diff --git a/ci/cases/yamls/soca_gfs_defaults_ci.yaml b/ci/cases/yamls/soca_gfs_defaults_ci.yaml
index c18eac9196..69971537c2 100644
--- a/ci/cases/yamls/soca_gfs_defaults_ci.yaml
+++ b/ci/cases/yamls/soca_gfs_defaults_ci.yaml
@@ -7,3 +7,5 @@ base:
 marineanl:
   SOCA_NINNER: 1
   DO_TEST_MODE: "YES"
+marineanl:
+  JCB_ALGO_YAML_VAR: "{{ HOMEgfs }}/sorc/gdas.cd/test/gw-ci/soca/jcb-prototype_3dfgat_3DVarAOWCDA.yaml.j2"
diff --git a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
index b956066f6b..b7344e8e35 100644
--- a/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
+++ b/ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml
@@ -5,10 +5,17 @@ base:
   DO_JEDIATMVAR: "YES"
   DO_JEDIATMENS: "YES"
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  DO_TEST_MODE: "YES"
 atmanl:
+  JCB_ALGO_YAML_VAR: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_3dvar_ufs_hybatmDA.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_3dvar-fv3inc_ufs_hybatmDA.yaml.j2"
   LAYOUT_X_ATMANL: 4
   LAYOUT_Y_ATMANL: 4
 atmensanl:
+  JCB_ALGO_YAML_LETKF: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_lgetkf_ufs_hybatmDA.yaml.j2"
+  JCB_ALGO_YAML_OBS: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_lgetkf_observer_ufs_hybatmDA.yaml.j2"
+  JCB_ALGO_YAML_SOL: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_lgetkf_solver_ufs_hybatmDA.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${HOMEgfs}/sorc/gdas.cd/test/gw-ci/atm/jcb-prototype_lgetkf-fv3inc_ufs_hybatmDA.yaml.j2"
   LAYOUT_X_ATMENSANL: 4
   LAYOUT_Y_ATMENSANL: 4
 esfc:
diff --git a/ci/platforms/config.gaea b/ci/platforms/config.gaea
index cce109d494..f4b8cc13ec 100644
--- a/ci/platforms/config.gaea
+++ b/ci/platforms/config.gaea
@@ -3,6 +3,6 @@
 export GFS_CI_ROOT=/gpfs/f5/epic/proj-shared/global/GFS_CI_ROOT
 export ICSDIR_ROOT=/gpfs/f5/epic/proj-shared/global/glopara/data/ICSDIR
 export STMP="/gpfs/f5/epic/scratch/${USER}"
-export SLURM_ACCOUNT=ufs-ard
+export HPC_ACCOUNT=ufs-ard
 export max_concurrent_cases=5
 export max_concurrent_pr=4
diff --git a/ci/platforms/config.hercules b/ci/platforms/config.hercules
index 5329adae49..4d5af21c78 100644
--- a/ci/platforms/config.hercules
+++ b/ci/platforms/config.hercules
@@ -2,7 +2,7 @@
 
 export GFS_CI_ROOT=/work2/noaa/stmp/GFS_CI_ROOT/HERCULES
 export ICSDIR_ROOT=/work/noaa/global/glopara/data/ICSDIR
-export HPC_ACCOUNT=nems
+export HPC_ACCOUNT=fv3-cpu
 export max_concurrent_cases=5
 export max_concurrent_pr=4
 
diff --git a/jobs/JGDAS_ENKF_SELECT_OBS b/jobs/JGDAS_ENKF_SELECT_OBS
index 3cfe48bb2b..2b876c0b3a 100755
--- a/jobs/JGDAS_ENKF_SELECT_OBS
+++ b/jobs/JGDAS_ENKF_SELECT_OBS
@@ -32,21 +32,25 @@ GPREFIX_DET="${GDUMP}.t${gcyc}z."
 export GSUFFIX=".ensmean.nc"
 
 # Generate COM variables from templates
-RUN=${RUN/enkf} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
-MEMDIR='ensstat' YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS
-declare -rx COM_ATMOS_ANALYSIS_ENS="${COM_ATMOS_ANALYSIS}"
+RUN=${RUN/enkf} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+	COMIN_OBS:COM_OBS_TMPL
+MEMDIR='ensstat' YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+	COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+declare -rx COMOUT_ATMOS_ANALYSIS_ENS="${COMOUT_ATMOS_ANALYSIS}"
 
-RUN=${RUN/enkf} YMD=${PDY} HH=${cyc} declare_from_tmpl -r COM_ATMOS_ANALYSIS_DET:COM_ATMOS_ANALYSIS_TMPL
+RUN=${RUN/enkf} YMD=${PDY} HH=${cyc} declare_from_tmpl -r \
+	COMOUT_ATMOS_ANALYSIS_DET:COM_ATMOS_ANALYSIS_TMPL
 
 MEMDIR='ensstat' RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
-    COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL \
+    COMIN_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
+    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL 
 
-RUN="${GDUMP}" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -r COM_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
+RUN="${GDUMP}" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -r \
+	COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
 
-mkdir -m 775 -p "${COM_ATMOS_ANALYSIS}"
+mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
-export ATMGES_ENSMEAN="${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}"
 if [[ ! -f ${ATMGES_ENSMEAN} ]]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
     exit 1
@@ -61,44 +65,44 @@ status=$?
 export LEVS
 
 # Link observational data
-export PREPQC="${COM_OBS}/${OPREFIX}prepbufr"
+export PREPQC="${COMIN_OBS}/${OPREFIX}prepbufr"
 if [[ ! -f ${PREPQC} ]]; then
     echo "WARNING: Global PREPBUFR FILE ${PREPQC} MISSING"
 fi
-export TCVITL="${COM_OBS}/${APREFIX_DET}syndata.tcvitals.tm00"
+export TCVITL="${COMIN_OBS}/${APREFIX_DET}syndata.tcvitals.tm00"
 if [[ ${DONST} = "YES" ]]; then
-   export NSSTBF="${COM_OBS}/${OPREFIX}nsstbufr"
+   export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
 fi
-export PREPQCPF="${COM_OBS}/${OPREFIX}prepbufr.acft_profiles"
+export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
 
 # Deterministic analysis and increment files
-export SFCANL="${COM_ATMOS_ANALYSIS_DET}/${APREFIX_DET}sfcanl.nc"
-export DTFANL="${COM_ATMOS_ANALYSIS_DET}/${APREFIX_DET}dtfanl.nc"
-export ATMANL="${COM_ATMOS_ANALYSIS_DET}/${APREFIX_DET}atmanl.nc"
-export ATMINC="${COM_ATMOS_ANALYSIS_DET}/${APREFIX_DET}atminc.nc"
+export SFCANL="${COMOUT_ATMOS_ANALYSIS_DET}/${APREFIX_DET}sfcanl.nc"
+export DTFANL="${COMOUT_ATMOS_ANALYSIS_DET}/${APREFIX_DET}dtfanl.nc"
+export ATMANL="${COMOUT_ATMOS_ANALYSIS_DET}/${APREFIX_DET}atmanl.nc"
+export ATMINC="${COMOUT_ATMOS_ANALYSIS_DET}/${APREFIX_DET}atminc.nc"
 
 # Guess Bias correction coefficients related to control
-export GBIAS=${COM_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias
-export GBIASPC=${COM_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_pc
-export GBIASAIR=${COM_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_air
-export GRADSTAT=${COM_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}radstat
+export GBIAS=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias
+export GBIASPC=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_pc
+export GBIASAIR=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_air
+export GRADSTAT=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}radstat
 
