diff --git a/.gitignore b/.gitignore
index 39d140fd65..943ad64e1a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -106,6 +106,7 @@ parm/post/ice.csv
 parm/post/ocnicepost.nml.jinja2
 parm/ufs/noahmptable.tbl
 parm/ufs/model_configure.IN
+parm/ufs/model_configure_nest.IN
 parm/ufs/MOM_input_*.IN
 parm/ufs/MOM6_data_table.IN
 parm/ufs/ice_in.IN
diff --git a/ci/cases/pr/C96_atm3DVar.yaml b/ci/cases/pr/C96_atm3DVar.yaml
index d992938f7f..8a89ff25ec 100644
--- a/ci/cases/pr/C96_atm3DVar.yaml
+++ b/ci/cases/pr/C96_atm3DVar.yaml
@@ -15,3 +15,6 @@ arguments:
   gfs_cyc: 1
   start: cold
   yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_defaults_ci.yaml
+
+skip_ci_on_hosts:
+  - wcoss2
diff --git a/ci/cases/pr/C96_atm3DVar_extended.yaml b/ci/cases/pr/C96_atm3DVar_extended.yaml
new file mode 100644
index 0000000000..994d3ef3a0
--- /dev/null
+++ b/ci/cases/pr/C96_atm3DVar_extended.yaml
@@ -0,0 +1,22 @@
+experiment:
+  system: gfs
+  mode: cycled
+
+arguments:
+  pslot: {{ 'pslot' | getenv }}
+  app: ATM
+  resdetatmos: 96
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C96C48
+  idate: 2021122018
+  edate: 2021122118
+  nens: 0
+  gfs_cyc: 4
+  start: cold
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/gfs_extended_ci.yaml
+
+skip_ci_on_hosts:
+  - hera
+  - orion
+  - hercules
diff --git a/ci/cases/yamls/gfs_extended_ci.yaml b/ci/cases/yamls/gfs_extended_ci.yaml
new file mode 100644
index 0000000000..4d4f79e0e8
--- /dev/null
+++ b/ci/cases/yamls/gfs_extended_ci.yaml
@@ -0,0 +1,12 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gfs/yaml/defaults.yaml
+
+base:
+  ACCOUNT: {{ 'SLURM_ACCOUNT' | getenv }}
+  DO_GOES: "YES"
+  DO_BUFRSND: "YES"
+  DO_GEMPAK: "YES"
+  DO_AWIPS: "NO"
+  DO_NPOESS: "YES"
+  DO_GENESIS_FSU: "NO"
+  FHMAX_GFS: 384
diff --git a/env/HERA.env b/env/HERA.env
index 6ce99f8e90..68dbd4d396 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -49,6 +49,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"
diff --git a/env/HERCULES.env b/env/HERCULES.env
index da5ad972f2..0b62120536 100755
--- a/env/HERCULES.env
+++ b/env/HERCULES.env
@@ -45,6 +45,10 @@ case ${step} in
 
     export APRUN_CALCFIMS="${launcher} -n 1"
  ;;
+ "prep_emissions")
+
+    export APRUN="${launcher} -n 1"
+ ;;
  "waveinit" | "waveprep" | "wavepostsbs" | "wavepostbndpnt" | "wavepostpnt" | "wavepostbndpntbll")
 
     export CFP_MP="YES"
diff --git a/env/JET.env b/env/JET.env
index 3b4c2c2c53..976e42a025 100755
--- a/env/JET.env
+++ b/env/JET.env
@@ -37,6 +37,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"
diff --git a/env/ORION.env b/env/ORION.env
index 6aac84a169..795346f0c6 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -44,6 +44,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || \
     [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostpnt" ]] || [[ "${step}" == "wavepostbndpntbll" ]]; then
 
diff --git a/env/S4.env b/env/S4.env
index 9cbf8b7bdb..ce68fddb89 100755
--- a/env/S4.env
+++ b/env/S4.env
@@ -37,6 +37,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export CFP_MP="YES"
diff --git a/env/WCOSS2.env b/env/WCOSS2.env
index ba55495655..ff0121e034 100755
--- a/env/WCOSS2.env
+++ b/env/WCOSS2.env
@@ -31,6 +31,10 @@ elif [[ "${step}" = "prepsnowobs" ]]; then
 
     export APRUN_CALCFIMS="${launcher} -n 1"
 
