config.update(local_dict)
+
 
     @logit(logger)
     def initialize(self: Task) -> None:
@@ -99,32 +100,18 @@ def initialize(self: Task) -> None:
         self._prep_scratch_dir()
 
         # fetch observations from COMROOT
-        # TODO(GV or AE): Keep a copy of the obs in the scratch fs after the obs prep job
+        # 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 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 backgrounds
-        # TODO(G): Check ocean backgrounds dates for consistency
+        # 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 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)
-        FileHandler(soca_utility_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 static B resources
+        # link the flow dependent static B resources from the B-matrix task of the same cycle
         os.symlink('../staticb', 'staticb')
 
         # hybrid EnVAR case
@@ -136,6 +123,10 @@ def initialize(self: Task) -> None:
         # 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
@@ -173,7 +164,8 @@ def _fetch_observations(self: Task) -> None:
 
     @logit(logger)
     def _prep_scratch_dir(self: Task) -> None:
-        """Create the necesssary directory structure to run the SOCA variational application
+        """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")
 
@@ -185,6 +177,20 @@ def _prep_scratch_dir(self: Task) -> None:
         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.HOMEgfs}/parm/gdas/soca")
+        soca_utility_list = parse_j2yaml(self.task_config.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
@@ -244,6 +250,51 @@ def _prep_variational_yaml(self: Task) -> None:
         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")
+        soca2mom6inc_config = parse_j2yaml(path=os.path.join(self.task_config.JCB_GDAS_ALGO, 'socaincr2mom6.yaml.j2'),
+                                           data=self.task_config)
+        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.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
@@ -258,6 +309,95 @@ def variational(self: Task) -> None:
         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 obs_space_stats(self: Task) -> None:
+        # obs space statistics
+        logger.info(f"---------------- Compute basic stats")
+        diags_list = glob.glob(os.path.join(os.path.join(com_ocean_analysis, 'diags', '*.nc4')))
+        obsstats_j2yaml = str(os.path.join(self.task_config.HOMEgdas,
+                                           'parm', '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(com_ocean_analysis,
+                                               f"{RUN}.t{cyc}z.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')
+        exec_cmd = Executable(f"{self.task_config.launcher} -n 1")
+        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)
+
+        
+
     @logit(logger)
     def finalize(self: Task) -> None:
         """Finalize the marine analysis job
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 8fccb91ee7..d18f0a3df0 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -58,7 +58,7 @@ 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)
@@ -135,8 +135,8 @@ def initialize(self: Task) -> None:
             hybridweights_config.save(os.path.join(self.task_config.DATA, 'soca_ensweights.yaml'))
 
         # create the symbolic link to the static B-matrix directory
-        link_target = os.path.join(self.task_config.DATA, '..', 'staticb')
-        link_name = os.path.join(self.task_config.DATA, 'diagb')
+        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)
@@ -290,12 +290,12 @@ 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 +308,17 @@ 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/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index 5b9aebc8ae..10353c6db5 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -46,7 +46,7 @@ def _get_app_configs(self):
             configs += ['prepoceanobs', 'marineanlinit', 'marinebmat', 'marineanlvar']
             if self.do_hybvar:
                 configs += ['ocnanalecen']
-            configs += ['ocnanalchkpt', 'ocnanalpost']
+            configs += ['marineanlchkpt', 'ocnanalpost']
             if self.do_vrfy_oceanda:
                 configs += ['ocnanalvrfy']
 
@@ -148,7 +148,7 @@ def get_task_names(self):
             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', 'ocnanalpost']
             if self.do_vrfy_oceanda:
                 gdas_gfs_common_tasks_before_fcst += ['ocnanalvrfy']
 
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index 11ab810dc3..ba9d42bd98 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -733,7 +733,7 @@ def ocnanalecen(self):
 
         return task
 
-    def ocnanalchkpt(self):
+    def marineanlchkpt(self):
 
         deps = []
         if self.app_config.do_hybvar:
@@ -747,14 +747,14 @@ 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;'
@@ -767,7 +767,7 @@ def ocnanalchkpt(self):
     def ocnanalpost(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)
 
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index 4f6b8df391..59b8fb47d0 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -16,7 +16,7 @@ class Tasks:
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch', "cleanup",
                    'prepatmiodaobs', 'atmanlinit', 'atmanlvar', 'atmanlfv3inc', 'atmanlfinal',
                    'prepoceanobs',
-                   'marineanlinit', 'marinebmat', 'marineanlvar', 'ocnanalecen', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
+                   'marineanlinit', 'marinebmat', 'marineanlvar', 'ocnanalecen', 'marineanlchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',
                    'atmensanlinit', 'atmensanlletkf', 'atmensanlfv3inc', 'atmensanlfinal',