 # Bias correction coefficients related to ensemble mean
-export ABIAS="${COM_ATMOS_ANALYSIS}/${APREFIX}abias.ensmean"
-export ABIASPC="${COM_ATMOS_ANALYSIS}/${APREFIX}abias_pc.ensmean"
-export ABIASAIR="${COM_ATMOS_ANALYSIS}/${APREFIX}abias_air.ensmean"
-export ABIASe="${COM_ATMOS_ANALYSIS}/${APREFIX}abias_int.ensmean"
+export ABIAS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias.ensmean"
+export ABIASPC="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc.ensmean"
+export ABIASAIR="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air.ensmean"
+export ABIASe="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int.ensmean"
 
 # Diagnostics related to ensemble mean
-export GSISTAT="${COM_ATMOS_ANALYSIS}/${APREFIX}gsistat.ensmean"
-export CNVSTAT="${COM_ATMOS_ANALYSIS}/${APREFIX}cnvstat.ensmean"
-export OZNSTAT="${COM_ATMOS_ANALYSIS}/${APREFIX}oznstat.ensmean"
-export RADSTAT="${COM_ATMOS_ANALYSIS}/${APREFIX}radstat.ensmean"
+export GSISTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat.ensmean"
+export CNVSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat.ensmean"
+export OZNSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat.ensmean"
+export RADSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.ensmean"
 
 # Select observations based on ensemble mean
 export RUN_SELECT="YES"
 export USE_SELECT="NO"
-export SELECT_OBS="${COM_ATMOS_ANALYSIS}/${APREFIX}obsinput.ensmean"
+export SELECT_OBS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.ensmean"
 
 export DIAG_SUFFIX="_ensmean"
 
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS b/jobs/JGLOBAL_ATMOS_ANALYSIS
index 5776aa6d13..b13f026ba2 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -31,18 +31,20 @@ export APREFIX="${rCDUMP}.t${cyc}z."
 export GPREFIX_ENS="${GDUMP_ENS}.t${gcyc}z."
 
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS COM_ATMOS_ANALYSIS
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+	COMIN_OBS:COM_OBS_TMPL \
+	COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
-    COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
+    COMIN_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL \
+    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 
 MEMDIR='ensstat' RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COM_ATMOS_HISTORY_ENS_PREV:COM_ATMOS_HISTORY_TMPL
+    COMIN_ATMOS_HISTORY_ENS_PREV:COM_ATMOS_HISTORY_TMPL
 
-mkdir -m 775 -p "${COM_ATMOS_ANALYSIS}"
+mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
-export ATMGES="${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
+export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
@@ -55,7 +57,7 @@ status=$?
 
 
 if [ ${DOHYBVAR} = "YES" ]; then
-    export ATMGES_ENSMEAN="${COM_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc"
+    export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
         echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
         exit 2
@@ -64,17 +66,17 @@ fi
 
 
 # Link observational data
-export PREPQC="${COM_OBS}/${OPREFIX}prepbufr"
+export PREPQC="${COMIN_OBS}/${OPREFIX}prepbufr"
 if [[ ! -f ${PREPQC} ]]; then
     echo "WARNING: Global PREPBUFR FILE ${PREPQC} MISSING"
 fi
-export TCVITL="${COM_OBS}/${OPREFIX}syndata.tcvitals.tm00"
+export TCVITL="${COMIN_OBS}/${OPREFIX}syndata.tcvitals.tm00"
 if [[ ${DONST} = "YES" ]]; then
    if [[ ${MAKE_NSSTBUFR} == "YES" ]]; then
-      export NSSTBF="${COM_OBS}/${OPREFIX}nsstbufr"
+      export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
    fi
 fi
-export PREPQCPF="${COM_OBS}/${OPREFIX}prepbufr.acft_profiles"
+export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
 
 # Copy fix file for obsproc  # TODO: Why is this necessary?
 if [[ ${RUN} = "gfs" ]]; then
@@ -95,9 +97,9 @@ status=$?
 # Send Alerts
 ##############################################
 if [ ${SENDDBN} = YES -a ${RUN} = gdas ] ; then
-    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias ${job} ${COM_ATMOS_ANALYSIS}/${APREFIX}abias
-    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias_pc ${job} ${COM_ATMOS_ANALYSIS}/${APREFIX}abias_pc
-    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias_air ${job} ${COM_ATMOS_ANALYSIS}/${APREFIX}abias_air
+    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias ${job} ${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias
+    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias_pc ${job} ${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc
+    ${DBNROOT}/bin/dbn_alert MODEL GDAS_MSC_abias_air ${job} ${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air
 fi
 
 
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
index 5b6073254a..063a006658 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -28,16 +28,19 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${RUN}.t${cyc}z."
 export GPREFIX_ENS="${GDUMP_ENS}.t${gcyc}z."
 
-RUN=${rCDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_OBS
+RUN=${rCDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+    COMIN_OBS:COM_OBS_TMPL
 
-YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COM_ATMOS_ANALYSIS COM_ATMOS_RESTART
+YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+    COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+    COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COM_OBS_PREV:COM_OBS_TMPL \
-    COM_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
+    COMIN_OBS_PREV:COM_OBS_TMPL \
+    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 
 
-export ATMGES="${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
+export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
diff --git a/parm/config/gfs/config.atmanl b/parm/config/gfs/config.atmanl
index 1d700a479c..df35a41d89 100644
--- a/parm/config/gfs/config.atmanl
+++ b/parm/config/gfs/config.atmanl
@@ -6,6 +6,7 @@
 echo "BEGIN: config.atmanl"
 
 export JCB_ALGO_YAML_VAR=@JCB_ALGO_YAML_VAR@
+export JCB_ALGO_YAML_FV3INC=@JCB_ALGO_YAML_FV3INC@
 
 export STATICB_TYPE=@STATICB_TYPE@
 export LOCALIZATION_TYPE="bump"
diff --git a/parm/config/gfs/config.atmensanl b/parm/config/gfs/config.atmensanl
index 2726f655bd..77f5e2ee86 100644
--- a/parm/config/gfs/config.atmensanl
+++ b/parm/config/gfs/config.atmensanl
@@ -8,6 +8,7 @@ echo "BEGIN: config.atmensanl"
 export JCB_ALGO_YAML_LETKF=@JCB_ALGO_YAML_LETKF@
 export JCB_ALGO_YAML_OBS=@JCB_ALGO_YAML_OBS@
 export JCB_ALGO_YAML_SOL=@JCB_ALGO_YAML_SOL@
+export JCB_ALGO_YAML_FV3INC=@JCB_ALGO_YAML_FV3INC@
 
 export INTERP_METHOD='barycentric'
 
diff --git a/parm/config/gfs/config.marineanl b/parm/config/gfs/config.marineanl
index 0b55fa447d..b0fbbedb54 100644
--- a/parm/config/gfs/config.marineanl
+++ b/parm/config/gfs/config.marineanl
@@ -6,6 +6,7 @@
 echo "BEGIN: config.marineanl"
 
 export JEDI_CONFIG_YAML="${PARMgfs}/gdas/soca_bmat_jedi_config.yaml.j2"
+export JCB_ALGO_YAML_VAR=@JCB_ALGO_YAML_VAR@
 