+elif [[ "${step}" = "prep_emissions" ]]; then
+
+    export APRUN="${launcher} -n 1"
+
 elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll"  ]] || [[ "${step}" = "wavepostpnt" ]]; then
 
     export USE_CFP="YES"
diff --git a/gempak/ush/gfs_meta_opc_na_ver b/gempak/ush/gfs_meta_opc_na_ver
index d38ddacee0..3aaf93db68 100755
--- a/gempak/ush/gfs_meta_opc_na_ver
+++ b/gempak/ush/gfs_meta_opc_na_ver
@@ -33,8 +33,8 @@ fcsthr="f00"
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
 case ${cyc} in
-    00 | 12) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 96 12 120)) ;;
-    06 | 18) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 90 12 126)) ;;
+    00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
+    06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
     *)
         echo "FATAL ERROR: Invalid cycle ${cyc} passed to ${BASH_SOURCE[0]}"
         exit 100
diff --git a/gempak/ush/gfs_meta_opc_np_ver b/gempak/ush/gfs_meta_opc_np_ver
index 9446417403..0968b55747 100755
--- a/gempak/ush/gfs_meta_opc_np_ver
+++ b/gempak/ush/gfs_meta_opc_np_ver
@@ -33,8 +33,8 @@ fcsthr="f00"
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
 case ${cyc} in
-    00 | 12) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 96 12 120)) ;;
-    06 | 18) IFS=$'\n' lookbacks=($(seq 6 6 84) $(seq 90 12 126)) ;;
+    00 | 12) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 96 12 120)) ;;
+    06 | 18) lookbacks=($(IFS=$'\n' seq 6 6 84) $(IFS=$'\n' seq 90 12 126)) ;;
     *)
         echo "FATAL ERROR: Invalid cycle ${cyc} passed to ${BASH_SOURCE[0]}"
         exit 100
diff --git a/gempak/ush/gfs_meta_ver.sh b/gempak/ush/gfs_meta_ver.sh
index 1e00cd3094..eb8b5b15c6 100755
--- a/gempak/ush/gfs_meta_ver.sh
+++ b/gempak/ush/gfs_meta_ver.sh
@@ -32,7 +32,7 @@ MDL2="GFSHPC"
 #GENERATING THE METAFILES.
 # seq won't give us any splitting problems, ignore warnings
 # shellcheck disable=SC2207,SC2312
-IFS=$'\n' lookbacks=($(seq 6 6 180) $(seq 192 12 216))
+lookbacks=($(IFS=$'\n' seq 6 6 180) $(IFS=$'\n' seq 192 12 216))
 for lookback in "${lookbacks[@]}"; do
     init_time="$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${lookback} hours")"
     init_PDY=${init_time:0:8}
diff --git a/jobs/JGLOBAL_PREP_EMISSIONS b/jobs/JGLOBAL_PREP_EMISSIONS
new file mode 100755
index 0000000000..84edac8e50
--- /dev/null
+++ b/jobs/JGLOBAL_PREP_EMISSIONS
@@ -0,0 +1,35 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "prep_emissions" -c "base prep_emissions"
+
+##############################################
+# Set variables used in the script
+##############################################
+# TODO: Set local variables used in this script e.g. GDATE may be needed for previous cycle
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+# Generate COM variables from templates
+# TODO: Add necessary COMIN, COMOUT variables for this job
+
+###############################################################
+# Run relevant script
+EXSCRIPT=${PREP_EMISSIONS_PY:-${SCRgfs}/exglobal_prep_emissions.py}
+${EXSCRIPT}
+status=$?
+(( status != 0 )) && ( echo "FATAL ERROR: Error executing ${EXSCRIPT}, ABORT!"; exit "${status}" )
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0
diff --git a/jobs/rocoto/prep_emissions.sh b/jobs/rocoto/prep_emissions.sh
new file mode 100755
index 0000000000..0677073947
--- /dev/null
+++ b/jobs/rocoto/prep_emissions.sh
@@ -0,0 +1,23 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+
+###############################################################
+# Source UFSDA workflow modules
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+status=$?
+(( status !=  0 )) && exit "${status}"
+
+export job="prep_emissions"
+export jobid="${job}.$$"
+
+###############################################################
+# setup python path for workflow utilities and tasks
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_PREP_EMISSIONS"
+status=$?
+exit "${status}"
diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index bc37c5abbc..90a75e3639 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -47,9 +47,9 @@ export NOSCRUB="@NOSCRUB@"
 export BASE_GIT="@BASE_GIT@"
 
 # Toggle to turn on/off GFS downstream processing.
-export DO_BUFRSND="NO"     # BUFR sounding products
-export DO_GEMPAK="NO"      # GEMPAK products
-export DO_AWIPS="NO"       # AWIPS products
+export DO_BUFRSND="@DO_BUFRSND@"     # BUFR sounding products
+export DO_GEMPAK="@DO_GEMPAK@"       # GEMPAK products
+export DO_AWIPS="@DO_AWIPS@"         # AWIPS products
 