From 4509b0c18868ac7ad916d45c2d75f07fd273fb0e Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 11 Sep 2024 15:28:55 -0500
Subject: [PATCH 04/16] working finalize

---
 ci/cases/pr/C48mx500_hybAOWCDA.yaml           |  24 +++
 ..._POST => JGLOBAL_MARINE_ANALYSIS_FINALIZE} |  39 ++---
 .../{ocnanalpost.sh => marineanlfinal.sh}     |   4 +-
 parm/archive/gdas.yaml.j2                     |   2 +-
 parm/config/gfs/config.marineanlfinal         |  10 ++
 parm/config/gfs/config.ocnanalpost            |  10 --
 parm/config/gfs/config.resources              |   4 +-
 scripts/exglobal_marine_analysis_finalize.py  |  27 +++
 .../exglobal_marine_analysis_variational.py   |   2 +
 ush/python/pygfs/task/marine_analysis.py      | 165 ++++++++++++++----
 ush/python/pygfs/task/marine_bmat.py          |  50 +++---
 ush/python/pygfs/utils/marine_da_utils.py     |  26 +--
 workflow/applications/gfs_cycled.py           |   4 +-
 workflow/rocoto/gfs_tasks.py                  |  12 +-
 workflow/rocoto/tasks.py                      |   2 +-
 15 files changed, 267 insertions(+), 114 deletions(-)
 create mode 100644 ci/cases/pr/C48mx500_hybAOWCDA.yaml
 rename jobs/{JGDAS_GLOBAL_OCEAN_ANALYSIS_POST => JGLOBAL_MARINE_ANALYSIS_FINALIZE} (50%)
 rename jobs/rocoto/{ocnanalpost.sh => marineanlfinal.sh} (82%)
 create mode 100644 parm/config/gfs/config.marineanlfinal
 delete mode 100644 parm/config/gfs/config.ocnanalpost
 create mode 100755 scripts/exglobal_marine_analysis_finalize.py

diff --git a/ci/cases/pr/C48mx500_hybAOWCDA.yaml b/ci/cases/pr/C48mx500_hybAOWCDA.yaml
new file mode 100644
index 0000000000..54d425e2ce
--- /dev/null
+++ b/ci/cases/pr/C48mx500_hybAOWCDA.yaml
@@ -0,0 +1,24 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: S2S
+  resdetatmos: 48
+  resdetocean: 5.0
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20240610
+  idate: 2021032412
+  edate: 2021032418
+  nens: 3
+  gfs_cyc: 0
+  start: warm
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_gfs_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - wcoss2
+  - gaea
+  - orion
+  - hercules
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
similarity index 50%
rename from jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
rename to jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
index 2d28569741..1430f45426 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
@@ -1,41 +1,38 @@
 #!/bin/bash
 source "${HOMEgfs}/ush/preamble.sh"
 export WIPE_DATA="NO"
-export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
-
+export DATAjob="${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
 ##############################################
-# 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}${cyc}}
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
 export GDUMP=${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
+# Generate COM variables from templates
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
+
+RUN=${GDUMP} YMD=${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=${GDASOCNPOSTPY:-${HOMEgfs}/sorc/gdas.cd/scripts/exgdas_global_marine_analysis_post.py}
+EXSCRIPT=${GDASMARINEANALYSIS:-${SCRgfs}/exglobal_marine_analysis_finalize.py}
 ${EXSCRIPT}
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
@@ -46,4 +43,4 @@ status=$?
 cd "${DATAROOT}" || exit 1
 #[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
-exit 1
+exit 0
diff --git a/jobs/rocoto/ocnanalpost.sh b/jobs/rocoto/marineanlfinal.sh
similarity index 82%
rename from jobs/rocoto/ocnanalpost.sh
rename to jobs/rocoto/marineanlfinal.sh
index b99a4e05ca..8f0c8fa3a3 100755
--- a/jobs/rocoto/ocnanalpost.sh
+++ b/jobs/rocoto/marineanlfinal.sh
@@ -8,11 +8,11 @@ source "${HOMEgfs}/ush/preamble.sh"
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-export job="ocnanalpost"
+export job="marineanlfinal"
 export jobid="${job}.$$"
 