 export MARINE_OBS_YAML_DIR="${PARMgfs}/gdas/soca/obs/config"
 export MARINE_OBS_LIST_YAML=@SOCA_OBS_LIST@
diff --git a/parm/config/gfs/config.resources.ORION b/parm/config/gfs/config.resources.ORION
index fceb8feeb1..a10588b6d0 100644
--- a/parm/config/gfs/config.resources.ORION
+++ b/parm/config/gfs/config.resources.ORION
@@ -30,10 +30,13 @@ case ${step} in
     export walltime="00:45:00"
   ;;
   "atmensanlobs")
-    # Run on 8 nodes for memory requirement
-    export tasks_per_node=8
+    # Run on 12 nodes for memory requirement
+    export tasks_per_node=12
     export walltime="00:45:00"
   ;;
+  "atmensanlsol")
+    export tasks_per_node=12
+  ;;  
   *)
   ;;
 esac
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index c9ecd11f5b..55f4b03f50 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -27,6 +27,7 @@ base:
 
 atmanl:
   JCB_ALGO_YAML_VAR: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${PARMgfs}/gdas/atm/jcb-prototype_3dvar-fv3inc.yaml.j2"
   STATICB_TYPE: "gsibec"
   LAYOUT_X_ATMANL: 8
   LAYOUT_Y_ATMANL: 8
@@ -37,6 +38,7 @@ atmensanl:
   JCB_ALGO_YAML_LETKF: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf.yaml.j2"
   JCB_ALGO_YAML_OBS: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_observer.yaml.j2"
   JCB_ALGO_YAML_SOL: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf_solver.yaml.j2"
+  JCB_ALGO_YAML_FV3INC: "${PARMgfs}/gdas/atm/jcb-prototype_lgetkf-fv3inc.yaml.j2"
   LAYOUT_X_ATMENSANL: 8
   LAYOUT_Y_ATMENSANL: 8
   IO_LAYOUT_X: 1
@@ -54,6 +56,7 @@ 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
+  JCB_ALGO_YAML_VAR: "${PARMgfs}/gdas/soca/marine-jcb-3dfgat.yaml.j2"
 