 # NO for retrospective parallel; YES for real-time parallel
 #  arch.sh uses REALTIME for MOS.  Need to set REALTIME=YES
diff --git a/parm/config/gefs/config.prep_emissions b/parm/config/gefs/config.prep_emissions
new file mode 100644
index 0000000000..fa411c27ad
--- /dev/null
+++ b/parm/config/gefs/config.prep_emissions
@@ -0,0 +1,11 @@
+#! /usr/bin/env bash
+
+########## config.prep_emissions ##########
+# aerosol emissions preprocessing specific
+
+echo "BEGIN: config.prep_emissions"
+
+# Get task specific resources
+source "${EXPDIR}/config.resources" prep_emissions
+
+echo "END: config.prep_emissions"
diff --git a/parm/config/gefs/config.resources b/parm/config/gefs/config.resources
index 9bf62cf514..d98e437359 100644
--- a/parm/config/gefs/config.resources
+++ b/parm/config/gefs/config.resources
@@ -69,6 +69,14 @@ case ${step} in
     export memory_waveinit="2GB"
     ;;
 
+  "prep_emissions")
+    export wtime_prep_emissions="00:10:00"
+    export npe_prep_emissions=1
+    export nth_prep_emissions=1
+    export npe_node_prep_emissions=$(( npe_node_max / nth_prep_emissions ))
+    export memory_prep_emissions="1GB"
+    ;;
+
   "fcst" | "efcs")
     export is_exclusive=True
 
diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
index d252e0d1b2..5c763ad29e 100644
--- a/parm/config/gefs/yaml/defaults.yaml
+++ b/parm/config/gefs/yaml/defaults.yaml
@@ -4,6 +4,9 @@ base:
   DO_JEDIOCNVAR: "NO"
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
   KEEPDATA: "NO" 
   FHMAX_GFS: 120
   USE_OCN_PERTURB_FILES: "false"
diff --git a/parm/config/gfs/config.aeroanl b/parm/config/gfs/config.aeroanl
index 972f393feb..24a5e92644 100644
--- a/parm/config/gfs/config.aeroanl
+++ b/parm/config/gfs/config.aeroanl
@@ -18,7 +18,7 @@ export JEDI_FIX_YAML="${PARMgfs}/gdas/aero_jedi_fix.yaml.j2"
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE="${EXECgfs}/fv3jedi_var.x"
+export JEDIEXE="${EXECgfs}/gdas.x"
 
 if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"
diff --git a/parm/config/gfs/config.atmanl b/parm/config/gfs/config.atmanl
index 7cfd0cb47f..5eb692b473 100644
--- a/parm/config/gfs/config.atmanl
+++ b/parm/config/gfs/config.atmanl
@@ -28,6 +28,6 @@ export layout_y_atmanl=@LAYOUT_Y_ATMANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_var.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmanl"
diff --git a/parm/config/gfs/config.atmensanl b/parm/config/gfs/config.atmensanl
index 8e824b22f6..23eab7f7b9 100644
--- a/parm/config/gfs/config.atmensanl
+++ b/parm/config/gfs/config.atmensanl
@@ -18,6 +18,6 @@ export layout_y_atmensanl=@LAYOUT_Y_ATMENSANL@
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
-export JEDIEXE=${EXECgfs}/fv3jedi_letkf.x
+export JEDIEXE=${EXECgfs}/gdas.x
 
 echo "END: config.atmensanl"
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index ab35f717cb..8ee1a2c17e 100644
--- a/parm/config/gfs/config.base
+++ b/parm/config/gfs/config.base
@@ -65,18 +65,18 @@ export NOSCRUB="@NOSCRUB@"
 export BASE_GIT="@BASE_GIT@"
 
 # Toggle to turn on/off GFS downstream processing.
-export DO_GOES="@DO_GOES@" # GOES products
-export DO_BUFRSND="NO"     # BUFR sounding products
-export DO_GEMPAK="NO"      # GEMPAK products
-export DO_AWIPS="NO"       # AWIPS products
-export DO_NPOESS="NO"      # NPOESS products
-export DO_TRACKER="YES"    # Hurricane track verification
-export DO_GENESIS="YES"    # Cyclone genesis verification
-export DO_GENESIS_FSU="NO" # Cyclone genesis verification (FSU)
-export DO_VERFOZN="YES"    # Ozone data assimilation monitoring
-export DO_VERFRAD="YES"    # Radiance data assimilation monitoring
-export DO_VMINMON="YES"    # GSI minimization monitoring
-export DO_MOS="NO"         # GFS Model Output Statistics - Only supported on WCOSS2
+export DO_GOES="@DO_GOES@"               # GOES products
+export DO_BUFRSND="@DO_BUFRSND@"         # BUFR sounding products
+export DO_GEMPAK="@DO_GEMPAK@"           # GEMPAK products
+export DO_AWIPS="@DO_AWIPS@"             # AWIPS products
+export DO_NPOESS="@DO_NPOESS@"           # NPOESS products
+export DO_TRACKER="@DO_TRACKER@"         # Hurricane track verification
+export DO_GENESIS="@DO_GENESIS@"         # Cyclone genesis verification
+export DO_GENESIS_FSU="@DO_GENESIS_FSU@" # Cyclone genesis verification (FSU)
+export DO_VERFOZN="YES"                  # Ozone data assimilation monitoring
+export DO_VERFRAD="YES"                  # Radiance data assimilation monitoring
+export DO_VMINMON="YES"                  # GSI minimization monitoring
+export DO_MOS="NO"                       # GFS Model Output Statistics - Only supported on WCOSS2
 