 ###############################################################
 # Execute the JJOB
-"${HOMEgfs}"/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
+"${HOMEgfs}"/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
 status=$?
 exit "${status}"
diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
index 066152368b..90c9d08aee 100644
--- a/parm/archive/gdas.yaml.j2
+++ b/parm/archive/gdas.yaml.j2
@@ -24,7 +24,7 @@ gdas:
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlinit.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marinebmat.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlvar.log"
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalpost.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlfinal.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}marineanlchkpt.log"
                 {% if DOHYBVAR %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ocnanalecen.log"
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
+. "${EXPDIR}/config.resources" marineanlfinal
+echo "END: config.marineanlfinal"
diff --git a/parm/config/gfs/config.ocnanalpost b/parm/config/gfs/config.ocnanalpost
deleted file mode 100644
index bc4d945865..0000000000
--- a/parm/config/gfs/config.ocnanalpost
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-########## config.ocnanalpost ##########
-# Post Ocn Analysis specific
-
-echo "BEGIN: config.ocnanalpost"
-
-# Get task specific resources
-. "${EXPDIR}/config.resources" ocnanalpost
-echo "END: config.ocnanalpost"
diff --git a/parm/config/gfs/config.resources b/parm/config/gfs/config.resources
index 14228d335c..ccfb9b125c 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 "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt ocnanalpost ocnanalvrfy"
+    echo "marineanlinit prepoceanobs marinebmat marineanlvar ocnanalecen marineanalletkf marineanlchkpt marineanlfinal ocnanalvrfy"
     exit 1
 
 fi
@@ -603,7 +603,7 @@ case ${step} in
     esac
     ;;
 
-  "ocnanalpost")
+  "marineanlfinal")
     walltime="00:30:00"
     ntasks=${max_tasks_per_node}
     threads_per_task=1
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_variational.py b/scripts/exglobal_marine_analysis_variational.py
index 5e15f410c6..e03c56b1e5 100755
--- a/scripts/exglobal_marine_analysis_variational.py
+++ b/scripts/exglobal_marine_analysis_variational.py
@@ -19,4 +19,6 @@
 
     # Create a MarineAnalysis object
     MarineAnl = MarineAnalysis(config)
+
+    # Run the variational application
     MarineAnl.variational()
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 3428da15ab..32b0963f93 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -4,7 +4,11 @@
 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
 
@@ -189,7 +193,7 @@ def _prep_scratch_dir(self: Task) -> None:
         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)
         FileHandler(soca_utility_list).sync()
-        
+
 
     @logit(logger)
     def _prep_variational_yaml(self: Task) -> None:
@@ -333,15 +337,115 @@ def checkpoint_mom6_iau(self: Task, socaincr2mom6yaml) -> None:
 
         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(com_ocean_analysis, 'diags', '*.nc4')))
-        obsstats_j2yaml = str(os.path.join(self.task_config.HOMEgdas,
+        diags_list = glob.glob(os.path.join(os.path.join(self.task_config.COMOUT_OCEAN_ANALYSIS, 'diags', '*.nc4')))
+        obsstats_j2yaml = str(os.path.join(os.getenv('HOMEgfs'), 'sorc', 'gdas.cd',
                                            'parm', 'soca', 'obs', 'obs_stats.yaml.j2'))
-        
+
         # function to create a minimalist ioda obs sapce
         def create_obs_space(data):
             os_dict = {"obs space": {
@@ -356,55 +460,48 @@ def create_obs_space(data):
                        "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(com_ocean_analysis,
-                                               f"{RUN}.t{cyc}z.ocn.{obs_space}.stats.csv")}
+                    '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')
-        exec_cmd = Executable(f"{self.task_config.launcher} -n 1")
-        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)
-
-        
-
-    @logit(logger)
-    def finalize(self: Task) -> None:
-        """Finalize the marine analysis job
-
-        This method will finalize the marine analysis job.
-        This includes:
-        -
-        - ...
 
-        """
+        # run the application
+        # TODO(GorA): this should be setup properly in the g-w once gdassoca_obsstats is in develop
+        gdassoca_obsstats_exec = os.path.join(os.getenv('HOMEgfs'),
+                                              'sorc', 'gdas.cd', 'build', 'bin', 'gdassoca_obsstats.x')
+        command = f"{os.getenv('launcher')} -n 1 {gdassoca_obsstats_exec} {stats_yaml}"
+        logger.info(f"{command}")
+        result = subprocess.run(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+        # issue a warning if the process has failed
+        if result.returncode != 0:
+            logger.warning(f"{command} has failed")
+        if result.stderr:
+            print("STDERR:", result.stderr.decode())
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index d18f0a3df0..b7ae69fb4b 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -26,28 +26,29 @@ 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
         _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,
-                '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.",
-            }
-        )
+        local_dict = AttrDict({
+           'HOMEgdas': _home_gdas,
+           '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."
+        })
 
         # Extend task_config with local_dict
         self.task_config = AttrDict(**self.task_config, **local_dict)
@@ -99,8 +100,9 @@ def initialize(self: Task) -> None:
 