 prepoceanobs:
   SOCA_INPUT_FIX_DIR: "${FIXgfs}/gdas/soca/72x35x25/soca"
diff --git a/parm/gdas/atmanl_jedi_config.yaml.j2 b/parm/gdas/atmanl_jedi_config.yaml.j2
index 4046ba0931..7a700c5cf6 100644
--- a/parm/gdas/atmanl_jedi_config.yaml.j2
+++ b/parm/gdas/atmanl_jedi_config.yaml.j2
@@ -10,4 +10,4 @@ atmanlfv3inc:
   exe_src: '{{ EXECgfs }}/fv3jedi_fv3inc.x'
   mpi_cmd: '{{ APRUN_ATMANLFV3INC }}'
   jcb_base_yaml: '{{ PARMgfs }}/gdas/atm/jcb-base.yaml.j2'
-  jcb_algo: fv3jedi_fv3inc_variational
+  jcb_algo_yaml: '{{ JCB_ALGO_YAML_FV3INC }}'
diff --git a/parm/gdas/atmensanl_jedi_config.yaml.j2 b/parm/gdas/atmensanl_jedi_config.yaml.j2
index 9ab2ec6ace..e5acba5db9 100644
--- a/parm/gdas/atmensanl_jedi_config.yaml.j2
+++ b/parm/gdas/atmensanl_jedi_config.yaml.j2
@@ -17,7 +17,7 @@ atmensanlfv3inc:
   exe_src: '{{ EXECgfs }}/fv3jedi_fv3inc.x'
   mpi_cmd: '{{ APRUN_ATMENSANLFV3INC }}'
   jcb_base_yaml: '{{ PARMgfs }}/gdas/atm/jcb-base.yaml.j2'
-  jcb_algo: fv3jedi_fv3inc_lgetkf
+  jcb_algo_yaml: '{{ JCB_ALGO_YAML_FV3INC }}'
 atmensanlletkf:
   rundir: '{{ DATA }}'
   exe_src: '{{ EXECgfs }}/gdas.x'
diff --git a/scripts/exglobal_atmos_analysis.sh b/scripts/exglobal_atmos_analysis.sh
index 932adf8e10..bd11b81c39 100755
--- a/scripts/exglobal_atmos_analysis.sh
+++ b/scripts/exglobal_atmos_analysis.sh
@@ -92,112 +92,112 @@ export hofx_2m_sfcfile=${hofx_2m_sfcfile:-".false."}
 # Observations
 OPREFIX=${OPREFIX:-""}
 OSUFFIX=${OSUFFIX:-""}
-PREPQC=${PREPQC:-${COM_OBS}/${OPREFIX}prepbufr${OSUFFIX}}
-PREPQCPF=${PREPQCPF:-${COM_OBS}/${OPREFIX}prepbufr.acft_profiles${OSUFFIX}}
-NSSTBF=${NSSTBF:-${COM_OBS}/${OPREFIX}nsstbufr${OSUFFIX}}
-SATWND=${SATWND:-${COM_OBS}/${OPREFIX}satwnd.tm00.bufr_d${OSUFFIX}}
-OSCATBF=${OSCATBF:-${COM_OBS}/${OPREFIX}oscatw.tm00.bufr_d${OSUFFIX}}
-RAPIDSCATBF=${RAPIDSCATBF:-${COM_OBS}/${OPREFIX}rapidscatw.tm00.bufr_d${OSUFFIX}}
-GSNDBF=${GSNDBF:-${COM_OBS}/${OPREFIX}goesnd.tm00.bufr_d${OSUFFIX}}
-GSNDBF1=${GSNDBF1:-${COM_OBS}/${OPREFIX}goesfv.tm00.bufr_d${OSUFFIX}}
-#B1HRS2=${B1HRS2:-${COM_OBS}/${OPREFIX}1bhrs2.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
-B1MSU=${B1MSU:-${COM_OBS}/${OPREFIX}1bmsu.tm00.bufr_d${OSUFFIX}}
-#B1HRS3=${B1HRS3:-${COM_OBS}/${OPREFIX}1bhrs3.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
-#B1HRS4=${B1HRS4:-${COM_OBS}/${OPREFIX}1bhrs4.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
-B1AMUA=${B1AMUA:-${COM_OBS}/${OPREFIX}1bamua.tm00.bufr_d${OSUFFIX}}
-B1AMUB=${B1AMUB:-${COM_OBS}/${OPREFIX}1bamub.tm00.bufr_d${OSUFFIX}}
-B1MHS=${B1MHS:-${COM_OBS}/${OPREFIX}1bmhs.tm00.bufr_d${OSUFFIX}}
-ESHRS3=${ESHRS3:-${COM_OBS}/${OPREFIX}eshrs3.tm00.bufr_d${OSUFFIX}}
-ESAMUA=${ESAMUA:-${COM_OBS}/${OPREFIX}esamua.tm00.bufr_d${OSUFFIX}}
-ESAMUB=${ESAMUB:-${COM_OBS}/${OPREFIX}esamub.tm00.bufr_d${OSUFFIX}}
-ESMHS=${ESMHS:-${COM_OBS}/${OPREFIX}esmhs.tm00.bufr_d${OSUFFIX}}
-HRS3DB=${HRS3DB:-${COM_OBS}/${OPREFIX}hrs3db.tm00.bufr_d${OSUFFIX}}
-AMUADB=${AMUADB:-${COM_OBS}/${OPREFIX}amuadb.tm00.bufr_d${OSUFFIX}}
-AMUBDB=${AMUBDB:-${COM_OBS}/${OPREFIX}amubdb.tm00.bufr_d${OSUFFIX}}
-MHSDB=${MHSDB:-${COM_OBS}/${OPREFIX}mhsdb.tm00.bufr_d${OSUFFIX}}
-AIRSBF=${AIRSBF:-${COM_OBS}/${OPREFIX}airsev.tm00.bufr_d${OSUFFIX}}
-IASIBF=${IASIBF:-${COM_OBS}/${OPREFIX}mtiasi.tm00.bufr_d${OSUFFIX}}
-ESIASI=${ESIASI:-${COM_OBS}/${OPREFIX}esiasi.tm00.bufr_d${OSUFFIX}}
-IASIDB=${IASIDB:-${COM_OBS}/${OPREFIX}iasidb.tm00.bufr_d${OSUFFIX}}
-AMSREBF=${AMSREBF:-${COM_OBS}/${OPREFIX}amsre.tm00.bufr_d${OSUFFIX}}
-AMSR2BF=${AMSR2BF:-${COM_OBS}/${OPREFIX}amsr2.tm00.bufr_d${OSUFFIX}}
-GMI1CRBF=${GMI1CRBF:-${COM_OBS}/${OPREFIX}gmi1cr.tm00.bufr_d${OSUFFIX}} # GMI temporarily disabled due to array overflow.
-SAPHIRBF=${SAPHIRBF:-${COM_OBS}/${OPREFIX}saphir.tm00.bufr_d${OSUFFIX}}
-SEVIRIBF=${SEVIRIBF:-${COM_OBS}/${OPREFIX}sevcsr.tm00.bufr_d${OSUFFIX}}
-AHIBF=${AHIBF:-${COM_OBS}/${OPREFIX}ahicsr.tm00.bufr_d${OSUFFIX}}
-SSTVIIRS=${SSTVIIRS:-${COM_OBS}/${OPREFIX}sstvcw.tm00.bufr_d${OSUFFIX}}
-ABIBF=${ABIBF:-${COM_OBS}/${OPREFIX}gsrcsr.tm00.bufr_d${OSUFFIX}}
-CRISBF=${CRISBF:-${COM_OBS}/${OPREFIX}cris.tm00.bufr_d${OSUFFIX}}
-ESCRIS=${ESCRIS:-${COM_OBS}/${OPREFIX}escris.tm00.bufr_d${OSUFFIX}}
-CRISDB=${CRISDB:-${COM_OBS}/${OPREFIX}crisdb.tm00.bufr_d${OSUFFIX}}
-CRISFSBF=${CRISFSBF:-${COM_OBS}/${OPREFIX}crisf4.tm00.bufr_d${OSUFFIX}}
-ESCRISFS=${ESCRISFS:-${COM_OBS}/${OPREFIX}escrsf.tm00.bufr_d${OSUFFIX}}
-CRISFSDB=${CRISFSDB:-${COM_OBS}/${OPREFIX}crsfdb.tm00.bufr_d${OSUFFIX}}
-ATMSBF=${ATMSBF:-${COM_OBS}/${OPREFIX}atms.tm00.bufr_d${OSUFFIX}}
-ESATMS=${ESATMS:-${COM_OBS}/${OPREFIX}esatms.tm00.bufr_d${OSUFFIX}}
-ATMSDB=${ATMSDB:-${COM_OBS}/${OPREFIX}atmsdb.tm00.bufr_d${OSUFFIX}}
-SSMITBF=${SSMITBF:-${COM_OBS}/${OPREFIX}ssmit.tm00.bufr_d${OSUFFIX}}
-SSMISBF=${SSMISBF:-${COM_OBS}/${OPREFIX}ssmisu.tm00.bufr_d${OSUFFIX}}
-SBUVBF=${SBUVBF:-${COM_OBS}/${OPREFIX}osbuv8.tm00.bufr_d${OSUFFIX}}
-OMPSNPBF=${OMPSNPBF:-${COM_OBS}/${OPREFIX}ompsn8.tm00.bufr_d${OSUFFIX}}
-OMPSTCBF=${OMPSTCBF:-${COM_OBS}/${OPREFIX}ompst8.tm00.bufr_d${OSUFFIX}}
-OMPSLPBF=${OMPSLPBF:-${COM_OBS}/${OPREFIX}ompslp.tm00.bufr_d${OSUFFIX}}
-GOMEBF=${GOMEBF:-${COM_OBS}/${OPREFIX}gome.tm00.bufr_d${OSUFFIX}}
-OMIBF=${OMIBF:-${COM_OBS}/${OPREFIX}omi.tm00.bufr_d${OSUFFIX}}
-MLSBF=${MLSBF:-${COM_OBS}/${OPREFIX}mls.tm00.bufr_d${OSUFFIX}}
-SMIPCP=${SMIPCP:-${COM_OBS}/${OPREFIX}spssmi.tm00.bufr_d${OSUFFIX}}
-TMIPCP=${TMIPCP:-${COM_OBS}/${OPREFIX}sptrmm.tm00.bufr_d${OSUFFIX}}
-GPSROBF=${GPSROBF:-${COM_OBS}/${OPREFIX}gpsro.tm00.bufr_d${OSUFFIX}}
-TCVITL=${TCVITL:-${COM_OBS}/${OPREFIX}syndata.tcvitals.tm00}
-B1AVHAM=${B1AVHAM:-${COM_OBS}/${OPREFIX}avcsam.tm00.bufr_d${OSUFFIX}}
-B1AVHPM=${B1AVHPM:-${COM_OBS}/${OPREFIX}avcspm.tm00.bufr_d${OSUFFIX}}
-HDOB=${HDOB:-${COM_OBS}/${OPREFIX}hdob.tm00.bufr_d${OSUFFIX}}
+PREPQC=${PREPQC:-${COMIN_OBS}/${OPREFIX}prepbufr${OSUFFIX}}
+PREPQCPF=${PREPQCPF:-${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles${OSUFFIX}}
+NSSTBF=${NSSTBF:-${COMIN_OBS}/${OPREFIX}nsstbufr${OSUFFIX}}
+SATWND=${SATWND:-${COMIN_OBS}/${OPREFIX}satwnd.tm00.bufr_d${OSUFFIX}}
+OSCATBF=${OSCATBF:-${COMIN_OBS}/${OPREFIX}oscatw.tm00.bufr_d${OSUFFIX}}
+RAPIDSCATBF=${RAPIDSCATBF:-${COMIN_OBS}/${OPREFIX}rapidscatw.tm00.bufr_d${OSUFFIX}}
+GSNDBF=${GSNDBF:-${COMIN_OBS}/${OPREFIX}goesnd.tm00.bufr_d${OSUFFIX}}
+GSNDBF1=${GSNDBF1:-${COMIN_OBS}/${OPREFIX}goesfv.tm00.bufr_d${OSUFFIX}}
+#B1HRS2=${B1HRS2:-${COMIN_OBS}/${OPREFIX}1bhrs2.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
+B1MSU=${B1MSU:-${COMIN_OBS}/${OPREFIX}1bmsu.tm00.bufr_d${OSUFFIX}}
+#B1HRS3=${B1HRS3:-${COMIN_OBS}/${OPREFIX}1bhrs3.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
+#B1HRS4=${B1HRS4:-${COMIN_OBS}/${OPREFIX}1bhrs4.tm00.bufr_d${OSUFFIX}} # HIRS temporarily disabled due to CRTM versioning issues
+B1AMUA=${B1AMUA:-${COMIN_OBS}/${OPREFIX}1bamua.tm00.bufr_d${OSUFFIX}}
+B1AMUB=${B1AMUB:-${COMIN_OBS}/${OPREFIX}1bamub.tm00.bufr_d${OSUFFIX}}
+B1MHS=${B1MHS:-${COMIN_OBS}/${OPREFIX}1bmhs.tm00.bufr_d${OSUFFIX}}
+ESHRS3=${ESHRS3:-${COMIN_OBS}/${OPREFIX}eshrs3.tm00.bufr_d${OSUFFIX}}
+ESAMUA=${ESAMUA:-${COMIN_OBS}/${OPREFIX}esamua.tm00.bufr_d${OSUFFIX}}
+ESAMUB=${ESAMUB:-${COMIN_OBS}/${OPREFIX}esamub.tm00.bufr_d${OSUFFIX}}
+ESMHS=${ESMHS:-${COMIN_OBS}/${OPREFIX}esmhs.tm00.bufr_d${OSUFFIX}}
+HRS3DB=${HRS3DB:-${COMIN_OBS}/${OPREFIX}hrs3db.tm00.bufr_d${OSUFFIX}}
+AMUADB=${AMUADB:-${COMIN_OBS}/${OPREFIX}amuadb.tm00.bufr_d${OSUFFIX}}
+AMUBDB=${AMUBDB:-${COMIN_OBS}/${OPREFIX}amubdb.tm00.bufr_d${OSUFFIX}}
+MHSDB=${MHSDB:-${COMIN_OBS}/${OPREFIX}mhsdb.tm00.bufr_d${OSUFFIX}}
+AIRSBF=${AIRSBF:-${COMIN_OBS}/${OPREFIX}airsev.tm00.bufr_d${OSUFFIX}}
+IASIBF=${IASIBF:-${COMIN_OBS}/${OPREFIX}mtiasi.tm00.bufr_d${OSUFFIX}}
+ESIASI=${ESIASI:-${COMIN_OBS}/${OPREFIX}esiasi.tm00.bufr_d${OSUFFIX}}
+IASIDB=${IASIDB:-${COMIN_OBS}/${OPREFIX}iasidb.tm00.bufr_d${OSUFFIX}}
+AMSREBF=${AMSREBF:-${COMIN_OBS}/${OPREFIX}amsre.tm00.bufr_d${OSUFFIX}}
+AMSR2BF=${AMSR2BF:-${COMIN_OBS}/${OPREFIX}amsr2.tm00.bufr_d${OSUFFIX}}
+GMI1CRBF=${GMI1CRBF:-${COMIN_OBS}/${OPREFIX}gmi1cr.tm00.bufr_d${OSUFFIX}} # GMI temporarily disabled due to array overflow.
+SAPHIRBF=${SAPHIRBF:-${COMIN_OBS}/${OPREFIX}saphir.tm00.bufr_d${OSUFFIX}}
+SEVIRIBF=${SEVIRIBF:-${COMIN_OBS}/${OPREFIX}sevcsr.tm00.bufr_d${OSUFFIX}}
+AHIBF=${AHIBF:-${COMIN_OBS}/${OPREFIX}ahicsr.tm00.bufr_d${OSUFFIX}}
+SSTVIIRS=${SSTVIIRS:-${COMIN_OBS}/${OPREFIX}sstvcw.tm00.bufr_d${OSUFFIX}}
+ABIBF=${ABIBF:-${COMIN_OBS}/${OPREFIX}gsrcsr.tm00.bufr_d${OSUFFIX}}
+CRISBF=${CRISBF:-${COMIN_OBS}/${OPREFIX}cris.tm00.bufr_d${OSUFFIX}}
+ESCRIS=${ESCRIS:-${COMIN_OBS}/${OPREFIX}escris.tm00.bufr_d${OSUFFIX}}
+CRISDB=${CRISDB:-${COMIN_OBS}/${OPREFIX}crisdb.tm00.bufr_d${OSUFFIX}}
+CRISFSBF=${CRISFSBF:-${COMIN_OBS}/${OPREFIX}crisf4.tm00.bufr_d${OSUFFIX}}
+ESCRISFS=${ESCRISFS:-${COMIN_OBS}/${OPREFIX}escrsf.tm00.bufr_d${OSUFFIX}}
+CRISFSDB=${CRISFSDB:-${COMIN_OBS}/${OPREFIX}crsfdb.tm00.bufr_d${OSUFFIX}}
+ATMSBF=${ATMSBF:-${COMIN_OBS}/${OPREFIX}atms.tm00.bufr_d${OSUFFIX}}
+ESATMS=${ESATMS:-${COMIN_OBS}/${OPREFIX}esatms.tm00.bufr_d${OSUFFIX}}
+ATMSDB=${ATMSDB:-${COMIN_OBS}/${OPREFIX}atmsdb.tm00.bufr_d${OSUFFIX}}
+SSMITBF=${SSMITBF:-${COMIN_OBS}/${OPREFIX}ssmit.tm00.bufr_d${OSUFFIX}}
+SSMISBF=${SSMISBF:-${COMIN_OBS}/${OPREFIX}ssmisu.tm00.bufr_d${OSUFFIX}}
+SBUVBF=${SBUVBF:-${COMIN_OBS}/${OPREFIX}osbuv8.tm00.bufr_d${OSUFFIX}}
+OMPSNPBF=${OMPSNPBF:-${COMIN_OBS}/${OPREFIX}ompsn8.tm00.bufr_d${OSUFFIX}}
+OMPSTCBF=${OMPSTCBF:-${COMIN_OBS}/${OPREFIX}ompst8.tm00.bufr_d${OSUFFIX}}
+OMPSLPBF=${OMPSLPBF:-${COMIN_OBS}/${OPREFIX}ompslp.tm00.bufr_d${OSUFFIX}}
+GOMEBF=${GOMEBF:-${COMIN_OBS}/${OPREFIX}gome.tm00.bufr_d${OSUFFIX}}
+OMIBF=${OMIBF:-${COMIN_OBS}/${OPREFIX}omi.tm00.bufr_d${OSUFFIX}}
+MLSBF=${MLSBF:-${COMIN_OBS}/${OPREFIX}mls.tm00.bufr_d${OSUFFIX}}
+SMIPCP=${SMIPCP:-${COMIN_OBS}/${OPREFIX}spssmi.tm00.bufr_d${OSUFFIX}}
+TMIPCP=${TMIPCP:-${COMIN_OBS}/${OPREFIX}sptrmm.tm00.bufr_d${OSUFFIX}}
+GPSROBF=${GPSROBF:-${COMIN_OBS}/${OPREFIX}gpsro.tm00.bufr_d${OSUFFIX}}
+TCVITL=${TCVITL:-${COMIN_OBS}/${OPREFIX}syndata.tcvitals.tm00}
+B1AVHAM=${B1AVHAM:-${COMIN_OBS}/${OPREFIX}avcsam.tm00.bufr_d${OSUFFIX}}
+B1AVHPM=${B1AVHPM:-${COMIN_OBS}/${OPREFIX}avcspm.tm00.bufr_d${OSUFFIX}}
+HDOB=${HDOB:-${COMIN_OBS}/${OPREFIX}hdob.tm00.bufr_d${OSUFFIX}}
 