 # NO for retrospective parallel; YES for real-time parallel
 #  arch.sh uses REALTIME for MOS.  Need to set REALTIME=YES
diff --git a/parm/config/gfs/config.snowanl b/parm/config/gfs/config.snowanl
index 7b3ffa47f3..a2984f190b 100644
--- a/parm/config/gfs/config.snowanl
+++ b/parm/config/gfs/config.snowanl
@@ -11,7 +11,7 @@ source "${EXPDIR}/config.resources" snowanl
 export OBS_LIST="${PARMgfs}/gdas/snow/obs/lists/gdas_snow.yaml.j2"
 
 # Name of the JEDI executable and its yaml template
-export JEDIEXE="${EXECgfs}/fv3jedi_letkf.x"
+export JEDIEXE="${EXECgfs}/gdas.x"
 export JEDIYAML="${PARMgfs}/gdas/snow/letkfoi/letkfoi.yaml.j2"
 
 # Ensemble member properties
diff --git a/parm/config/gfs/yaml/defaults.yaml b/parm/config/gfs/yaml/defaults.yaml
index 445fee144e..bdb5f47f04 100644
--- a/parm/config/gfs/yaml/defaults.yaml
+++ b/parm/config/gfs/yaml/defaults.yaml
@@ -6,6 +6,13 @@ base:
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
   DO_GOES: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
+  DO_NPOESS: "NO"
+  DO_TRACKER: "YES"
+  DO_GENESIS: "YES"
+  DO_GENESIS_FSU: "NO"
   FHMAX_GFS: 120
   DO_VRFY_OCEANDA: "NO"
   GSI_SOILANAL: "NO"
diff --git a/scripts/exgfs_atmos_grib2_special_npoess.sh b/scripts/exgfs_atmos_grib2_special_npoess.sh
index 3877b50b77..8d182469ed 100755
--- a/scripts/exgfs_atmos_grib2_special_npoess.sh
+++ b/scripts/exgfs_atmos_grib2_special_npoess.sh
@@ -153,7 +153,8 @@ for (( fhr=SHOUR; fhr <= FHOUR; fhr = fhr + FHINC )); do
    # existence of the restart files
    ###############################
    export pgm="postcheck"
-   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   # grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.special.grb2f${fhr3}"
    if ! wait_for_file "${grib_file}" "${SLEEP_INT}" "${SLEEP_LOOP_MAX}"; then
       echo "FATAL ERROR: GOES master grib file ${grib_file} not available after max sleep time"
       export err=9
diff --git a/scripts/exglobal_prep_emissions.py b/scripts/exglobal_prep_emissions.py
new file mode 100755
index 0000000000..ef0e709142
--- /dev/null
+++ b/scripts/exglobal_prep_emissions.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exglobal_prep_emissions.py
+# This script creates a emissions object
+# which perform the pre-processing for aerosol emissions
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs import AerosolEmissions
+
+
+# Initialize root logger
+logger = Logger(level=os.environ.get("LOGGING_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)
+
+    # Instantiate the emissions pre-processing task
+    emissions = AerosolEmissions(config)
+    emissions.initialize()
+    emissions.configure()
+    emissions.execute(emissions.task_config.DATA, emissions.task_config.APRUN)
+    emissions.finalize()
diff --git a/sorc/gdas.cd b/sorc/gdas.cd
index 1b07517a22..70f1319139 160000
--- a/sorc/gdas.cd
+++ b/sorc/gdas.cd
@@ -1 +1 @@
-Subproject commit 1b07517a22cd569d35ee24d341c15a97fc6ad932
+Subproject commit 70f13191391d0909e92da47dc7d17ddf1dc4c6c6
diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
index 2a9d9d04db..0041ce083b 100755
--- a/sorc/link_workflow.sh
+++ b/sorc/link_workflow.sh
@@ -333,33 +333,16 @@ fi
 
 # GDASApp
 if [[ -d "${HOMEgfs}/sorc/gdas.cd/build" ]]; then
-  declare -a JEDI_EXE=("fv3jedi_addincrement.x" \
-                       "fv3jedi_diffstates.x" \
-                       "fv3jedi_ensvariance.x" \
-                       "fv3jedi_hofx.x" \
-                       "fv3jedi_var.x" \
-                       "fv3jedi_convertincrement.x" \
-                       "fv3jedi_dirac.x" \
-                       "fv3jedi_error_covariance_training.x" \
-                       "fv3jedi_letkf.x" \
-                       "fv3jedi_convertstate.x" \
-                       "fv3jedi_eda.x" \
-                       "fv3jedi_forecast.x" \
+  declare -a JEDI_EXE=("gdas.x" \
+                       "gdas_soca_gridgen.x" \
+                       "gdas_soca_error_covariance_toolbox.x" \
+                       "gdas_soca_setcorscales.x" \
                        "fv3jedi_plot_field.x" \
-                       "fv3jedi_data_checker.py" \
-                       "fv3jedi_enshofx.x" \
-                       "fv3jedi_hofx_nomodel.x" \
-                       "fv3jedi_testdata_downloader.py" \
                        "fv3jedi_fv3inc.x" \
                        "gdas_ens_handler.x" \
                        "gdas_incr_handler.x" \
                        "gdas_obsprovider2ioda.x" \
                        "gdas_socahybridweights.x" \
-                       "soca_convertincrement.x" \
-                       "soca_error_covariance_training.x" \
-                       "soca_setcorscales.x" \
-                       "soca_gridgen.x" \
-                       "soca_var.x" \
                        "bufr2ioda.x" \
                        "calcfIMS.exe" \
                        "apply_incr.exe" )
diff --git a/ush/python/pygfs/__init__.py b/ush/python/pygfs/__init__.py
index e69de29bb2..fa6b0b373e 100644
--- a/ush/python/pygfs/__init__.py
+++ b/ush/python/pygfs/__init__.py
@@ -0,0 +1,16 @@
+
+import os
+
+from .task.analysis import Analysis
+from .task.aero_emissions import AerosolEmissions
+from .task.aero_analysis import AerosolAnalysis
+from .task.atm_analysis import AtmAnalysis
+from .task.atmens_analysis import AtmEnsAnalysis
+from .task.snow_analysis import SnowAnalysis
+from .task.upp import UPP
+from .task.oceanice_products import OceanIceProducts
+from .task.gfs_forecast import GFSForecast
+
+__docformat__ = "restructuredtext"
+__version__ = "0.1.0"
+pygfs_directory = os.path.dirname(__file__)
diff --git a/ush/python/pygfs/task/aero_analysis.py b/ush/python/pygfs/task/aero_analysis.py
index a61b7c82f3..16d2735090 100644
--- a/ush/python/pygfs/task/aero_analysis.py
+++ b/ush/python/pygfs/task/aero_analysis.py
@@ -109,8 +109,10 @@ def execute(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_AEROANL)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_var.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('variational')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:
diff --git a/ush/python/pygfs/task/aero_emissions.py b/ush/python/pygfs/task/aero_emissions.py
new file mode 100644
index 0000000000..17d2f528e4
--- /dev/null
+++ b/ush/python/pygfs/task/aero_emissions.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+
+import os
+from logging import getLogger
+from typing import Dict, Any, Union
+from pprint import pformat
+
+from wxflow import (AttrDict,
+                    parse_j2yaml,
+                    FileHandler,
+                    Jinja,
+                    logit,
+                    Task,
+                    add_to_datetime, to_timedelta,
+                    WorkflowException,
+                    Executable, which)
+
+logger = getLogger(__name__.split('.')[-1])
+
+
+class AerosolEmissions(Task):
+    """Aerosol Emissions pre-processing Task
+    """
+
+    @logit(logger, name="AerosolEmissions")
+    def __init__(self, config: Dict[str, Any]) -> None:
+        """Constructor for the Aerosol Emissions task
+
+        Parameters
+        ----------
+        config : Dict[str, Any]
+            Incoming configuration for the task from the environment
+
+        Returns
+        -------
+        None
+        """
+        super().__init__(config)
+
+        local_variable = "something"
+
+        localdict = AttrDict(
+            {'variable_used_repeatedly': local_variable}
+        )
+        self.task_config = AttrDict(**self.config, **self.runtime_config, **localdict)
+
+    @staticmethod
+    @logit(logger)
+    def initialize() -> None:
+        """Initialize the work directory
+        """
+
+    @staticmethod
+    @logit(logger)
+    def configure() -> None:
+        """Configure the artifacts in the work directory.
+        Copy run specific data to run directory
+        """
+
+    @staticmethod
+    @logit(logger)
+    def execute(workdir: Union[str, os.PathLike], aprun_cmd: str) -> None:
+        """Run the executable (if any)
+
+        Parameters
+        ----------
+        workdir : str | os.PathLike
+            work directory with the staged data, parm files, namelists, etc.
+        aprun_cmd : str
+            launcher command for executable.x
+
+        Returns
+        -------
+        None
+        """
+
+    @staticmethod
+    @logit(logger)
+    def finalize() -> None:
+        """Perform closing actions of the task.
+        Copy data back from the DATA/ directory to COM/
+        """
diff --git a/ush/python/pygfs/task/analysis.py b/ush/python/pygfs/task/analysis.py
index 02011423b7..5a516a02c8 100644
--- a/ush/python/pygfs/task/analysis.py
+++ b/ush/python/pygfs/task/analysis.py
@@ -292,46 +292,6 @@ def get_fv3ens_dict(config: Dict[str, Any]) -> Dict[str, Any]:
         }
         return ens_dict
 
-    @staticmethod
-    @logit(logger)
-    def execute_jediexe(workdir: Union[str, os.PathLike], aprun_cmd: str, jedi_exec: str, jedi_yaml: str) -> None:
-        """
-        Run a JEDI executable
-
-        Parameters
-        ----------
-        workdir : str | os.PathLike
-            Working directory where to run containing the necessary files and executable
-        aprun_cmd : str
-            Launcher command e.g. mpirun -np <ntasks> or srun, etc.
-        jedi_exec : str
-            Name of the JEDI executable e.g. fv3jedi_var.x
-        jedi_yaml : str | os.PathLike
-            Name of the yaml file to feed the JEDI executable e.g. fv3jedi_var.yaml
-
-        Raises
-        ------
-        OSError
-            Failure due to OS issues
-        WorkflowException
-            All other exceptions
-        """
-
-        os.chdir(workdir)
-
-        exec_cmd = Executable(aprun_cmd)
-        exec_cmd.add_default_arg([os.path.join(workdir, jedi_exec), jedi_yaml])
-
-        logger.info(f"Executing {exec_cmd}")
-        try:
-            exec_cmd()
-        except OSError:
-            logger.exception(f"FATAL ERROR: Failed to execute {exec_cmd}")
-            raise OSError(f"{exec_cmd}")
-        except Exception:
-            logger.exception(f"FATAL ERROR: Error occured during execution of {exec_cmd}")
-            raise WorkflowException(f"{exec_cmd}")
-
     @staticmethod
     @logit(logger)
     def tgz_diags(statfile: str, diagdir: str) -> None:
diff --git a/ush/python/pygfs/task/atm_analysis.py b/ush/python/pygfs/task/atm_analysis.py
index ebeb0c7ba6..47d291268e 100644
--- a/ush/python/pygfs/task/atm_analysis.py
+++ b/ush/python/pygfs/task/atm_analysis.py
@@ -118,8 +118,10 @@ def variational(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_ATMANLVAR)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_var.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('variational')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:
@@ -144,10 +146,17 @@ def init_fv3_increment(self: Analysis) -> None:
     @logit(logger)
     def fv3_increment(self: Analysis) -> None:
         # Run executable
-        self.execute_jediexe(self.runtime_config.DATA,
-                             self.task_config.APRUN_ATMANLFV3INC,
-                             self.task_config.jedi_exe,
-                             self.task_config.jedi_yaml)
+        exec_cmd = Executable(self.task_config.APRUN_ATMANLFV3INC)
+        exec_cmd.add_default_arg(self.task_config.jedi_exe)
+        exec_cmd.add_default_arg(self.task_config.jedi_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd}")
+            exec_cmd()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd}")
 
     @logit(logger)
     def finalize(self: Analysis) -> None:
diff --git a/ush/python/pygfs/task/atmens_analysis.py b/ush/python/pygfs/task/atmens_analysis.py
index 1037b557c2..a1aecfe07c 100644
--- a/ush/python/pygfs/task/atmens_analysis.py
+++ b/ush/python/pygfs/task/atmens_analysis.py
@@ -148,8 +148,10 @@ def execute(self: Analysis) -> None:
         chdir(self.task_config.DATA)
 
         exec_cmd = Executable(self.task_config.APRUN_ATMENSANL)
-        exec_name = os.path.join(self.task_config.DATA, 'fv3jedi_letkf.x')
+        exec_name = os.path.join(self.task_config.DATA, 'gdas.x')
         exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('localensembleda')
         exec_cmd.add_default_arg(self.task_config.jedi_yaml)
 
         try:
diff --git a/ush/python/pygfs/task/snow_analysis.py b/ush/python/pygfs/task/snow_analysis.py
index c149f140b6..fe21a67536 100644
--- a/ush/python/pygfs/task/snow_analysis.py
+++ b/ush/python/pygfs/task/snow_analysis.py
@@ -310,10 +310,20 @@ def execute(self) -> None:
                              AttrDict({key: localconf[key] for key in ['DATA', 'ntiles', 'current_cycle']}))
 
         logger.info("Running JEDI LETKF")
-        self.execute_jediexe(localconf.DATA,
-                             localconf.APRUN_SNOWANL,
-                             os.path.basename(localconf.JEDIEXE),
-                             localconf.jedi_yaml)
+        exec_cmd = Executable(localconf.APRUN_SNOWANL)
+        exec_name = os.path.join(localconf.DATA, 'gdas.x')
+        exec_cmd.add_default_arg(exec_name)
+        exec_cmd.add_default_arg('fv3jedi')
+        exec_cmd.add_default_arg('localensembleda')
+        exec_cmd.add_default_arg(localconf.jedi_yaml)
+
+        try:
+            logger.debug(f"Executing {exec_cmd}")
+            exec_cmd()
+        except OSError:
+            raise OSError(f"Failed to execute {exec_cmd}")
+        except Exception:
+            raise WorkflowException(f"An error occured during execution of {exec_cmd}")
 
         logger.info("Creating analysis from backgrounds and increments")
         self.add_increments(localconf)
diff --git a/versions/run.hera.ver b/versions/run.hera.ver
index d612619acc..6280e8e115 100644
--- a/versions/run.hera.ver
+++ b/versions/run.hera.ver
@@ -4,7 +4,7 @@ export spack_env=gsi-addon-dev-rocky8
 
 export hpss_ver=hpss
 export ncl_ver=6.6.2
-export R_ver=3.5.0
+export R_ver=3.6.1
 export gempak_ver=7.17.0
 export perl_ver=5.38.0
 
diff --git a/workflow/applications/gefs.py b/workflow/applications/gefs.py
index b14c1a9003..c165f9d1ca 100644
--- a/workflow/applications/gefs.py
+++ b/workflow/applications/gefs.py
@@ -27,6 +27,9 @@ def _get_app_configs(self):
         if self.do_ocean or self.do_ice:
             configs += ['oceanice_products']
 
+        if self.do_aero:
+            configs += ['prep_emissions']
+
         return configs
 
     @staticmethod
@@ -45,6 +48,9 @@ def get_task_names(self):
         if self.do_wave:
             tasks += ['waveinit']
 
+        if self.do_aero:
+            tasks += ['prep_emissions']
+
         tasks += ['fcst']
 
         if self.nens > 0:
diff --git a/workflow/applications/gfs_cycled.py b/workflow/applications/gfs_cycled.py
index c2a6a32f02..4d785bc4da 100644
--- a/workflow/applications/gfs_cycled.py
+++ b/workflow/applications/gfs_cycled.py
@@ -264,7 +264,7 @@ def get_task_names(self):
                 gfs_tasks += ['gempakpgrb2spec']
 
         if self.do_awips:
-            gfs_tasks += ['awips_20km_1p0deg', 'awips_g2', 'fbwind']
+            gfs_tasks += ['awips_20km_1p0deg', 'fbwind']
 
         if self.do_mos:
             gfs_tasks += ['mos_stn_prep', 'mos_grd_prep', 'mos_ext_stn_prep', 'mos_ext_grd_prep',
diff --git a/workflow/applications/gfs_forecast_only.py b/workflow/applications/gfs_forecast_only.py
index 0a9648ee65..89881af8c9 100644
--- a/workflow/applications/gfs_forecast_only.py
+++ b/workflow/applications/gfs_forecast_only.py
@@ -124,7 +124,7 @@ def get_task_names(self):
                 tasks += ['gempak', 'gempakmeta', 'gempakncdcupapgif', 'gempakpgrb2spec']
 
             if self.do_awips:
-                tasks += ['awips_20km_1p0deg', 'awips_g2', 'fbwind']
+                tasks += ['awips_20km_1p0deg', 'fbwind']
 
         if self.do_ocean:
             tasks += ['ocean_prod']
diff --git a/workflow/prod.yml b/workflow/prod.yml
index 64783dd611..55717772b5 100644
--- a/workflow/prod.yml
+++ b/workflow/prod.yml
@@ -113,17 +113,6 @@ suites:
                 jgfs_atmos_awips_f( 3,27,6 ):
                   edits:
                     TRDRUN: 'NO'
-            awips_g2:
-              tasks:
-                jgfs_atmos_awips_g2_f( 0,64,6 ):
-                  template: jgfs_atmos_awips_g2_master
-                  triggers:
-                  - task: jgfs_atmos_post_f( )
-                  edits:
-                    FHRGRP: '( )'
-                    FHRLST: 'f( )'
-                    FCSTHR: '( )'
-                    TRDRUN: 'YES'
             gempak:
               tasks:
                 jgfs_atmos_gempak:
diff --git a/workflow/rocoto/gefs_tasks.py b/workflow/rocoto/gefs_tasks.py
index 6ee079fdfa..86be494549 100644
--- a/workflow/rocoto/gefs_tasks.py
+++ b/workflow/rocoto/gefs_tasks.py
@@ -89,6 +89,27 @@ def waveinit(self):
 
         return task
 
+    def prep_emissions(self):
+        deps = []
+        dep_dict = {'type': 'task', 'name': f'stage_ic'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep=deps)
+
+        resources = self.get_resource('prep_emissions')
+        task_name = 'prep_emissions'
+        task_dict = {'task_name': task_name,
+                     'resources': resources,
+                     'envars': self.envars,
+                     'cycledef': 'gefs',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/prep_emissions.sh',
+                     'job_name': f'{self.pslot}_{task_name}_@H',
+                     'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
+                     'maxtries': '&MAXTRIES;'
+                     }
+        task = rocoto.create_task(task_dict)
+
+        return task
+
     def fcst(self):
         dependencies = []
         dep_dict = {'type': 'task', 'name': f'stage_ic'}
@@ -98,6 +119,10 @@ def fcst(self):
             dep_dict = {'type': 'task', 'name': f'wave_init'}
             dependencies.append(rocoto.add_dependency(dep_dict))
 
+        if self.app_config.do_aero:
+            dep_dict = {'type': 'task', 'name': f'prep_emissions'}
+            dependencies.append(rocoto.add_dependency(dep_dict))
+
         dependencies = rocoto.create_dependency(dep_condition='and', dep=dependencies)
 
         resources = self.get_resource('fcst')
@@ -125,6 +150,10 @@ def efcs(self):
             dep_dict = {'type': 'task', 'name': f'wave_init'}
             dependencies.append(rocoto.add_dependency(dep_dict))
 
+        if self.app_config.do_aero:
+            dep_dict = {'type': 'task', 'name': f'prep_emissions'}
+            dependencies.append(rocoto.add_dependency(dep_dict))
+
         dependencies = rocoto.create_dependency(dep_condition='and', dep=dependencies)
 
         efcsenvars = self.envars.copy()
diff --git a/workflow/rocoto/gfs_tasks.py b/workflow/rocoto/gfs_tasks.py
index bba7bac3dd..6125a33dec 100644
--- a/workflow/rocoto/gfs_tasks.py
+++ b/workflow/rocoto/gfs_tasks.py
@@ -1433,47 +1433,6 @@ def awips_20km_1p0deg(self):
 
         return task
 
-    def awips_g2(self):
-
-        deps = []
-        dep_dict = {'type': 'metatask', 'name': f'{self.cdump}atmos_prod'}
-        deps.append(rocoto.add_dependency(dep_dict))
-        dependencies = rocoto.create_dependency(dep=deps)
-
-        awipsenvars = self.envars.copy()
-        awipsenvar_dict = {'FHRGRP': '#grp#',
-                           'FHRLST': '#lst#',
-                           'ROTDIR': self.rotdir}
-        for key, value in awipsenvar_dict.items():
-            awipsenvars.append(rocoto.create_envar(name=key, value=str(value)))
-
-        varname1, varname2, varname3 = 'grp', 'dep', 'lst'
-        varval1, varval2, varval3 = self._get_awipsgroups(self.cdump, self._configs['awips'])
-        var_dict = {varname1: varval1, varname2: varval2, varname3: varval3}
-
-        resources = self.get_resource('awips')
-
-        task_name = f'{self.cdump}awips_g2#{varname1}#'
-        task_dict = {'task_name': task_name,
-                     'resources': resources,
-                     'dependency': dependencies,
-                     'envars': awipsenvars,
-                     'cycledef': self.cdump.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/awips_g2.sh',
-                     'job_name': f'{self.pslot}_{task_name}_@H',
-                     'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
-                     'maxtries': '&MAXTRIES;'
-                     }
-
-        metatask_dict = {'task_name': f'{self.cdump}awips_g2',
-                         'task_dict': task_dict,
-                         'var_dict': var_dict
-                         }
-
-        task = rocoto.create_task(metatask_dict)
-
-        return task
-
     def gempak(self):
 
         deps = []
diff --git a/workflow/rocoto/tasks.py b/workflow/rocoto/tasks.py
index 3abae9b5b7..a8b4eb9fac 100644
--- a/workflow/rocoto/tasks.py
+++ b/workflow/rocoto/tasks.py
@@ -27,7 +27,7 @@ class Tasks:
                    'verfozn', 'verfrad', 'vminmon',
                    'metp',
                    'tracker', 'genesis', 'genesis_fsu',
-                   'postsnd', 'awips_g2', 'awips_20km_1p0deg', 'fbwind',
+                   'postsnd', 'awips_20km_1p0deg', 'fbwind',
                    'gempak', 'gempakmeta', 'gempakmetancdc', 'gempakncdcupapgif', 'gempakpgrb2spec', 'npoess_pgrb2_0p5deg'
                    'waveawipsbulls', 'waveawipsgridded', 'wavegempak', 'waveinit',
                    'wavepostbndpnt', 'wavepostbndpntbll', 'wavepostpnt', 'wavepostsbs', 'waveprep',