         # 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)
+        diffvz_config = parse_j2yaml(
+            path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_parameters_diffusion_vt.yaml.j2'),
+            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
@@ -112,8 +114,9 @@ def initialize(self: Task) -> None:
 
             # 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)
+            diffhz_config = parse_j2yaml(
+                path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_parameters_diffusion_hz.yaml.j2'),
+                data=self.task_config)
             diffhz_config.save(os.path.join(self.task_config.DATA, 'soca_parameters_diffusion_hz.yaml'))
 
         # hybrid EnVAR case
@@ -130,8 +133,9 @@ def initialize(self: Task) -> None:
 
             # 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)
+            hybridweights_config = parse_j2yaml(
+                path=os.path.join(self.task_config.BERROR_YAML_DIR, 'soca_ensweights.yaml.j2'),
+                data=self.task_config)
             hybridweights_config.save(os.path.join(self.task_config.DATA, 'soca_ensweights.yaml'))
 
         # create the symbolic link to the static B-matrix directory
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 450678b2fc..abfaf8c30e 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -1,11 +1,16 @@
 from netCDF4 import Dataset
 from datetime import datetime, timedelta
 import dateutil.parser as dparser
-import f90nml
 import os
+import glob
+import re
+import netCDF4
+from multiprocessing import Process
+import subprocess
 from logging import getLogger
 import xarray as xr
 import yaml
+from jinja2 import Template
 
 from wxflow import (FileHandler,
                     logit,
@@ -48,22 +53,19 @@ 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.HOMEgdas, 'parm', 'soca', '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)
diff --git a/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index 10353c6db5..3077c99312 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -46,7 +46,7 @@ def _get_app_configs(self):
             configs += ['prepoceanobs', 'marineanlinit', 'marinebmat', 'marineanlvar']
             if self.do_hybvar:
                 configs += ['ocnanalecen']
-            configs += ['marineanlchkpt', 'ocnanalpost']
+            configs += ['marineanlchkpt', 'marineanlfinal']
             if self.do_vrfy_oceanda:
                 configs += ['ocnanalvrfy']
 
@@ -148,7 +148,7 @@ def get_task_names(self):
             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 += ['marineanlchkpt', '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/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index ba9d42bd98..60f0a29141 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -764,21 +764,21 @@ def marineanlchkpt(self):
 
         return task
 
-    def ocnanalpost(self):
+    def marineanlfinal(self):
 
         deps = []
         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;'
@@ -791,7 +791,7 @@ 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)
 
@@ -897,7 +897,7 @@ 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 59b8fb47d0..37d8e5e400 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -16,7 +16,7 @@ class Tasks:
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch', "cleanup",
                    'prepatmiodaobs', 'atmanlinit', 'atmanlvar', 'atmanlfv3inc', 'atmanlfinal',
                    'prepoceanobs',
-                   'marineanlinit', 'marinebmat', 'marineanlvar', 'ocnanalecen', 'marineanlchkpt', 'ocnanalpost', 'ocnanalvrfy',
+                   'marineanlinit', 'marinebmat', 'marineanlvar', 'ocnanalecen', 'marineanlchkpt', 'marineanlfinal', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',
                    'atmensanlinit', 'atmensanlletkf', 'atmensanlfv3inc', 'atmensanlfinal',

From 317e35149cfee9f363eb43242462d9dd2186f352 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 13 Sep 2024 06:55:16 -0500
Subject: [PATCH 05/16] ...

---
 sorc/link_workflow.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 18b2314f55..80a8e65526 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -286,8 +286,8 @@ fi
 case "${machine}" in
   "wcoss2")   EXPOBS_DIR="" ;;
   "hera")     EXPOBS_DIR="/scratch1/NCEPDEV/global/glopara/data/experimental_obs" ;;
-  "orion")    EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs/" ;;
-  "hercules") EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs/" ;;
+  "orion")    EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs" ;;
+  "hercules") EXPOBS_DIR="/work/noaa/global/glopara/data/experimental_obs" ;;
   "jet")      EXPOBS_DIR="" ;;
   "s4")       EXPOBS_DIR="" ;;
   "gaea")     EXPOBS_DIR="" ;;

From ea6ae912e0ef3aa118af6a9ccd6af31d3a082ab0 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 13 Sep 2024 12:57:06 -0500
Subject: [PATCH 06/16] removed envar test yaml