 # Guess files
 GPREFIX=${GPREFIX:-""}
 GSUFFIX=${GSUFFIX:-".nc"}
-SFCG03=${SFCG03:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf003${GSUFFIX}}
-SFCG04=${SFCG04:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf004${GSUFFIX}}
-SFCG05=${SFCG05:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf005${GSUFFIX}}
-SFCGES=${SFCGES:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf006${GSUFFIX}}
-SFCG07=${SFCG07:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf007${GSUFFIX}}
-SFCG08=${SFCG08:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf008${GSUFFIX}}
-SFCG09=${SFCG09:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf009${GSUFFIX}}
-ATMG03=${ATMG03:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf003${GSUFFIX}}
-ATMG04=${ATMG04:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf004${GSUFFIX}}
-ATMG05=${ATMG05:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf005${GSUFFIX}}
-ATMGES=${ATMGES:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}}
-ATMG07=${ATMG07:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf007${GSUFFIX}}
-ATMG08=${ATMG08:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf008${GSUFFIX}}
-ATMG09=${ATMG09:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf009${GSUFFIX}}
-GBIAS=${GBIAS:-${COM_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias}
-GBIASPC=${GBIASPC:-${COM_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias_pc}
-GBIASAIR=${GBIASAIR:-${COM_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias_air}
-GRADSTAT=${GRADSTAT:-${COM_ATMOS_ANALYSIS_PREV}/${GPREFIX}radstat}
+SFCG03=${SFCG03:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf003${GSUFFIX}}
+SFCG04=${SFCG04:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf004${GSUFFIX}}
+SFCG05=${SFCG05:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf005${GSUFFIX}}
+SFCGES=${SFCGES:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf006${GSUFFIX}}
+SFCG07=${SFCG07:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf007${GSUFFIX}}
+SFCG08=${SFCG08:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf008${GSUFFIX}}
+SFCG09=${SFCG09:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf009${GSUFFIX}}
+ATMG03=${ATMG03:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf003${GSUFFIX}}
+ATMG04=${ATMG04:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf004${GSUFFIX}}
+ATMG05=${ATMG05:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf005${GSUFFIX}}
+ATMGES=${ATMGES:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}}
+ATMG07=${ATMG07:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf007${GSUFFIX}}
+ATMG08=${ATMG08:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf008${GSUFFIX}}
+ATMG09=${ATMG09:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf009${GSUFFIX}}
+GBIAS=${GBIAS:-${COMIN_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias}
+GBIASPC=${GBIASPC:-${COMIN_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias_pc}
+GBIASAIR=${GBIASAIR:-${COMIN_ATMOS_ANALYSIS_PREV}/${GPREFIX}abias_air}
+GRADSTAT=${GRADSTAT:-${COMIN_ATMOS_ANALYSIS_PREV}/${GPREFIX}radstat}
 
 # Analysis files
 export APREFIX=${APREFIX:-""}
-SFCANL=${SFCANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc}
-DTFANL=${DTFANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}
-ATMANL=${ATMANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmanl.nc}
-ABIAS=${ABIAS:-${COM_ATMOS_ANALYSIS}/${APREFIX}abias}
-ABIASPC=${ABIASPC:-${COM_ATMOS_ANALYSIS}/${APREFIX}abias_pc}
-ABIASAIR=${ABIASAIR:-${COM_ATMOS_ANALYSIS}/${APREFIX}abias_air}
-ABIASe=${ABIASe:-${COM_ATMOS_ANALYSIS}/${APREFIX}abias_int}
-RADSTAT=${RADSTAT:-${COM_ATMOS_ANALYSIS}/${APREFIX}radstat}
-GSISTAT=${GSISTAT:-${COM_ATMOS_ANALYSIS}/${APREFIX}gsistat}
-PCPSTAT=${PCPSTAT:-${COM_ATMOS_ANALYSIS}/${APREFIX}pcpstat}
-CNVSTAT=${CNVSTAT:-${COM_ATMOS_ANALYSIS}/${APREFIX}cnvstat}
-OZNSTAT=${OZNSTAT:-${COM_ATMOS_ANALYSIS}/${APREFIX}oznstat}
+SFCANL=${SFCANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc}
+DTFANL=${DTFANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}
+ATMANL=${ATMANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmanl.nc}
+ABIAS=${ABIAS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias}
+ABIASPC=${ABIASPC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc}
+ABIASAIR=${ABIASAIR:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air}
+ABIASe=${ABIASe:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int}
+RADSTAT=${RADSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat}
+GSISTAT=${GSISTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat}
+PCPSTAT=${PCPSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}pcpstat}
+CNVSTAT=${CNVSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat}
+OZNSTAT=${OZNSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat}
 
 # Increment files
-ATMINC=${ATMINC:-${COM_ATMOS_ANALYSIS}/${APREFIX}atminc.nc}
+ATMINC=${ATMINC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atminc.nc}
 
 # Obs diag
 RUN_SELECT=${RUN_SELECT:-"NO"}
 USE_SELECT=${USE_SELECT:-"NO"}
 USE_RADSTAT=${USE_RADSTAT:-"YES"}
-SELECT_OBS=${SELECT_OBS:-${COM_ATMOS_ANALYSIS}/${APREFIX}obsinput}
+SELECT_OBS=${SELECT_OBS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput}
 GENDIAG=${GENDIAG:-"YES"}
 DIAG_SUFFIX=${DIAG_SUFFIX:-""}
 if [ ${netcdf_diag} = ".true." ] ; then
@@ -211,7 +211,7 @@ nm=""
 if [ ${CFP_MP} = "YES" ]; then
     nm=0
 fi
-DIAG_DIR=${DIAG_DIR:-${COM_ATMOS_ANALYSIS}/gsidiags}
+DIAG_DIR=${DIAG_DIR:-${COMOUT_ATMOS_ANALYSIS}/gsidiags}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -242,8 +242,8 @@ JCAP=${JCAP:--9999} # there is no jcap in these files
 
 # Get header information from Ensemble Guess files
 if [ ${DOHYBVAR} = "YES" ]; then
-   SFCGES_ENSMEAN=${SFCGES_ENSMEAN:-${COM_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}sfcf006.ensmean.nc}
-   export ATMGES_ENSMEAN=${ATMGES_ENSMEAN:-${COM_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc}
+   SFCGES_ENSMEAN=${SFCGES_ENSMEAN:-${COMIN_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}sfcf006.ensmean.nc}
+   export ATMGES_ENSMEAN=${ATMGES_ENSMEAN:-${COMIN_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc}
    LONB_ENKF=${LONB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_xt)} # get LONB_ENKF
    LATB_ENKF=${LATB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_yt)} # get LATB_ENFK
    LEVS_ENKF=${LEVS_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} pfull)} # get LATB_ENFK
@@ -335,18 +335,18 @@ fi
 
 # Set 4D-EnVar specific variables
 if [ ${DOHYBVAR} = "YES" -a ${l4densvar} = ".true." -a ${lwrite4danl} = ".true." ]; then
-   ATMA03=${ATMA03:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma003.nc}
-   ATMI03=${ATMI03:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi003.nc}
-   ATMA04=${ATMA04:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma004.nc}
-   ATMI04=${ATMI04:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi004.nc}
-   ATMA05=${ATMA05:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma005.nc}
-   ATMI05=${ATMI05:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi005.nc}
-   ATMA07=${ATMA07:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma007.nc}
-   ATMI07=${ATMI07:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi007.nc}
-   ATMA08=${ATMA08:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma008.nc}
-   ATMI08=${ATMI08:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi008.nc}
-   ATMA09=${ATMA09:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma009.nc}
-   ATMI09=${ATMI09:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi009.nc}
+   ATMA03=${ATMA03:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma003.nc}
+   ATMI03=${ATMI03:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi003.nc}
+   ATMA04=${ATMA04:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma004.nc}
+   ATMI04=${ATMI04:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi004.nc}
+   ATMA05=${ATMA05:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma005.nc}
+   ATMI05=${ATMI05:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi005.nc}
+   ATMA07=${ATMA07:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma007.nc}
+   ATMI07=${ATMI07:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi007.nc}
+   ATMA08=${ATMA08:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma008.nc}
+   ATMI08=${ATMI08:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi008.nc}
+   ATMA09=${ATMA09:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma009.nc}
+   ATMI09=${ATMI09:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi009.nc}
 fi
 
 ################################################################################
@@ -545,12 +545,13 @@ if [ ${DOHYBVAR} = "YES" ]; then
 
    for imem in $(seq 1 ${NMEM_ENS}); do
       memchar="mem$(printf %03i "${imem}")"
-      MEMDIR=${memchar} RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl COM_ATMOS_HISTORY
+      MEMDIR=${memchar} RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl \
+	      COMIN_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
 
       for fhr in ${fhrs}; do
-         ${NLN} ${COM_ATMOS_HISTORY}/${GPREFIX_ENS}atmf0${fhr}${ENKF_SUFFIX}.nc ./ensemble_data/sigf${fhr}_ens_${memchar}
+         ${NLN} ${COMIN_ATMOS_HISTORY}/${GPREFIX_ENS}atmf0${fhr}${ENKF_SUFFIX}.nc ./ensemble_data/sigf${fhr}_ens_${memchar}
          if [ ${cnvw_option} = ".true." ]; then
-            ${NLN} ${COM_ATMOS_HISTORY}/${GPREFIX_ENS}sfcf0${fhr}.nc ./ensemble_data/sfcf${fhr}_ens_${memchar}
+            ${NLN} ${COMIN_ATMOS_HISTORY}/${GPREFIX_ENS}sfcf0${fhr}.nc ./ensemble_data/sfcf${fhr}_ens_${memchar}
          fi
       done
    done
@@ -990,7 +991,7 @@ cd ${pwd}
 if [ ${SENDECF} = "YES" -a "${RUN}" != "enkf" ]; then
    ecflow_client --event release_fcst
 fi
-echo "${rCDUMP} ${CDATE} atminc done at $(date)" > ${COM_ATMOS_ANALYSIS}/${APREFIX}loginc.txt
+echo "${rCDUMP} ${CDATE} atminc done at $(date)" > ${COMOUT_ATMOS_ANALYSIS}/${APREFIX}loginc.txt
 
 ################################################################################
 
diff --git a/scripts/exglobal_atmos_analysis_calc.sh b/scripts/exglobal_atmos_analysis_calc.sh
index 423e800879..74455ee2cb 100755
--- a/scripts/exglobal_atmos_analysis_calc.sh
+++ b/scripts/exglobal_atmos_analysis_calc.sh
@@ -69,22 +69,22 @@ SENDDBN=${SENDDBN:-"NO"}
 
 # Guess files
 GPREFIX=${GPREFIX:-""}
-ATMG03=${ATMG03:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf003.nc}
-ATMG04=${ATMG04:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf004.nc}
-ATMG05=${ATMG05:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf005.nc}
-ATMGES=${ATMGES:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc}
-ATMG07=${ATMG07:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf007.nc}
-ATMG08=${ATMG08:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf008.nc}
-ATMG09=${ATMG09:-${COM_ATMOS_HISTORY_PREV}/${GPREFIX}atmf009.nc}
+ATMG03=${ATMG03:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf003.nc}
+ATMG04=${ATMG04:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf004.nc}
+ATMG05=${ATMG05:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf005.nc}
+ATMGES=${ATMGES:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc}
+ATMG07=${ATMG07:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf007.nc}
+ATMG08=${ATMG08:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf008.nc}
+ATMG09=${ATMG09:-${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf009.nc}
 
 # Analysis files
 export APREFIX=${APREFIX:-""}
-SFCANL=${SFCANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc}
-DTFANL=${DTFANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}
-ATMANL=${ATMANL:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmanl.nc}
+SFCANL=${SFCANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc}
+DTFANL=${DTFANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}dtfanl.nc}
+ATMANL=${ATMANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmanl.nc}
 
 # Increment files
-ATMINC=${ATMINC:-${COM_ATMOS_ANALYSIS}/${APREFIX}atminc.nc}
+ATMINC=${ATMINC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atminc.nc}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -101,18 +101,18 @@ fi
 
 # Set 4D-EnVar specific variables
 if [ $DOHYBVAR = "YES" -a $l4densvar = ".true." -a $lwrite4danl = ".true." ]; then
-   ATMA03=${ATMA03:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma003.nc}
-   ATMI03=${ATMI03:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi003.nc}
-   ATMA04=${ATMA04:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma004.nc}
-   ATMI04=${ATMI04:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi004.nc}
-   ATMA05=${ATMA05:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma005.nc}
-   ATMI05=${ATMI05:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi005.nc}
-   ATMA07=${ATMA07:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma007.nc}
-   ATMI07=${ATMI07:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi007.nc}
-   ATMA08=${ATMA08:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma008.nc}
-   ATMI08=${ATMI08:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi008.nc}
-   ATMA09=${ATMA09:-${COM_ATMOS_ANALYSIS}/${APREFIX}atma009.nc}
-   ATMI09=${ATMI09:-${COM_ATMOS_ANALYSIS}/${APREFIX}atmi009.nc}
+   ATMA03=${ATMA03:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma003.nc}
+   ATMI03=${ATMI03:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi003.nc}
+   ATMA04=${ATMA04:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma004.nc}
+   ATMI04=${ATMI04:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi004.nc}
+   ATMA05=${ATMA05:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma005.nc}
+   ATMI05=${ATMI05:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi005.nc}
+   ATMA07=${ATMA07:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma007.nc}
+   ATMI07=${ATMI07:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi007.nc}
+   ATMA08=${ATMA08:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma008.nc}
+   ATMI08=${ATMI08:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi008.nc}
+   ATMA09=${ATMA09:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atma009.nc}
+   ATMI09=${ATMI09:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}atmi009.nc}
 fi
 
 ################################################################################
@@ -181,7 +181,7 @@ if [ $DOGAUSFCANL = "YES" ]; then
     export err=$?; err_chk
 fi
 
-echo "${rCDUMP} ${PDY}${cyc} atmanl and sfcanl done at $(date)" > "${COM_ATMOS_ANALYSIS}/${APREFIX}loganl.txt"
+echo "${rCDUMP} ${PDY}${cyc} atmanl and sfcanl done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}loganl.txt"
 
 ################################################################################
 # Postprocessing
diff --git a/sorc/gdas.cd b/sorc/gdas.cd
index d91663bb58..d9b40c9bde 160000
--- a/sorc/gdas.cd
+++ b/sorc/gdas.cd
@@ -1 +1 @@
-Subproject commit d91663bb585fbfa30db99d6126a1d4f24906b69b
+Subproject commit d9b40c9bde1e5e70451f309a5e010267aaadba00
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 8c1c0658e7..ecbad78693 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -235,13 +235,12 @@ fi
 #------------------------------
 if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
   cd "${HOMEgfs}/ush" || exit 1
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/soca" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_json.py" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_yaml.py" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py" .
-  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py" .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/soca"                              .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ufsda"                              .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_json.py"    .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/gen_bufr2ioda_yaml.py"    .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
   declare -a gdasapp_ocn_insitu_profile_platforms=("argo" "bathy" "glider" "marinemammal" "tesac" "xbtctd")
   for platform in "${gdasapp_ocn_insitu_profile_platforms[@]}"; do
     ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/marine/bufr2ioda_insitu_profile_${platform}.py" .
diff --git a/ush/calcanl_gfs.py b/ush/calcanl_gfs.py
index 9dc6ff9fa6..f5e65f3824 100755
--- a/ush/calcanl_gfs.py
+++ b/ush/calcanl_gfs.py
@@ -346,9 +346,9 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix,
     DoIAU = gsi_utils.isTrue(os.getenv('DOIAU', 'NO'))
     l4DEnsVar = gsi_utils.isTrue(os.getenv('l4densvar', 'NO'))
     Write4Danl = gsi_utils.isTrue(os.getenv('lwrite4danl', 'NO'))
-    ComIn_Ges = os.getenv('COM_ATMOS_HISTORY_PREV', './')
+    ComIn_Ges = os.getenv('COMIN_ATMOS_HISTORY_PREV', './')
     GPrefix = os.getenv('GPREFIX', './')
-    ComOut = os.getenv('COM_ATMOS_ANALYSIS', './')
+    ComOut = os.getenv('COMOUT_ATMOS_ANALYSIS', './')
     APrefix = os.getenv('APREFIX', '')
     NThreads = os.getenv('NTHREADS_CHGRES', 1)
     FixDir = os.path.join(os.getenv('FIXgfs', './'), 'am')
diff --git a/ush/calcinc_gfs.py b/ush/calcinc_gfs.py
index cb334ac836..770ed79f3d 100755
--- a/ush/calcinc_gfs.py
+++ b/ush/calcinc_gfs.py
@@ -70,7 +70,7 @@ def calcinc_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, IAUHrs,
     DoIAU = gsi_utils.isTrue(os.getenv('DOIAU', 'NO'))
     l4DEnsVar = gsi_utils.isTrue(os.getenv('l4densvar', 'NO'))
     Write4Danl = gsi_utils.isTrue(os.getenv('lwrite4danl', 'NO'))
-    ComOut = os.getenv('COM_ATMOS_ANALYSIS', './')
+    ComOut = os.getenv('COMOUT_ATMOS_ANALYSIS', './')
     APrefix = os.getenv('APREFIX', '')
     NThreads = os.getenv('NTHREADS_CALCINC', 1)
     IMP_Physics = os.getenv('imp_physics', 11)
diff --git a/ush/gaussian_sfcanl.sh b/ush/gaussian_sfcanl.sh
index 4ac762824b..8b8f066cfe 100755
--- a/ush/gaussian_sfcanl.sh
+++ b/ush/gaussian_sfcanl.sh
@@ -77,7 +77,7 @@
 #                  ${FIXWGTS}
 #                  ${FIXgfs}/am/global_hyblev.l65.txt
 #
-#     input data : ${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile*.nc
+#     input data : ${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile*.nc
 #
 #     output data: $PGMOUT
 #                  $PGMERR
@@ -133,8 +133,7 @@ export REDERR=${REDERR:-'2>'}
 ${INISCRIPT:-}
 pwd=$(pwd)
 cd "${DATA}" || exit 99
-[[ -d "${COM_ATMOS_ANALYSIS}" ]] || mkdir -p "${COM_ATMOS_ANALYSIS}"
-[[ -d "${COM_ATMOS_RESTART}" ]] || mkdir -p "${COM_ATMOS_RESTART}"
+[[ -d "${COMOUT_ATMOS_ANALYSIS}" ]] || mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 ################################################################################
 #  Make surface analysis
@@ -153,12 +152,12 @@ export OMP_NUM_THREADS=${OMP_NUM_THREADS_SFC:-1}
 ${NLN} "${FIXWGTS}" "./weights.nc"
 
 # input analysis tiles (with nst records)
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile1.nc" "./anal.tile1.nc"
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile2.nc" "./anal.tile2.nc"
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile3.nc" "./anal.tile3.nc"
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile4.nc" "./anal.tile4.nc"
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile5.nc" "./anal.tile5.nc"
-${NLN} "${COM_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile6.nc" "./anal.tile6.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile1.nc" "./anal.tile1.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile2.nc" "./anal.tile2.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile3.nc" "./anal.tile3.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile4.nc" "./anal.tile4.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile5.nc" "./anal.tile5.nc"
+${NLN} "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile6.nc" "./anal.tile6.nc"
 
 # input orography tiles
 ${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile1.nc" "./orog.tile1.nc"
@@ -171,7 +170,7 @@ ${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile6.nc" "./orog.tile6.
 ${NLN} "${SIGLEVEL}" "./vcoord.txt"
 
 # output gaussian global surface analysis files
-${NLN} "${COM_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc" "./sfc.gaussian.analysis.file"
+${NLN} "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc" "./sfc.gaussian.analysis.file"
 
 # Namelist uses booleans now
 if [[ ${DONST} == "YES" ]]; then do_nst='.true.'; else do_nst='.false.'; fi
diff --git a/ush/python/pygfs/task/marine_analysis.py b/ush/python/pygfs/task/marine_analysis.py
index ebb1502634..dd48c9f80f 100644
--- a/ush/python/pygfs/task/marine_analysis.py
+++ b/ush/python/pygfs/task/marine_analysis.py
@@ -214,6 +214,10 @@ def _prep_variational_yaml(self: Task) -> None:
         envconfig_jcb['cyc'] = os.getenv('cyc')
         envconfig_jcb['SOCA_NINNER'] = self.task_config.SOCA_NINNER
         envconfig_jcb['obs_list'] = ['adt_rads_all']
+        envconfig_jcb['HOMEgfs'] = self.task_config.HOMEgfs
+        envconfig_jcb['DO_TEST_MODE'] = self.task_config.DO_TEST_MODE
+        envconfig_jcb['RUN'] = self.task_config.RUN
+        envconfig_jcb['current_cycle'] = self.task_config.current_cycle
         envconfig_jcb['MOM6_LEVS'] = mdau.get_mom6_levels(str(self.task_config.OCNRES).zfill(3))
 
         # Write obs_list_short
@@ -222,7 +226,7 @@ def _prep_variational_yaml(self: Task) -> None:
 
         # Render the JCB configuration files
         jcb_base_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-base.yaml')
-        jcb_algo_yaml = os.path.join(self.task_config.PARMsoca, 'marine-jcb-3dfgat.yaml.j2')
+        jcb_algo_yaml = self.task_config.JCB_ALGO_YAML_VAR
 
         jcb_base_config = parse_j2yaml(path=jcb_base_yaml, data=envconfig_jcb)
         jcb_algo_config = parse_j2yaml(path=jcb_algo_yaml, data=envconfig_jcb)