---
 ci/cases/pr/C48mx500_hybAOWCDA.yaml | 24 ------------------------
 1 file changed, 24 deletions(-)
 delete mode 100644 ci/cases/pr/C48mx500_hybAOWCDA.yaml

diff --git a/ci/cases/pr/C48mx500_hybAOWCDA.yaml b/ci/cases/pr/C48mx500_hybAOWCDA.yaml
deleted file mode 100644
index 54d425e2ce..0000000000
--- a/ci/cases/pr/C48mx500_hybAOWCDA.yaml
+++ /dev/null
@@ -1,24 +0,0 @@
-experiment:
-  system: gfs
-  mode: cycled
-
-arguments:
-  pslot: {{ 'pslot' | getenv }}
-  app: S2S
-  resdetatmos: 48
-  resdetocean: 5.0
-  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
-  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
-  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48mx500/20240610
-  idate: 2021032412
-  edate: 2021032418
-  nens: 3
-  gfs_cyc: 0
-  start: warm
-  yaml: {{ HOMEgfs }}/ci/cases/yamls/soca_gfs_defaults_ci.yaml
-
-skip_ci_on_hosts:
-  - wcoss2
-  - gaea
-  - orion
-  - hercules

From 5c7eb428727cd7b3968dc783230618d965ba968b Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 13 Sep 2024 13:30:51 -0500
Subject: [PATCH 07/16] norms, try 1

---
 jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT   |  3 ---
 ush/python/pygfs/task/marine_analysis.py  | 11 +----------
 ush/python/pygfs/task/marine_bmat.py      | 22 +++++++++++-----------
 ush/python/pygfs/utils/marine_da_utils.py |  8 +++++---
 4 files changed, 17 insertions(+), 27 deletions(-)

diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT b/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
index 12e19564d8..75e5b84fdb 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_CHECKPOINT
@@ -11,9 +11,6 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "marineanlchkpt" -c "base marineanl ma
 ##############################################
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
-GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-gPDY=${GDATE:0:8}
-gcyc=${GDATE:8:2}
 export GDUMP=${GDUMP:-"gdas"}
 
 ##############################################
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 32b0963f93..97e706d47a 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -84,7 +84,6 @@ def __init__(self, config):
         # Extend task_config with local_dict
         self.task_config.update(local_dict)
 
-
     @logit(logger)
     def initialize(self: Task) -> None:
         """Initialize the marine analysis
@@ -130,7 +129,6 @@ def initialize(self: Task) -> None:
         # 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
@@ -165,7 +163,6 @@ def _fetch_observations(self: Task) -> None:
 
         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
@@ -194,7 +191,6 @@ def _prep_scratch_dir(self: Task) -> None:
         soca_utility_list = parse_j2yaml(self.task_config.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
@@ -253,7 +249,6 @@ def _prep_variational_yaml(self: Task) -> None:
         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
         """
@@ -278,7 +273,7 @@ def _prep_checkpoint(self: Task) -> None:
 
         # 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')
+        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
@@ -298,7 +293,6 @@ def _prep_checkpoint(self: Task) -> None:
                                             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
@@ -312,7 +306,6 @@ def variational(self: Task) -> None:
 
         mdau.run(exec_cmd)
 
-
     @logit(logger)
     def checkpoint_cice6(self: Task, soca2ciceyaml) -> None:
         # link gdas_soca_gridgen.x
@@ -337,7 +330,6 @@ def checkpoint_mom6_iau(self: Task, socaincr2mom6yaml) -> None:
 
         mdau.run(exec_cmd)
 
-
     @logit(logger)
     def finalize(self: Task) -> None:
         """Finalize the marine analysis job
@@ -433,7 +425,6 @@ def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
 
         FileHandler({'copy': fh_list}).sync()
 
-
     @logit(logger)
     def obs_space_stats(self: Task) -> None:
         """Observation space statistics
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index b7ae69fb4b..8cc48cf464 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -36,18 +36,18 @@ def __init__(self, config):
 
         # Create a local dictionary that is repeatedly used across this class
         local_dict = AttrDict({
-           'HOMEgdas': _home_gdas,
-           '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(
+            'HOMEgdas': _home_gdas,
+            '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."
+            '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."
         })
 
         # Extend task_config with local_dict
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index abfaf8c30e..331269d2b6 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -62,8 +62,8 @@ def prep_input_nml(task_config: AttrDict) -> None:
 
     # swap date and stacksize
     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 }
+    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')
 
@@ -82,6 +82,7 @@ def stage_ens_mem(task_config: AttrDict) -> None:
     logger.info(f"{letkf_stage_list}")
     FileHandler(letkf_stage_list).sync()
 
+
 @logit(logger)
 def test_hist_date(histfile: str, ref_date: datetime) -> None:
     """
@@ -126,7 +127,7 @@ def gen_bkg_list(bkg_path: str, window_begin=' ', yaml_name='bkg.yaml', ice_rst=
         # 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'
+        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")
@@ -144,6 +145,7 @@ def gen_bkg_list(bkg_path: str, window_begin=' ', yaml_name='bkg.yaml', ice_rst=
     f = open(yaml_name, 'w')
     yaml.dump(bkg_list, f, sort_keys=False, default_flow_style=False)
 
+
 @logit(logger)
 def clean_empty_obsspaces(config, target, app='var'):
     """

From 3b15dc610dc5f75dd19c12561873df1d0c714e0d Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 13 Sep 2024 13:37:29 -0500
Subject: [PATCH 08/16] norms, try 2

---
 .../exglobal_marine_analysis_checkpoint.py    |  4 +--
 ush/python/pygfs/task/marine_analysis.py      |  1 -
 ush/python/pygfs/task/marine_bmat.py          | 29 ++++++++++---------
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/scripts/exglobal_marine_analysis_checkpoint.py b/scripts/exglobal_marine_analysis_checkpoint.py
index 233b267186..84b180b287 100755
--- a/scripts/exglobal_marine_analysis_checkpoint.py
+++ b/scripts/exglobal_marine_analysis_checkpoint.py
@@ -22,8 +22,8 @@
     MarineAnl = MarineAnalysis(config)
 
     # Prepare the SOCA increment for MOM6 IAU
-    MarineAnl.checkpoint_mom6_iau('socaincr2mom6.yaml')    
-    
+    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/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 97e706d47a..42b91cf5df 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -452,7 +452,6 @@ def create_obs_space(data):
                        }
             return os_dict
 
-
         # get the experiment id
         pslot = self.task_config.PSLOT
 
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 8cc48cf464..8001682235 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -35,20 +35,21 @@ def __init__(self, config):
         _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,
-            '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."
-        })
+        local_dict =
+            AttrDict({
+                'HOMEgdas': _home_gdas,
+                '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."
+            })
 
         # Extend task_config with local_dict
         self.task_config = AttrDict(**self.task_config, **local_dict)

From 90ad1d3bb3aff827318e079a37be94ba712493a3 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 13 Sep 2024 13:43:27 -0500
Subject: [PATCH 09/16] norms, try 3

---
 ush/python/pygfs/task/marine_bmat.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 8001682235..2242b0a583 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -35,21 +35,21 @@ def __init__(self, config):
         _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({
+        local_dict = AttrDict(
+            {
                 'HOMEgdas': _home_gdas,
                 '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_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."
-            })
+            }
+        )
 
         # Extend task_config with local_dict
         self.task_config = AttrDict(**self.task_config, **local_dict)

From f1d7f8bf3f6c6fcc5b3989e46b643fa7acbe47b8 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Mon, 16 Sep 2024 17:54:25 -0500
Subject: [PATCH 10/16] addressed review comments

---
 jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE     |  2 +-
 parm/config/gfs/config.marineanl          | 12 +++---
 parm/config/gfs/config.marinebmat         |  8 ++++
 parm/config/gfs/config.prepoceanobs       |  2 +-
 ush/python/pygfs/task/marine_analysis.py  | 47 ++++++++++-------------
 ush/python/pygfs/task/marine_bmat.py      | 45 ++++++++--------------
 ush/python/pygfs/utils/marine_da_utils.py |  2 +-
 7 files changed, 53 insertions(+), 65 deletions(-)

diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
index 1430f45426..59767008c6 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
@@ -41,6 +41,6 @@ status=$?
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || exit 1
-#[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
+[[ "${KEEPDATA}" = "NO" ]] && rm -rf "${DATA}"
 
 exit 0
diff --git a/parm/config/gfs/config.marineanl b/parm/config/gfs/config.marineanl
index 86ffe80f85..a19fc015e2 100644
--- a/parm/config/gfs/config.marineanl
+++ b/parm/config/gfs/config.marineanl
@@ -5,16 +5,16 @@
 
 echo "BEGIN: config.marineanl"
 
-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 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 JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin  # TODO(GA): remove once analysis "run"
-                                                   #          and "checkpoint" are refactored
+export MARINE_UTILITY_YAML_TMPL="${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.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="${PARMgfs}/gdas/soca/berror/soca_ensweights.yaml.j2"
+
 echo "END: config.marinebmat"
diff --git a/parm/config/gfs/config.prepoceanobs b/parm/config/gfs/config.prepoceanobs
index 746ce79257..0963a5c42d 100644
--- a/parm/config/gfs/config.prepoceanobs
+++ b/parm/config/gfs/config.prepoceanobs
@@ -8,7 +8,7 @@ export OCNOBS2IODAEXEC=${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/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index 42b91cf5df..cb5b7628b5 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -24,17 +24,16 @@
 logger = getLogger(__name__.split('.')[-1])
 
 
-def parse_obs_list_file(gdas_home):
+def parse_obs_list_file(obs_list_yaml_path):
     # Get the list of observation types from the obs_list.yaml
-    obs_list_path = os.path.join(gdas_home, 'parm', 'soca', 'obs', 'obs_list.yaml')
     obs_types = []
-    with open(obs_list_path, 'r') as file:
+    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'\$\{OBS_YAML_DIR\}/(.+)\.yaml', line)
+                match = re.search(r'\$\{MARINE_OBS_YAML_DIR\}/(.+)\.yaml', line)
                 if match:
                     obs_types.append(str(match.group(1)))
     return obs_types
@@ -47,7 +46,6 @@ class MarineAnalysis(Task):
     @logit(logger, name="MarineAnalysis")
     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)
@@ -61,22 +59,15 @@ def __init__(self, config):
         # 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_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'),
-                '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'),
-                'JCB_GDAS_ALGO': os.path.join(_home_gdas, 'parm', 'jcb-gdas', 'algorithm', 'marine'),
-                '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'),
-                'MARINE_OBS_LIST_YAML': os.path.join(_home_gdas, 'parm', 'soca', 'obs', 'obs_list.yaml'),
                 'ENSPERT_RELPATH': _enspert_relpath,
                 'CALC_SCALE_EXEC': _calc_scale_exec,
-                'APREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",
                 'OPREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z."
             }
         )
@@ -145,8 +136,8 @@ def _fetch_observations(self: Task) -> None:
 
         obs_files = []
         for ob in obs_list_config['observations']['observers']:
-            logger.info(f"******** {self.task_config.APREFIX}{ob['obs space']['name'].lower()}.{to_YMD(self.task_config.PDY)}{self.task_config.cyc}.nc4")
-            obs_files.append(f"{self.task_config.APREFIX}{ob['obs space']['name'].lower()}.{to_YMD(self.task_config.PDY)}{self.task_config.cyc}.nc4")
+            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
@@ -187,8 +178,8 @@ def _prep_scratch_dir(self: Task) -> None:
         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.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 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)
@@ -221,12 +212,12 @@ def _prep_variational_yaml(self: Task) -> None:
 
         # Write obs_list_short
         with open('obs_list_short.yaml', 'w') as file:
-            yaml.dump(parse_obs_list_file(self.task_config.HOMEgdas), file, default_flow_style=False)
+            yaml.dump(parse_obs_list_file(self.task_config.MARINE_OBS_LIST_YAML), file, default_flow_style=False)
         os.environ['OBS_LIST_SHORT'] = 'obs_list_short.yaml'
 
         # Render the JCB configuration files
-        jcb_base_yaml = os.path.join(self.task_config.HOMEgdas, 'parm', 'soca', 'marine-jcb-base.yaml')
-        jcb_algo_yaml = os.path.join(self.task_config.HOMEgdas, 'parm', 'soca', 'marine-jcb-3dfgat.yaml.j2')
+        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)
@@ -254,8 +245,10 @@ def _prep_checkpoint(self: Task) -> None:
         """
         # prepare the socaincr2mom6.yaml
         logger.info("Generate the SOCA to MOM6 IAU increment YAML file")
-        soca2mom6inc_config = parse_j2yaml(path=os.path.join(self.task_config.JCB_GDAS_ALGO, 'socaincr2mom6.yaml.j2'),
-                                           data=self.task_config)
+        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
@@ -278,10 +271,10 @@ def _prep_checkpoint(self: Task) -> None:
 
         # 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
+            "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}")
 
@@ -289,7 +282,7 @@ def _prep_checkpoint(self: Task) -> None:
         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.JCB_GDAS_ALGO, f'{varchgyaml}.j2'),
+            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))
 
diff --git a/ush/python/pygfs/task/marine_bmat.py b/ush/python/pygfs/task/marine_bmat.py
index 2242b0a583..93329f05ac 100644
--- a/ush/python/pygfs/task/marine_bmat.py
+++ b/ush/python/pygfs/task/marine_bmat.py
@@ -37,14 +37,10 @@ def __init__(self, config):
         # 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."
@@ -83,41 +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
@@ -128,15 +118,12 @@ 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'))
 
         # create the symbolic link to the static B-matrix directory
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 331269d2b6..ff64af556c 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -56,7 +56,7 @@ def prep_input_nml(task_config: AttrDict) -> None:
     """Prepare the mom_input.nml file
     """
     # stage input.nml.j2
-    mom_input_nml_tmpl_src = os.path.join(task_config.HOMEgdas, 'parm', 'soca', 'fms', '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()
 

From 9e8bbada6463b8bd969a5bd91a93aa9959fd4420 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 18 Sep 2024 11:00:43 -0500
Subject: [PATCH 11/16] module tidy

---
 sorc/link_workflow.sh                     | 4 +++-
 ush/python/pygfs/utils/marine_da_utils.py | 7 -------
 2 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 5d401578d4..dcc83401eb 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -293,7 +293,9 @@ case "${machine}" in
     ;;
 esac
 if [[ -d "${EXPOBS_DIR}" ]]; then
-  ${LINK_OR_COPY} "${EXPOBS_DIR}" "${HOMEgfs}/parm/gdas/experimental_obs"
+  if [[ ! -L "${HOMEgfs}/parm/gdas/experimental_obs" ]]; then
+    ${LINK_OR_COPY} "${EXPOBS_DIR}" "${HOMEgfs}/parm/gdas/experimental_obs"
+  fi
 fi
 
 #------------------------------
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index ff64af556c..8981697eb1 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -1,16 +1,9 @@
-from netCDF4 import Dataset
 from datetime import datetime, timedelta
 import dateutil.parser as dparser
 import os
-import glob
 import re
-import netCDF4
-from multiprocessing import Process
-import subprocess
 from logging import getLogger
-import xarray as xr
 import yaml
-from jinja2 import Template
 
 from wxflow import (FileHandler,
                     logit,

From a4d83917eaaf1e204da08bff14bf7462f3ab4dda Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Wed, 18 Sep 2024 12:19:03 -0500
Subject: [PATCH 12/16] updated gdas and jcb-gdas hashes

---
 sorc/gdas.cd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sorc/gdas.cd b/sorc/gdas.cd
index faa95efb18..55e895f1dc 160000
--- a/sorc/gdas.cd
+++ b/sorc/gdas.cd
@@ -1 +1 @@
-Subproject commit faa95efb18f0f52acab2cf09b17f78406f9b48b1
+Subproject commit 55e895f1dcf4e6be36eb0eb4c8a7995d429157e0

From 2a5e9bffe6cdc5affea60d23a9efb6992b2fa808 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Thu, 19 Sep 2024 07:25:37 -0500
Subject: [PATCH 13/16] fixed logging

---
 ush/python/pygfs/task/marine_analysis.py  | 2 +-
 ush/python/pygfs/utils/marine_da_utils.py | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index cb5b7628b5..26be0ecc3d 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -487,4 +487,4 @@ def create_obs_space(data):
         if result.returncode != 0:
             logger.warning(f"{command} has failed")
         if result.stderr:
-            print("STDERR:", result.stderr.decode())
+            logger.warning("STDERR:", result.stderr.decode())
diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 8981697eb1..4c746049a8 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -26,9 +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)

From a2eb39e7ddf4dfa9bfb3009c8db08418de7300bf Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@gmail.com>
Date: Fri, 20 Sep 2024 03:41:07 +0000
Subject: [PATCH 14/16] missing module

---
 ush/python/pygfs/utils/marine_da_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ush/python/pygfs/utils/marine_da_utils.py b/ush/python/pygfs/utils/marine_da_utils.py
index 4c746049a8..6145798e16 100644
--- a/ush/python/pygfs/utils/marine_da_utils.py
+++ b/ush/python/pygfs/utils/marine_da_utils.py
@@ -1,7 +1,7 @@
 from datetime import datetime, timedelta
 import dateutil.parser as dparser
 import os
-import re
+from netCDF4 import Dataset
 from logging import getLogger
 import yaml
 

From 77f3ddc26be5a6a7efdd9b7ba89556429bb9df5b Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 20 Sep 2024 16:49:40 -0400
Subject: [PATCH 15/16] Update jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
index 59767008c6..878a1d9faa 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
@@ -24,7 +24,7 @@ RUN=${GDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
    COMOUT_ICE_ANALYSIS:COM_ICE_ANALYSIS_TMPL \
    COMOUT_ICE_RESTART:COM_ICE_RESTART_TMPL
 
-mkdir -p "${COMOUT_OCEAN_ANALYSIS}"
+if [[ -d "${COMOUT_OCEAN_ANALYSIS}" ]]; then mkdir -p "${COMOUT_OCEAN_ANALYSIS}"; fi
 mkdir -p "${COMOUT_ICE_ANALYSIS}"
 mkdir -p "${COMOUT_ICE_RESTART}"
 

From 98ace0690d720cc3388b351bbdee1a40ba0a181d Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Fri, 20 Sep 2024 16:50:12 -0400
Subject: [PATCH 16/16] Update jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE

Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
---
 jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
index 878a1d9faa..be775cb011 100755
--- a/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
+++ b/jobs/JGLOBAL_MARINE_ANALYSIS_FINALIZE
@@ -17,7 +17,7 @@ export GDUMP=${GDUMP:-"gdas"}
 ##############################################
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL
 
 RUN=${GDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
    COMOUT_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL \