diff --git a/dev/parm/config/gfs/config.resources b/dev/parm/config/gfs/config.resources
index 1c8ca9d24a1..f6bd3ab387f 100644
--- a/dev/parm/config/gfs/config.resources
+++ b/dev/parm/config/gfs/config.resources
@@ -758,12 +758,19 @@ case ${step} in
     fi
     ;;
 
-  "analdiag")
+  "analdiag" | "ediag")
     walltime="00:15:00"
     ntasks=96             # Should be at least twice ediag's tasks
+    memory="48GB"
+    #if [[ "${step}" == "ediag" ]]; then
+    #  ntasks=48
+    #fi
     threads_per_task=1
+    if [[ ${ntasks} -gt ${max_tasks_per_node} ]]; then
+      ntasks=${max_tasks_per_node}
+      export is_exclusive=True
+    fi
     tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
-    memory="48GB"
     ;;
 
   "anlstat")
@@ -853,7 +860,7 @@ case ${step} in
     MEDTHREADS=${nthreads_mediator:-1}
     MEDPETS=${MEDPETS:-${FV3PETS}}
     (( MEDPETS = FV3PETS ))
-    (( MEDTHREADS = FV3THREADS )) 
+    (( MEDTHREADS = FV3THREADS ))
     (( "${MEDPETS}" > 4800 )) && MEDPETS=4800
     export MEDPETS MEDTHREADS
     echo "MEDIATOR using (threads, PETS) = (${MEDTHREADS}, ${MEDPETS})"
@@ -979,7 +986,7 @@ case ${step} in
     ;;
 
   "upp")
-    #ntasks cannot be greater than $CASE_HIST      
+    #ntasks cannot be greater than $CASE_HIST
     #define resources based on $CASE_HIST for upp
     case "${CASE_HIST}" in
       "C48" | "C96")
@@ -1255,14 +1262,6 @@ case ${step} in
     fi
     ;;
 
-  "ediag")
-    walltime="00:15:00"
-    ntasks=48
-    threads_per_task=1
-    tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
-    memory="30GB"
-    ;;
-
   "eupd")
     walltime="00:45:00"
     case "${CASE}" in
diff --git a/env/GAEAC6.env b/env/GAEAC6.env
index 77e7bdd05d3..5ab863acb16 100755
--- a/env/GAEAC6.env
+++ b/env/GAEAC6.env
@@ -199,7 +199,10 @@ case ${step} in
     ntasks_gausfcanl=${ntasks_gausfcanl:-1}
     export APRUN_GAUSFCANL="${launcher} -n ${ntasks_gausfcanl} --cpus-per-task=${NTHREADS_GAUSFCANL}"
  ;;
-  "offlineanl")
+ "analdiag" | "ediag")
+    export USE_CFP="YES"
+ ;;
+ "offlineanl")
 
     export NTHREADS_CHGRES=${threads_per_task_chgres:-12}
     if [[ ${NTHREADS_CHGRES} -gt ${max_tasks_per_node} ]]; then
diff --git a/env/HERA.env b/env/HERA.env
index 8d6619e0da1..76af27e6748 100755
--- a/env/HERA.env
+++ b/env/HERA.env
@@ -203,6 +203,10 @@ elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
     ntasks_gausfcanl=${ntasks_gausfcanl:-1}
     export APRUN_GAUSFCANL="${launcher} -n ${ntasks_gausfcanl} --cpus-per-task=${NTHREADS_GAUSFCANL}"
 
+elif [[ "${step}" = "analdiag" ]] || [[ "${step}" = "ediag" ]]; then
+
+    export USE_CFP="YES"
+
 elif [[ "${step}" = "offlineanl" ]]; then
 
     export NTHREADS_CHGRES=${threads_per_task_chgres:-12}
diff --git a/env/HERCULES.env b/env/HERCULES.env
index 9aa6feb9ed8..493e23db4a3 100755
--- a/env/HERCULES.env
+++ b/env/HERCULES.env
@@ -158,7 +158,7 @@ case ${step} in
  "anlstat")
 
     export NTHREADS_ANLSTAT=${NTHREADSmax}
-    export APRUN_ANLSTAT="${APRUN_default} --cpus-per-task=${NTHREADS_ANLSTAT}" 
+    export APRUN_ANLSTAT="${APRUN_default} --cpus-per-task=${NTHREADS_ANLSTAT}"
  ;;
  "ecen_fv3jedi")
 
@@ -218,6 +218,9 @@ case ${step} in
     # REGRID requires 6 tasks for reproducibility
     ntasks_regrid=6
     export APRUN_REGRID="${launcher} -n ${ntasks_regrid} "
+ ;;
+  "analdiag" | "ediag")
+    export USE_CFP="YES"
  ;;
   "offlineanl")
 
diff --git a/env/ORION.env b/env/ORION.env
index ca1d9334dc5..6634fda665f 100755
--- a/env/ORION.env
+++ b/env/ORION.env
@@ -157,7 +157,7 @@ elif [[ "${step}" = "marineanlletkf" ]]; then
 elif [[ "${step}" = "anlstat" ]]; then
 
     export NTHREADS_ANLSTAT=${NTHREADSmax}
-    export APRUN_ANLSTAT="${APRUN_default} --cpus-per-task=${NTHREADS_ANLSTAT}" 
+    export APRUN_ANLSTAT="${APRUN_default} --cpus-per-task=${NTHREADS_ANLSTAT}"
 
 elif [[ "${step}" = "ecen_fv3jedi" ]]; then
 
@@ -216,6 +216,10 @@ elif [[ "${step}" = "sfcanl" ]]; then
     ntasks_regrid=6
     export APRUN_REGRID="${launcher} -n ${ntasks_regrid} "
 
+elif [[ "${step}" = "analdiag" ]] || [[ "${step}" = "ediag" ]]; then
+
+    export USE_CFP="YES"
+
 elif [[ "${step}" = "offlineanl" ]]; then
 
     export NTHREADS_CHGRES=${threads_per_task:-12}
diff --git a/env/URSA.env b/env/URSA.env
index 4ee5a07b7e5..80711ea2b3b 100644
--- a/env/URSA.env
+++ b/env/URSA.env
@@ -192,6 +192,10 @@ elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then
     ntasks_gausfcanl=${ntasks_gausfcanl:-1}
     export APRUN_GAUSFCANL="${launcher} -n ${ntasks_gausfcanl} --cpus-per-task=${NTHREADS_GAUSFCANL}"
 
+elif [[ "${step}" = "analdiag" ]] || [[ "${step}" = "ediag" ]]; then
+
+    export USE_CFP="YES"
+
 elif [[ "${step}" = "offlineanl" ]]; then
 
     export NTHREADS_CHGRES=${threads_per_task_chgres:-12}
diff --git a/env/WCOSS2.env b/env/WCOSS2.env
index 5d89728674c..867c0a4eab2 100755
--- a/env/WCOSS2.env
+++ b/env/WCOSS2.env
@@ -205,6 +205,10 @@ elif [[ "${step}" = "sfcanl" ]]; then
     ntasks_regrid=6
     export APRUN_REGRID="${launcher} -n ${ntasks_regrid} "
 
+elif [[ "${step}" = "analdiag" ]] || [[ "${step}" = "ediag" ]]; then
+
+    export USE_CFP="YES"
+
 elif [[ "${step}" = "offlineanl" ]]; then
 
     export NTHREADS_CHGRES=${threads_per_task_chgres:-14}
diff --git a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
index ad83614bff8..553a58e1160 100755
--- a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
+++ b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
@@ -1,27 +1,28 @@
 #! /usr/bin/env bash
 
-source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal analdiag"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "analdiag" -c "base anal analdiag"
 
 ##############################################
 # Set variables used in the script
 ##############################################
-export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
+#export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 # shellcheck disable=SC2153
-GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP="gdas"
-export GDUMP_ENS="enkf${GDUMP}"
+#GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+#export gPDY=${GDATE:0:8}
+#export gcyc=${GDATE:8:2}
+#export GDUMP="gdas"
+#export GDUMP_ENS="enkf${GDUMP}"
 
-export OPREFIX="${RUN/enkf/}.t${cyc}z."
-export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${RUN}.t${cyc}z."
+#export OPREFIX="${RUN/enkf/}.t${cyc}z."
+#export GPREFIX="${GDUMP}.t${gcyc}z."
+#export APREFIX="${RUN}.t${cyc}z."
 
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
+    COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
diff --git a/jobs/JGDAS_ENKF_DIAG b/jobs/JGDAS_ENKF_DIAG
index 70567283f2f..fa494dfb847 100755
--- a/jobs/JGDAS_ENKF_DIAG
+++ b/jobs/JGDAS_ENKF_DIAG
@@ -1,6 +1,6 @@
 #! /usr/bin/env bash
 
-source "${HOMEgfs}/ush/jjob_header.sh" -e "eobs" -c "base anal eobs analdiag ediag"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "ediag" -c "base anal eobs analdiag ediag"
 
 ##############################################
 # Set variables used in the script
@@ -10,83 +10,76 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "eobs" -c "base anal eobs analdiag edi
 # Begin JOB SPECIFIC work
 ##############################################
 # shellcheck disable=SC2153
-GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP="gdas"
-export GDUMP_ENS="enkf${GDUMP}"
+#GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+#export gPDY=${GDATE:0:8}
+#export gcyc=${GDATE:8:2}
+#export GDUMP="gdas"
+#export GDUMP_ENS="enkf${GDUMP}"
 
 export CASE=${CASE_ENS}
 
-export OPREFIX="${RUN/enkf/}.t${cyc}z."
+#export OPREFIX="${RUN/enkf/}.t${cyc}z."
 export APREFIX="${RUN}.t${cyc}z."
-export GPREFIX="${GDUMP_ENS}.t${gcyc}z."
-GPREFIX_DET="${GDUMP}.t${gcyc}z."
+#export GPREFIX="${GDUMP_ENS}.t${gcyc}z."
+#GPREFIX_DET="${GDUMP}.t${gcyc}z."
 
-RUN=${RUN/enkf/} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-    COMIN_OBS:COM_OBS_TMPL
+#RUN=${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 \
+    COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 
-RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COMIN_OBS_PREV:COM_OBS_TMPL \
-    COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
+#RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+#    COMIN_OBS_PREV:COM_OBS_TMPL \
+#    COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
 
-MEMDIR="ensstat" RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
+#MEMDIR="ensstat" RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+#    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 
-export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}ensmean.atm.f006.nc"
-if [[ ! -f "${ATMGES_ENSMEAN}" ]]; then
-    export err=1
-    err_exit "FILE MISSING: ATMGES_ENSMEAN == ${ATMGES_ENSMEAN}"
-fi
+#export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}ensmean.atm.f006.nc"
+#if [[ ! -f "${ATMGES_ENSMEAN}" ]]; then
+#    export err=1
+#    err_exit "FILE MISSING: ATMGES_ENSMEAN == ${ATMGES_ENSMEAN}"
+#fi
 
 # Link observational data
-export PREPQC="${COMIN_OBS}/${OPREFIX}prepbufr"
-if [[ ! -f ${PREPQC} ]]; then
-    echo "WARNING: Global PREPBUFR FILE ${PREPQC} MISSING"
-fi
-export TCVITL="${COMIN_OBS}/${OPREFIX}syndata.tcvitals.tm00"
-if [[ ${DONST} == "YES" ]]; then
-    export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
-fi
-export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
+#export PREPQC="${COMIN_OBS}/${OPREFIX}prepbufr"
+#if [[ ! -f ${PREPQC} ]]; then
+#    echo "WARNING: Global PREPBUFR FILE ${PREPQC} MISSING"
+#fi
+#export TCVITL="${COMIN_OBS}/${OPREFIX}syndata.tcvitals.tm00"
+#if [[ ${DONST} == "YES" ]]; then
+#    export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
+#fi
+#export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
 
 # Guess Bias correction coefficients related to control
-export GBIAS=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias.txt
-export GBIASPC=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_pc.txt
-export GBIASAIR=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_air.txt
-export GRADSTAT=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}radstat.tar
+#export GBIAS=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias.txt
+#export GBIASPC=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_pc.txt
+#export GBIASAIR=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}abias_air.txt
+#export GRADSTAT=${COMIN_ATMOS_ANALYSIS_DET_PREV}/${GPREFIX_DET}radstat.tar
 
 # Bias correction coefficients related to ensemble mean
-export ABIAS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias.txt"
-export ABIASPC="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc.txt"
-export ABIASAIR="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air.txt"
-export ABIASe="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int.txt"
+#export ABIAS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias.txt"
+#export ABIASPC="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc.txt"
+#export ABIASAIR="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air.txt"
+#export ABIASe="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int.txt"
 
 # Diagnostics related to ensemble mean
-export GSISTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat.ensmean.tar"
-export CNVSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat.ensmean.tar"
-export OZNSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat.ensmean.tar"
-export RADSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.ensmean.tar"
+export CNVSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat_ensmean.tar"
+export OZNSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat_ensmean.tar"
+export RADSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat_ensmean.tar"
 
 # Select observations based on ensemble mean
-export RUN_SELECT="YES"
-export USE_SELECT="NO"
-export SELECT_OBS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.ensmean"
+#export RUN_SELECT="YES"
+#export USE_SELECT="NO"
+#export SELECT_OBS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.ensmean"
 
 export DIAG_SUFFIX="_ensmean"
 export DIAG_COMPRESS="NO"
 
 # GSI namelist options specific to eobs
-export SETUP_INVOBS="passive_bc=.false.,${SETUP_INVOBS}"
-
-# Ensure clean stat tarballs for ensemble mean
-for fstat in ${CNVSTAT} ${OZNSTAT} ${RADSTAT}; do
-    if [[ -f "${fstat}" ]]; then
-        rm -f "${fstat}"
-    fi
-done
+#export SETUP_INVOBS="passive_bc=.false.,${SETUP_INVOBS}"
 
 ###############################################################
 # Run relevant script
diff --git a/jobs/JGDAS_ENKF_SELECT_OBS b/jobs/JGDAS_ENKF_SELECT_OBS
index 3417f6f6e77..f5fe813ef9d 100755
--- a/jobs/JGDAS_ENKF_SELECT_OBS
+++ b/jobs/JGDAS_ENKF_SELECT_OBS
@@ -84,15 +84,15 @@ export ABIASAIR="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air.txt"
 export ABIASe="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int.txt"
 
 # Diagnostics related to ensemble mean
-export GSISTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat.ensmean.txt"
-export CNVSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat.ensmean.tar"
-export OZNSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat.ensmean.tar"
-export RADSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.ensmean.tar"
+export GSISTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat_ensmean.txt"
+export CNVSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat_ensmean.tar"
+export OZNSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat_ensmean.tar"
+export RADSTAT="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat_ensmean.tar"
 
 # Select observations based on ensemble mean
 export RUN_SELECT="YES"
 export USE_SELECT="NO"
-export SELECT_OBS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.ensmean"
+export SELECT_OBS="${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput_ensmean.tar"
 
 export DIAG_SUFFIX="_ensmean"
 
diff --git a/jobs/JGDAS_ENKF_UPDATE b/jobs/JGDAS_ENKF_UPDATE
index 3b0d829591b..43d39b21735 100755
--- a/jobs/JGDAS_ENKF_UPDATE
+++ b/jobs/JGDAS_ENKF_UPDATE
@@ -9,15 +9,12 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "eupd" -c "base anal eupd"
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
-# shellcheck disable=SC2153
-GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
-export gPDY=${GDATE:0:8}
-export gcyc=${GDATE:8:2}
-export GDUMP="gdas"
-export GDUMP_ENS="enkf${GDUMP}"
+# shellcheck disable=SC2155
+export GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+export GDUMP="enkfgdas" # EnKF ensemble always uses RUN=enkfgdas for prior members
 
 export APREFIX="${RUN}.t${cyc}z."
-export GPREFIX="${GDUMP_ENS}.t${gcyc}z."
+export GPREFIX="${GDUMP}.t${GDATE:8:2}z."
 
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL
@@ -25,7 +22,7 @@ MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS_STAT:COM_ATMOS_ANALYSIS_TMPL
 
-MEMDIR="ensstat" RUN="enkfgdas" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
+MEMDIR="ensstat" RUN="enkfgdas" YMD=${GDATE:0:8} HH=${GDATE:8:2} declare_from_tmpl -rx \
     COMIN_ATMOS_HISTORY_STAT_PREV:COM_ATMOS_HISTORY_TMPL
 
 ###############################################################
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
index cf59158117a..bfb5c74a3ad 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -28,6 +28,7 @@ RUN=${rCDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
+    COMIN_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
     COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
diff --git a/parm/archive/enkf.yaml.j2 b/parm/archive/enkf.yaml.j2
index c19781a1c3e..73c92aeb806 100644
--- a/parm/archive/enkf.yaml.j2
+++ b/parm/archive/enkf.yaml.j2
@@ -69,10 +69,10 @@ enkf:
         # Ensemble mean state
         {% if not DO_JEDIATMENS %}
             {% set da_stat_files = ["enkfstat.txt",
-                                    "gsistat.ensmean.txt",
-                                    "cnvstat.ensmean.tar",
-                                    "oznstat.ensmean.tar",
-                                    "radstat.ensmean.tar"] %}
+                                    "gsistat_ensmean.txt",
+                                    "cnvstat_ensmean.tar",
+                                    "oznstat_ensmean.tar",
+                                    "radstat_ensmean.tar"] %}
             {% set da_conf_files = [] %}
         {% else %}
             {% if lobsdiag_forenkf %}
@@ -109,7 +109,7 @@ enkf:
         # soil DA increments
         {% if DO_GSISOILDA %}
             {% for fhr in IAUFHRS %}
-        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}increment.sfc.i{{ '%03d' % fhr }}.nc"
+        - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}ensmean_increment.sfc.i{{ '%03d' % fhr }}.nc"
             {% endfor %}
         {% endif %}
 
diff --git a/parm/archive/gcafs_arcdir.yaml.j2 b/parm/archive/gcafs_arcdir.yaml.j2
index c4a548c4e94..325ffba80e6 100644
--- a/parm/archive/gcafs_arcdir.yaml.j2
+++ b/parm/archive/gcafs_arcdir.yaml.j2
@@ -83,7 +83,7 @@
     {% else %}
         {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "enkfstat.txt",
                                  ARCDIR ~ "/enkfstat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
-        {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "gsistat.ensmean.txt",
+        {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "gsistat_ensmean.txt",
                                  ARCDIR ~ "/gsistat." ~ RUN ~ "." ~ cycle_YMDH ~ ".ensmean"]) %}
     {% endif %}
 
diff --git a/parm/archive/gdas_restarta.yaml.j2 b/parm/archive/gdas_restarta.yaml.j2
index 60615e0c7ad..94074d2239b 100644
--- a/parm/archive/gdas_restarta.yaml.j2
+++ b/parm/archive/gdas_restarta.yaml.j2
@@ -46,7 +46,7 @@ gdas_restarta:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}cnvstat.tar"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}abias_int.txt"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}analysis.dtf.a006.nc"
-        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}increment.done.txt"
+        - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}analysis.done.txt"
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}rad_varbc_params.tar"
         {% endif %}
diff --git a/parm/archive/gfs_arcdir.yaml.j2 b/parm/archive/gfs_arcdir.yaml.j2
index 877691ff5f9..ed873b21c8b 100644
--- a/parm/archive/gfs_arcdir.yaml.j2
+++ b/parm/archive/gfs_arcdir.yaml.j2
@@ -140,7 +140,7 @@
     {% else %}
         {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "enkfstat.txt",
                                  ARCDIR ~ "/enkfstat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
-        {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "gsistat.ensmean.txt",
+        {% do enkf_files.append([COMIN_ATMOS_ANALYSIS_ENSSTAT ~ "/" ~ head ~ "gsistat_ensmean.txt",
                                  ARCDIR ~ "/gsistat." ~ RUN ~ "." ~ cycle_YMDH ~ ".ensmean"]) %}
     {% endif %}
 
diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
index df981d16973..c44ba3e2bb9 100755
--- a/scripts/exgdas_enkf_update.sh
+++ b/scripts/exgdas_enkf_update.sh
@@ -18,56 +18,32 @@
 ################################################################################
 
 # Directories.
-pwd=$(pwd)
+cd "${DATA}" || exit 1
 
 # Utilities
 NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
-USE_CFP=${USE_CFP:-"NO"}
-CFP_MP=${CFP_MP:-"NO"}
-APRUNCFP=${APRUNCFP:-""}
 APRUN_ENKF=${APRUN_ENKF:-${APRUN:-""}}
 NTHREADS_ENKF=${NTHREADS_ENKF:-${NTHREADS:-1}}
 
 # Executables
 ENKFEXEC=${ENKFEXEC:-${EXECgfs}/enkf.x}
 
-# Filenames.
-GPREFIX=${GPREFIX:-""}
-APREFIX=${APREFIX:-""}
+APREFIX=${APREFIX:-${RUN}.t${cyc}z.}
+GPREFIX=${GPREFIX:-${RUN}.t${GDATE:8:2}z.}
 
-SMOOTH_ENKF=${SMOOTH_ENKF:-"YES"}
-
-GBIASe=${GBIASe:-${APREFIX}abias_int.ensmean.txt}
-CNVSTAT=${CNVSTAT:-${APREFIX}cnvstat.tar}
-OZNSTAT=${OZNSTAT:-${APREFIX}oznstat.tar}
-RADSTAT=${RADSTAT:-${APREFIX}radstat.tar}
-ENKFSTAT=${ENKFSTAT:-${APREFIX}enkfstat.txt}
+# GBIASe=${GBIASe:-${APREFIX}abias_int.ensmean.txt}  # TODO: remove (see comment and TODO below) Also, this is not a "G"BIAS (See the name, it has APREFIX in its name)
+CNVSTAT="${APREFIX}cnvstat_ensmean.tar"
+OZNSTAT="${APREFIX}oznstat_ensmean.tar"
+RADSTAT="${APREFIX}radstat_ensmean.tar"
 
 # Namelist parameters
-USE_CORRELATED_OBERRS=${USE_CORRELATED_OBERRS:-"NO"}
-NAM_ENKF=${NAM_ENKF:-""}
-SATOBS_ENKF=${SATOBS_ENKF:-""}
-OZOBS_ENKF=${OZOBS_ENKF:-""}
-use_correlated_oberrs=${use_correlated_oberrs:-".false."}
-if [[ "${USE_CORRELATED_OBERRS}" == "YES" ]]; then
+if [[ "${USE_CORRELATED_OBERRS:-}" == "YES" ]]; then
     use_correlated_oberrs=".true."
 fi
-imp_physics=${imp_physics:-"99"}
-lupp=${lupp:-".true."}
 corrlength=${corrlength:-1250}
 lnsigcutoff=${lnsigcutoff:-2.5}
 analpertwt=${analpertwt:-0.85}
-readin_localization_enkf=${readin_localization_enkf:-".true."}
-reducedgrid=${reducedgrid:-".false."}
-letkf_flag=${letkf_flag:-".false."}
-getkf=${getkf:-".false."}
-denkf=${denkf:-".false."}
-nobsl_max=${nobsl_max:-10000}
-write_spread_diag=${write_spread_diag:-".false."}
 cnvw_option=${cnvw_option:-".false."}
-netcdf_diag=${netcdf_diag:-".true."}
-modelspace_vloc=${modelspace_vloc:-".false."} # if true, 'vlocal_eig.dat' is needed
-taperanalperts=${taperanalperts:-".false."}
 IAUFHRS_ENKF=${IAUFHRS_ENKF:-"6,"}
 NMEM_ENS_MAX=${NMEM_ENS:-80}
 if [[ "${RUN}" == "enkfgfs" ]]; then
@@ -90,9 +66,6 @@ ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_STAT_PREV}/${GPREFIX}ensmean.atm.f006.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 LEVS_ENFK
-use_gfs_ncio=".true."
-use_gfs_nemsio=".false."
-paranc=${paranc:-".true."}
 WRITE_INCR_ZERO="incvars_to_zero= ${INCREMENTS_TO_ZERO},"
 if [[ "${DO_CALC_INCREMENT}" == "YES" ]]; then
     write_fv3_incr=".false."
@@ -110,71 +83,55 @@ HYBENSINFO=${HYBENSINFO:-${FIXgfs}/gsi/global_hybens_info.l${LEVS_ENKF}.txt}
 ANAVINFO=${ANAVINFO:-${FIXgfs}/gsi/global_anavinfo.l${LEVS_ENKF}.txt}
 VLOCALEIG=${VLOCALEIG:-${FIXgfs}/gsi/vlocal_eig_l${LEVS_ENKF}.dat}
 ENKF_SUFFIX="s"
-if [[ "${SMOOTH_ENKF}" == "NO" ]]; then
+if [[ "${SMOOTH_ENKF:-YES}" == "NO" ]]; then
     ENKF_SUFFIX=""
 fi
 
 ################################################################################
 # Fixed files
+cpreq "${SATANGL}" satbias_angle
+cpreq "${SCANINFO}" scaninfo
+cpreq "${HYBENSINFO}" hybens_info
+cpreq "${ANAVINFO}" anavinfo
+cpreq "${VLOCALEIG}" vlocal_eig.dat
 if [[ "${SATINFO}" == "generate" ]]; then
     "${USHgfs}/create_gsi_info.sh" sat "${PDY}${cyc}" "${DATA}"
 else
-    ${NLN} "${SATINFO}" satinfo
+    cpreq "${SATINFO}" satinfo
 fi
 if [[ "${CONVINFO}" == "generate" ]]; then
     "${USHgfs}/create_gsi_info.sh" conv "${PDY}${cyc}" "${DATA}" "${USE_2M_OBS}"
 else
-    ${NLN} "${CONVINFO}" convinfo
+    cpreq "${CONVINFO}" convinfo
 fi
 if [[ "${OZINFO}" == "generate" ]]; then
     "${USHgfs}/create_gsi_info.sh" oz "${PDY}${cyc}" "${DATA}"
 else
-    ${NLN} "${OZINFO}" ozinfo
+    cpreq "${OZINFO}" ozinfo
 fi
-${NLN} "${SATANGL}" satbias_angle
-${NLN} "${SCANINFO}" scaninfo
-${NLN} "${HYBENSINFO}" hybens_info
-${NLN} "${ANAVINFO}" anavinfo
-${NLN} "${VLOCALEIG}" vlocal_eig.dat
 
 # Bias correction coefficients based on the ensemble mean
-${NLN} "${COMIN_ATMOS_ANALYSIS_STAT}/${GBIASe}" "satbias_in"
+#${NLN} "${COMIN_ATMOS_ANALYSIS_STAT}/${GBIASe}" "satbias_in"  # This file does not exist when test was run # TODO: remove
 
 ################################################################################
+# Ensemble guess, observational data and analyses/increments
 
-if [[ "${USE_CFP}" == "YES" ]]; then
-    rm -f "${DATA}/untar.sh" "${DATA}/mp_untar.sh"
-    cat > "${DATA}/untar.sh" << EOFuntar
-#!/bin/sh
-memchar=\$1
-COMOUT_ATMOS_ANALYSIS=\$2
 flist="${CNVSTAT} ${OZNSTAT} ${RADSTAT}"
-for ftype in \$flist; do
-   if [[ "\${memchar}" == "ensmean" ]]; then
-      fname=\${COMOUT_ATMOS_ANALYSIS}/\${ftype%.tar}.ensmean.tar
-   else
-      fname=\${COMOUT_ATMOS_ANALYSIS}/\${ftype}
-   fi
-   tar -xvf \$fname
+for ftype in ${flist}; do
+    fname="${COMIN_ATMOS_ANALYSIS_STAT}/${ftype}"
+    tar -xvf "${fname}"
 done
-EOFuntar
-    chmod 755 "${DATA}/untar.sh"
-fi
-
-################################################################################
-# Ensemble guess, observational data and analyses/increments
 
-echo "${DATA}/untar.sh ensmean ${COMIN_ATMOS_ANALYSIS_STAT}" | tee -a "${DATA}/mp_untar.sh"
 nfhrs="${IAUFHRS_ENKF//,/ }"
 for imem in $(seq 1 "${NMEM_ENS}"); do
     smem=$((imem + mem_offset))
-    if ((smem > NMEM_ENS_MAX)); then
+    if [[ ${smem} -gt ${NMEM_ENS_MAX} ]]; then
         smem=$((smem - NMEM_ENS_MAX))
     fi
     gmemchar="mem"$(printf "%03i" "${smem}")
     memchar="mem"$(printf "%03i" "${imem}")
 
-    MEMDIR=${gmemchar} RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -x \
+    MEMDIR=${gmemchar} RUN=${GDUMP} YMD=${GDATE:0:8} HH=${GDATE:8:2} declare_from_tmpl -x \
         COMIN_ATMOS_HISTORY_MEM_PREV:COM_ATMOS_HISTORY_TMPL
 
     MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl -x \
@@ -220,18 +177,11 @@ for FHR in ${nfhrs}; do
     if [[ "${DO_GSISOILDA}" == "YES" ]]; then
         ${NLN} "${COMIN_ATMOS_HISTORY_STAT_PREV}/${GPREFIX}ensmean.sfc.f00${FHR}.nc" \
             "bfg_${PDY}${cyc}_fhr0${FHR}_ensmean"
-        ${NLN} "${COMIN_ATMOS_ANALYSIS_STAT}/${APREFIX}increment.sfc.i00${FHR}.nc" \
+        ${NLN} "${COMIN_ATMOS_ANALYSIS_STAT}/${APREFIX}ensmean_increment.sfc.i00${FHR}.nc" \
             "sfcincr_${PDY}${cyc}_fhr0${FHR}_ensmean"
     fi
 done
 
-# Run with MPMD or serial
-"${USHgfs}/run_mpmd.sh" "${DATA}/mp_untar.sh" && true
-export err=$?
-if [[ ${err} -ne 0 ]]; then
-    err_exit "Failed to untar input data!"
-fi
-
 ################################################################################
 # Create global_enkf namelist
 cat > enkf.nml << EOFnml
@@ -248,19 +198,19 @@ cat > enkf.nml << EOFnml
    sprd_tol=1.e30,paoverpb_thresh=0.98,
    nlons=${LONA_ENKF},nlats=${LATA_ENKF},nlevs=${LEVS_ENKF},nanals=${NMEM_ENS},
    deterministic=.true.,sortinc=.true.,lupd_satbiasc=.false.,
-   reducedgrid=${reducedgrid},readin_localization=${readin_localization_enkf}.,
-   use_gfs_nemsio=${use_gfs_nemsio},use_gfs_ncio=${use_gfs_ncio},imp_physics=${imp_physics},lupp=${lupp},
+   reducedgrid=${reducedgrid:-.false.},readin_localization=${readin_localization_enkf:-.true.},
+   use_gfs_nemsio=.false.,use_gfs_ncio=.true.,imp_physics=${imp_physics:-99},lupp=${lupp:-.true.},
    univaroz=.false.,adp_anglebc=.true.,angord=4,use_edges=.false.,emiss_bc=.true.,
-   letkf_flag=${letkf_flag},nobsl_max=${nobsl_max},denkf=${denkf},getkf=${getkf}.,
+   letkf_flag=${letkf_flag:-.false.},nobsl_max=${nobsl_max:-10000},denkf=${denkf:-.false.},getkf=${getkf:-.false.},
    nhr_anal=${IAUFHRS_ENKF},nhr_state=${IAUFHRS_ENKF},
-   lobsdiag_forenkf=.true.,taperanalperts=${taperanalperts},
-   write_spread_diag=${write_spread_diag},
-   modelspace_vloc=${modelspace_vloc},
-   use_correlated_oberrs=${use_correlated_oberrs},
-   netcdf_diag=${netcdf_diag},cnvw_option=${cnvw_option},
-   paranc=${paranc},write_fv3_incr=${write_fv3_incr},
+   lobsdiag_forenkf=.true.,taperanalperts=${taperanalperts:-.false.},
+   write_spread_diag=${write_spread_diag:-".false."},
+   modelspace_vloc=${modelspace_vloc:-.false.},
+   use_correlated_oberrs=${use_correlated_oberrs:-.false.},
+   netcdf_diag=.true.,cnvw_option=${cnvw_option},
+   paranc=${paranc:-.true.},write_fv3_incr=${write_fv3_incr},
    ${WRITE_INCR_ZERO}
-   ${NAM_ENKF}
+   ${NAM_ENKF:-}
 /
 &satobs_enkf
    sattypes_rad(1) = 'amsua_n15',     dsis(1) = 'amsua_n15',
@@ -343,7 +293,7 @@ cat > enkf.nml << EOFnml
    sattypes_rad(78)= 'atms_n21',      dsis(78)= 'atms_n21',
    sattypes_rad(79)= 'cris-fsr_n21',  dsis(79)= 'cris-fsr_n21',
    sattypes_rad(80)= 'abi_g19',       dsis(80)= 'abi_g19',
-   ${SATOBS_ENKF}
+   ${SATOBS_ENKF:-}
 /
 &ozobs_enkf
    sattypes_oz(1) = 'sbuv2_n16',
@@ -362,7 +312,7 @@ cat > enkf.nml << EOFnml
    sattypes_oz(14) = 'ompstc8_n21',
    sattypes_oz(15) = 'ompsnp_n21',
    sattypes_oz(16) = 'gome_metop-c',
-   ${OZOBS_ENKF}
+   ${OZOBS_ENKF:-}
 /
 EOFnml
 
@@ -381,10 +331,10 @@ if [[ ${err} -ne 0 ]]; then
 fi
 
 # Cat runtime output files.
-cat stdout stderr > "${COMOUT_ATMOS_ANALYSIS_STAT}/${ENKFSTAT}"
+cat stdout stderr > enkfstat.txt
+cpfs enkfstat.txt "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX}enkfstat.txt"
 
 ################################################################################
 #  Postprocessing
-cd "${pwd}" || exit 1
 
-exit "${err}"
+exit 0
diff --git a/scripts/exglobal_atmos_analysis.sh b/scripts/exglobal_atmos_analysis.sh
index 604350dcf45..6eb8804a59d 100755
--- a/scripts/exglobal_atmos_analysis.sh
+++ b/scripts/exglobal_atmos_analysis.sh
@@ -20,8 +20,7 @@
 #  Set environment.
 
 #  Directories.
-pwd=$(pwd)
-
+cd "${DATA}" || exit 1
 # Base variables
 rCDUMP=${rCDUMP:-"gdas"}
 GDUMP=${GDUMP:-"gdas"}
@@ -39,7 +38,6 @@ export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 COMPRESS=${COMPRESS:-gzip}
 UNCOMPRESS=${UNCOMPRESS:-gunzip}
-APRUNCFP=${APRUNCFP:-""}
 APRUN_GSI=${APRUN_GSI:-${APRUN:-""}}
 NTHREADS_GSI=${NTHREADS_GSI:-${NTHREADS:-1}}
 
@@ -57,8 +55,6 @@ IASI_CADS=${IASI_CADS:-".false."}
 CRIS_CADS=${CRIS_CADS:-".false."}
 
 # Diagnostic files options
-netcdf_diag=${netcdf_diag:-".true."}
-binary_diag=${binary_diag:-".false."}
 lobsdiag_forenkf=${lobsdiag_forenkf:-".false."}
 
 # IAU
@@ -186,11 +182,7 @@ ABIAS=${ABIAS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias.txt}
 ABIASPC=${ABIASPC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_pc.txt}
 ABIASAIR=${ABIASAIR:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_air.txt}
 ABIASe=${ABIASe:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}abias_int.txt}
-RADSTAT=${RADSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.tar}
 GSISTAT=${GSISTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsistat.txt}
-PCPSTAT=${PCPSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}pcpstat}
-CNVSTAT=${CNVSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat.tar}
-OZNSTAT=${OZNSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat.tar}
 
 # Increment files
 ATMINC=${ATMINC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.atm.i006.nc}
@@ -199,17 +191,8 @@ ATMINC=${ATMINC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.atm.i006.nc}
 RUN_SELECT=${RUN_SELECT:-"NO"}
 USE_SELECT=${USE_SELECT:-"NO"}
 USE_RADSTAT=${USE_RADSTAT:-"YES"}
-SELECT_OBS=${SELECT_OBS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput}
+SELECT_OBS=${SELECT_OBS:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}obsinput.tar}
 GENDIAG=${GENDIAG:-"YES"}
-DIAG_SUFFIX=${DIAG_SUFFIX:-""}
-if [[ "${netcdf_diag}" == ".true." ]]; then
-    DIAG_SUFFIX="${DIAG_SUFFIX}.nc4"
-fi
-DIAG_COMPRESS=${DIAG_COMPRESS:-"YES"}
-DIAG_TARBALL=${DIAG_TARBALL:-"YES"}
-USE_CFP=${USE_CFP:-"NO"}
-CFP_MP=${CFP_MP:-"NO"}
-DIAG_DIR=${DIAG_DIR:-${COMOUT_ATMOS_ANALYSIS}/gsidiags}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -332,8 +315,7 @@ RAPIDREFRESH_CLDSURF=${RAPIDREFRESH_CLDSURF:-""}
 CHEM=${CHEM:-""}
 NST=${NST:-""}
 
-#uGSI Namelist parameters
-lrun_subdirs=${lrun_subdirs:-".true."}
+# GSI Namelist parameters
 if [[ "${DOHYBVAR}" == "YES" ]]; then
     l_hyb_ens=.true.
     export l4densvar=${l4densvar:-".false."}
@@ -632,25 +614,6 @@ if [[ "${JCAP}" -ne "${JCAP_A}" ]]; then
     fi
 fi
 
-##############################################################
-# Diagnostic files
-# if requested, link GSI diagnostic file directories for use later
-if [[ "${GENDIAG}" == "YES" ]]; then
-    if [[ "${lrun_subdirs}" == ".true." ]]; then
-        if [[ -d "${DIAG_DIR}" ]]; then
-            rm -rf "${DIAG_DIR}"
-        fi
-        ntasks_m1="$((ntasks - 1))"
-        for pe in $(seq 0 "${ntasks_m1}"); do
-            pedir="dir.$(printf %04i "${pe}")"
-            mkdir -p "${DIAG_DIR}/${pedir}"
-            ${NLN} "${DIAG_DIR}/${pedir}" "${pedir}"
-        done
-    else
-        err_exit "lrun_subdirs must be true. lrun_subdirs=${lrun_subdirs}"
-    fi
-fi
-
 ##############################################################
 # Output files
 ${NLN} "${ATMANL}" siganl
@@ -698,39 +661,32 @@ fi
 ##############################################################
 # If requested, copy and de-tar guess radstat file
 if [[ "${USE_RADSTAT}" == "YES" ]]; then
-    if [[ -f "${DATA}/unzip.sh" ]]; then
-        rm -f "${DATA}/unzip.sh"
-    fi
-    if [[ -f "${DATA}/mp_unzip.sh" ]]; then
-        rm -f "${DATA}/mp_unzip.sh"
-    fi
-    cat > "${DATA}/unzip.sh" << EOFunzip
-#!/bin/sh
-   diag_file=\$1
-   diag_suffix=\$2
-   fname=\$(echo \$diag_file | cut -d'.' -f1)
-   fdate=\$(echo \$diag_file | cut -d'.' -f2)
-   ${UNCOMPRESS} \$diag_file
-   fnameges=\$(echo \$fname | sed 's/_ges//g')
-   ${NMV} \$fname.\$fdate\$diag_suffix \$fnameges
-EOFunzip
-
-    chmod 755 "${DATA}/unzip.sh"
+    rm -f "${DATA}/unzip_radstat.sh"
+    cat > "${DATA}/unzip_radstat.sh" << EOF
+#!/bin/bash
+diag_file=\$1
+diag_suffix=\$2
+fname=\$(echo \$diag_file | cut -d'.' -f1)
+fdate=\$(echo \$diag_file | cut -d'.' -f2)
+${UNCOMPRESS} \$diag_file
+fnameges=\$(echo \$fname | sed 's/_ges//g')
+${NMV} \$fname.\$fdate\$diag_suffix \$fnameges
+EOF
+    chmod 755 "${DATA}/unzip_radstat.sh"
 
+    rm -f "${DATA}/cmdfile"
     #shellcheck disable=SC2312
-    listdiag="$(tar xvf radstat.gdas | cut -d' ' -f2 | grep _ges)"
+    listdiag=$(tar -xvf radstat.gdas | cut -d' ' -f2 | grep _ges)
     for type in ${listdiag}; do
         diag_file=$(echo "${type}" | cut -d',' -f1)
-        echo "${DATA}/unzip.sh ${diag_file} ${DIAG_SUFFIX}" | tee -a "${DATA}/mp_unzip.sh"
+        echo "${DATA}/unzip_radstat.sh ${diag_file} ${DIAG_SUFFIX:-}.nc4" >> "${DATA}/cmdfile"
     done
-    chmod 755 "${DATA}/mp_unzip.sh"
-    "${USHgfs}/run_mpmd.sh" "${DATA}/mp_unzip.sh" && true
+
+    "${USHgfs}/run_mpmd.sh" "${DATA}/cmdfile" && true
     export err=$?
     if [[ ${err} -ne 0 ]]; then
-        export pgm="run_mpmd.sh"
-        err_exit "run_mpmd failed while unziping diagnotic files."
+        err_exit "Failed to unzip radstat.gdas file!"
     fi
-
 fi # if [[ $USE_RADSTAT == "YES" ]
 
 ##############################################################
@@ -768,12 +724,12 @@ cat > gsiparm.anl << EOF
   use_pbl=.false.,use_compress=.true.,nsig_ext=45,gpstop=50.,commgpstop=45.,commgpserrinf=1.0,
   use_gfs_nemsio=.false.,use_gfs_ncio=.true.,sfcnst_comb=.true.,
   use_readin_anl_sfcmask=${USE_READIN_ANL_SFCMASK},
-  lrun_subdirs=${lrun_subdirs},
+  lrun_subdirs=.true.,
   crtm_coeffs_path='./crtm_coeffs/',
   newpc4pred=.true.,adp_anglebc=.true.,angord=4,passive_bc=.true.,use_edges=.false.,
   diag_precon=.true.,step_start=1.e-3,emiss_bc=.true.,nhr_obsbin=${nhr_obsbin:-3},
   cwoption=3,imp_physics=${imp_physics},lupp=${lupp},cnvw_option=${cnvw_option},cao_check=${cao_check},
-  netcdf_diag=${netcdf_diag},binary_diag=${binary_diag},
+  netcdf_diag=.true.,binary_diag=.false.,
   lobsdiag_forenkf=${lobsdiag_forenkf},
   write_fv3_incr=${write_fv3_increment},
   nhr_anal=${IAUFHRS},
@@ -927,7 +883,7 @@ fi
 
 ################################################################################
 # Postprocessing
-cd "${pwd}" || exit 1
+cd "${DATA}" || exit 1
 
 ##############################################################
 # Add this statement to release the forecast job once the
@@ -937,6 +893,18 @@ cd "${pwd}" || exit 1
 if [[ "${SENDECF}" == "YES" && "${RUN}" != "enkf" ]]; then
     ecflow_client --event release_fcst
 fi
+
+# Diagnostic files
+# if requested, GSI diagnostic file directories for use later
+if [[ "${GENDIAG}" == "YES" ]]; then
+    tar -cvf gsidiags.tar dir.????
+    export err=$?
+    if [[ ${err} -ne 0 ]]; then
+        err_exit "Failed to tar GSI diagnostic directories!"
+    fi
+    cpfs gsidiags.tar "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}gsidiags${DIAG_SUFFIX:-}.tar"
+fi
+
 # shellcheck disable=SC2312
 echo "${rCDUMP} ${PDY}${cyc} atminc done at $(date)" > "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.done.txt"
 
diff --git a/scripts/exglobal_diag.sh b/scripts/exglobal_diag.sh
index 92ea7bdaa8f..68231b6fb72 100755
--- a/scripts/exglobal_diag.sh
+++ b/scripts/exglobal_diag.sh
@@ -18,233 +18,218 @@
 ################################################################################
 
 #  Set environment.
+cd "${DATA}" || exit 8
 
 # Base variables
-GDUMP="${GDUMP:-gdas}"
 
 # Utilities
-export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
-export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
-export CATEXEC=${CATEXEC:-${ncdiag_ROOT:-${gsi_ncdiag_ROOT}}/bin/ncdiag_cat_serial.x}
+CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
+CATEXEC=${CATEXEC:-${ncdiag_ROOT:-${gsi_ncdiag_ROOT}}/bin/ncdiag_cat_serial.x}
 COMPRESS=${COMPRESS:-gzip}
-UNCOMPRESS=${UNCOMPRESS:-gunzip}
-APRUNCFP=${APRUNCFP:-""}
-
-# Diagnostic files options
-netcdf_diag=${netcdf_diag:-".true."}
-binary_diag=${binary_diag:-".false."}
 
 # Analysis files
-export APREFIX=${APREFIX:-""}
-RADSTAT=${RADSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.tar}
-PCPSTAT=${PCPSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}pcpstat}
+APREFIX=${APREFIX:-"${RUN}.t${cyc}z."}
 CNVSTAT=${CNVSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}cnvstat.tar}
+PCPSTAT=${PCPSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}pcpstat}
 OZNSTAT=${OZNSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}oznstat.tar}
+RADSTAT=${RADSTAT:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}radstat.tar}
 
 # Remove stat file if file already exists
 rm -f "${RADSTAT}" "${PCPSTAT}" "${CNVSTAT}" "${OZNSTAT}"
 
 # Obs diag
 GENDIAG=${GENDIAG:-"YES"}
-DIAG_SUFFIX=${DIAG_SUFFIX:-""}
-if [[ "${netcdf_diag}" == ".true." ]]; then
-    DIAG_SUFFIX="${DIAG_SUFFIX}.nc4"
-fi
+GSIDIAG=${GSIDIAG:-"${COMIN_ATMOS_ANALYSIS}/${APREFIX}gsidiags${DIAG_SUFFIX:-}.tar"}
+USE_BUILD_GSINFO=${USE_BUILD_GSINFO:-"NO"}
 DIAG_COMPRESS=${DIAG_COMPRESS:-"YES"}
-COMPRESS_SUFFIX=${COMPRESS_SUFFIX:-""}
-if [[ ${DIAG_COMPRESS} == "YES" ]]; then
-    COMPRESS_SUFFIX="${COMPRESS_SUFFIX}.gz"
+if [[ "${DIAG_COMPRESS:-}" == "YES" ]]; then
+    COMPRESS_SUFFIX=".gz"
 fi
 DIAG_TARBALL=${DIAG_TARBALL:-"YES"}
-USE_CFP=${USE_CFP:-"NO"}
-CFP_MP=${CFP_MP:-"NO"}
-DIAG_DIR=${DIAG_DIR:-${COMOUT_ATMOS_ANALYSIS}/gsidiags}
-REMOVE_DIAG_DIR=${REMOVE_DIAG_DIR:-"NO"}
 
 # Set script / GSI control parameters
-lrun_subdirs=${lrun_subdirs:-".true."}
 
 ################################################################################
-# If requested, generate diagnostic files
-if [[ "${GENDIAG}" == "YES" ]]; then
-    if [[ "${lrun_subdirs}" == ".true." ]]; then
-        for pe in "${DIAG_DIR}/"dir.*; do
-            pedir="$(basename -- "${pe}")"
-            ${NLN} "${pe}" "${DATA}/${pedir}"
-        done
-    else
-        err_exit "lrun_subdirs must be true.  Abort job"
-    fi
+if [[ "${GENDIAG}" != "YES" ]]; then
+    echo "INFO: GENDIAG set to NO.  Skipping diagnostic file generation."
+    exit 0
+fi
 
-    # Set up lists and variables for various types of diagnostic files.
-    diagtype[0]="conv conv_gps conv_ps conv_pw conv_q conv_sst conv_t conv_tcp conv_uv conv_spd"
-    diagtype[1]="pcp_ssmi_dmsp pcp_tmi_trmm"
-    if [[ "${USE_BUILD_GSINFO}" == "YES" ]]; then
-        diagtype[2]=$(cat "${BUILD_GSINFO_DIR}/ozinfo/satellites")
-        diagtype[3]=$(cat "${BUILD_GSINFO_DIR}/satinfo/satellites")
-    else
-        diagtype[2]="sbuv2_n16 sbuv2_n17 sbuv2_n18 sbuv2_n19 gome_metop-a gome_metop-b omi_aura mls30_aura ompsnp_npp ompstc8_npp  ompstc8_n20 ompsnp_n20 ompstc8_n21 ompsnp_n21 ompslp_npp gome_metop-c"
-        diagtype[3]="msu_n14 sndr_g08 sndr_g11 sndr_g12 sndr_g13 sndr_g08_prep sndr_g11_prep sndr_g12_prep sndr_g13_prep sndrd1_g11 sndrd2_g11 sndrd3_g11 sndrd4_g11 sndrd1_g12 sndrd2_g12 sndrd3_g12 sndrd4_g12 sndrd1_g13 sndrd2_g13 sndrd3_g13 sndrd4_g13 sndrd1_g14 sndrd2_g14 sndrd3_g14 sndrd4_g14 sndrd1_g15 sndrd2_g15 sndrd3_g15 sndrd4_g15 amsua_n15 amsua_n16 amsua_n17 amsub_n15 amsub_n16 amsub_n17 hsb_aqua airs_aqua amsua_aqua imgr_g08 imgr_g11 imgr_g12 imgr_g14 imgr_g15 ssmi_f13 ssmi_f15 amsua_n18 amsua_metop-a mhs_n18 mhs_metop-a amsre_low_aqua amsre_mid_aqua amsre_hig_aqua ssmis_f16 ssmis_f17 ssmis_f18 ssmis_f19 ssmis_f20 iasi_metop-a amsua_n19 mhs_n19 seviri_m08 seviri_m09 seviri_m10 seviri_m11 cris_npp cris-fsr_npp cris-fsr_n20 atms_npp atms_n20 amsua_metop-b mhs_metop-b iasi_metop-b avhrr_metop-b avhrr_n18 avhrr_n19 avhrr_metop-a amsr2_gcom-w1 gmi_gpm saphir_meghat ahi_himawari8 abi_g16 abi_g17 amsua_metop-c mhs_metop-c iasi_metop-c avhrr_metop-c viirs-m_npp viirs-m_j1 abi_g18 ahi_himawari9 viirs-m_j2 cris-fsr_n21 atms_n21 abi_g19"
-    fi
+################################################################################
+# Copy gsidiags.tar file from COMIN to DATA and untar
+cpreq "${GSIDIAG}" ./gsidiags.tar
+tar -xvf gsidiags.tar
+export err=$?
+if [[ ${err} -ne 0 ]]; then
+    err_exit "Unable to unpack gsidiags.tar file!"
+fi
 
-    diaglist[0]=listcnv
-    diaglist[1]=listpcp
-    diaglist[2]=listozn
-    diaglist[3]=listrad
-
-    diagfile[0]="${CNVSTAT}"
-    diagfile[1]="${PCPSTAT}"
-    diagfile[2]="${OZNSTAT}"
-    diagfile[3]="${RADSTAT}"
-
-    # Set diagnostic file prefix based on lrun_subdirs variable
-    if [[ "${lrun_subdirs}" == ".true." ]]; then
-        prefix="dir.*/"
-    else
-        prefix="pe*"
-    fi
+# Set up lists and variables for various types of diagnostic files.
+ntype=3
 
-    rm -f "${DATA}/diag.sh" "${DATA}/mp_diag.sh"
-    cat > "${DATA}/diag.sh" << EOFdiag
-#!/bin/sh
-lrun_subdirs=\$1
-binary_diag=\$2
-type=\$3
-loop=\$4
-string=\$5
-PDY=\$6
-cyc=\$7
-DIAG_COMPRESS=\$8
-DIAG_SUFFIX=\$9
-if [[ "\${lrun_subdirs}" == ".true." ]]; then
-    prefix="dir.*/"
+diagtype[0]="conv conv_gps conv_ps conv_pw conv_q conv_sst conv_t conv_tcp conv_uv conv_spd"
+diagtype[1]="pcp_ssmi_dmsp pcp_tmi_trmm"
+if [[ ${USE_BUILD_GSINFO} == "YES" ]]; then
+    diagtype[2]=$(cat "${BUILD_GSINFO_DIR}/ozinfo/satellites")
+    diagtype[3]=$(cat "${BUILD_GSINFO_DIR}/satinfo/satellites")
 else
-    prefix="pe*"
-fi
-count=\$(find -L ./ -path "./\${prefix}\${type}_\${loop}*" -type f -printf '.' | wc -c)
-file="diag_\${type}_\${string}.\${PDY}\${cyc}\${DIAG_SUFFIX}"
-if [[ "\${binary_diag}" == ".true." ]] || [[ "\${count}" -eq 1 ]]; then
-    cat \${prefix}\${type}_\${loop}* > "\${file}"
-else    
-    ${CATEXEC} -o "\${file}" \${prefix}\${type}_\${loop}*
+    diagtype[2]="sbuv2_n16 sbuv2_n17 sbuv2_n18 sbuv2_n19 gome_metop-a gome_metop-b omi_aura mls30_aura ompsnp_npp ompstc8_npp  ompstc8_n20 ompsnp_n20 ompstc8_n21 ompsnp_n21 ompslp_npp gome_metop-c"
+    diagtype[3]="msu_n14 sndr_g08 sndr_g11 sndr_g12 sndr_g13 sndr_g08_prep sndr_g11_prep sndr_g12_prep sndr_g13_prep sndrd1_g11 sndrd2_g11 sndrd3_g11 sndrd4_g11 sndrd1_g12 sndrd2_g12 sndrd3_g12 sndrd4_g12 sndrd1_g13 sndrd2_g13 sndrd3_g13 sndrd4_g13 sndrd1_g14 sndrd2_g14 sndrd3_g14 sndrd4_g14 sndrd1_g15 sndrd2_g15 sndrd3_g15 sndrd4_g15 amsua_n15 amsua_n16 amsua_n17 amsub_n15 amsub_n16 amsub_n17 hsb_aqua airs_aqua amsua_aqua imgr_g08 imgr_g11 imgr_g12 imgr_g14 imgr_g15 ssmi_f13 ssmi_f15 amsua_n18 amsua_metop-a mhs_n18 mhs_metop-a amsre_low_aqua amsre_mid_aqua amsre_hig_aqua ssmis_f16 ssmis_f17 ssmis_f18 ssmis_f19 ssmis_f20 iasi_metop-a amsua_n19 mhs_n19 seviri_m08 seviri_m09 seviri_m10 seviri_m11 cris_npp cris-fsr_npp cris-fsr_n20 atms_npp atms_n20 amsua_metop-b mhs_metop-b iasi_metop-b avhrr_metop-b avhrr_n18 avhrr_n19 avhrr_metop-a amsr2_gcom-w1 gmi_gpm saphir_meghat ahi_himawari8 abi_g16 abi_g17 amsua_metop-c mhs_metop-c iasi_metop-c avhrr_metop-c viirs-m_npp viirs-m_j1 abi_g18 ahi_himawari9 viirs-m_j2 cris-fsr_n21 atms_n21 abi_g19"
 fi
-if [[ "\${DIAG_COMPRESS}" == "YES" ]]; then
-    ${COMPRESS} "\${file}"
+
+diaglist[0]=listcnv
+diaglist[1]=listpcp
+diaglist[2]=listozn
+diaglist[3]=listrad
+
+diagfile[0]="${CNVSTAT}"
+diagfile[1]="${PCPSTAT}"
+diagfile[2]="${OZNSTAT}"
+diagfile[3]="${RADSTAT}"
+
+numfile[0]=0
+numfile[1]=0
+numfile[2]=0
+numfile[3]=0
+
+rm -f "${DATA}/diag.sh"
+cat > "${DATA}/diag.sh" << EOF
+#!/bin/bash
+set -x
+
+type=\$1
+loop=\$2
+string=\$3
+count=\$4
+suffix=\$5
+
+# Match files with this prefix
+diag_files=dir.*/\${type}_\${loop}
+
+# Name of combined diagnostic file from matched files
+out_diag_file=diag_\${type}_\${string}.${PDY}${cyc}\${suffix}
+
+# Combine diagnostic files
+if [[ \${count} -gt 1 ]]; then
+    ${CATEXEC} -o \${out_diag_file} \${diag_files}*
+else
+    cat \${diag_files}* > "\${out_diag_file}"
 fi
-EOFdiag
-    chmod 755 "${DATA}/diag.sh"
-
-    # Collect diagnostic files as a function of loop and type.
-    # Loop over first and last outer loops to generate innovation
-    # diagnostic files for indicated observation types (groups)
-    #
-    # NOTE:  Since we set miter=2 in GSI namelist SETUP, outer
-    #        loop 03 will contain innovations with respect to
-    #        the analysis.  Creation of o-a innovation files
-    #        is triggered by write_diag(3)=.true.  The setting
-    #        write_diag(1)=.true. turns on creation of o-g
-    #        innovation files.
-
-    loops="01 03"
-    for loop in ${loops}; do
-        case ${loop} in
-            01) string=ges ;;
-            03) string=anl ;;
-            *) string=${loop} ;;
-        esac
-        # shellcheck disable=SC2312
-        echo "$(date) START loop ${string}" >&2
-        for ((n = 0; n < ${#diagtype[@]}; n++)); do
-            for type in ${diagtype[n]}; do
-                # shellcheck disable=SC2312
-                count=$(find -L ./ -path "./${prefix}${type}_${loop}*" -type f -printf '.' | wc -c)
-                if [[ "${count}" -gt 0 ]]; then
-                    echo "${DATA}/diag.sh ${lrun_subdirs} ${binary_diag} ${type} ${loop} ${string} ${PDY} ${cyc} ${DIAG_COMPRESS} ${DIAG_SUFFIX}" | tee -a "${DATA}/mp_diag.sh"
-                    echo "diag_${type}_${string}.${PDY}${cyc}${DIAG_SUFFIX}${COMPRESS_SUFFIX}" >> "${diaglist[n]}"
-                fi
-            done
-        done
-        # shellcheck disable=SC2312
-        echo "$(date) END loop ${string}" >&2
-    done
 
-    # We should already be in $DATA, but extra cd to be sure.
-    cd "${DATA}" || exit 1
+# Compress diagnostic file if requested
+if [[ "${DIAG_COMPRESS:-}" == "YES" ]]; then
+    ${COMPRESS} "\${out_diag_file}"
+fi
 
-    export err=0
-    if [[ -s "${DATA}/mp_diag.sh" ]]; then
-        chmod 755 "${DATA}/mp_diag.sh"
-        "${USHgfs}/run_mpmd.sh" "${DATA}/mp_diag.sh" && true
-        # Delay err exit to avoid rstprod leakage
-        err=$?
-    fi
+exit 0
+EOF
+chmod 755 "${DATA}/diag.sh"
 
-    # Restrict diagnostic files containing rstprod data
-    if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
-        rlist="conv_gps conv_ps conv_pw conv_q conv_sst conv_t conv_uv saphir"
-        for rtype in ${rlist}; do
-            for rfile in *"${rtype}"*; do
-                if [[ -s "${rfile}" ]]; then
-                    ${CHGRP_CMD} "${rfile}"
-                fi
-            done
+# Collect diagnostic files as a function of loop and type.
+# Loop over first and last outer loops to generate innovation
+# diagnostic files for indicated observation types (groups)
+#
+# NOTE:  Since we set miter=2 in GSI namelist SETUP, outer
+#        loop 03 will contain innovations with respect to
+#        the analysis.  Creation of o-a innovation files
+#        is triggered by write_diag(3)=.true.  The setting
+#        write_diag(1)=.true. turns on creation of o-g
+#        innovation files.
+
+rm -f cmdfile
+touch cmdfile
+loops="01 03"
+for loop in ${loops}; do
+    case ${loop} in
+        01) string=ges ;;
+        03) string=anl ;;
+        *) string=${loop} ;;
+    esac
+    echo "START loop ${string}"
+    n=-1
+    while [[ ${n} -lt ${ntype} ]]; do
+        n=$((n + 1))
+        for type in ${diagtype[n]}; do
+            #shellcheck disable=SC2012,SC2312
+            count=$(ls dir.*/"${type}_${loop}"* 2> /dev/null | wc -l)
+            if [[ ${count} -eq 0 ]]; then
+                continue
+            fi
+            echo "${DATA}/diag.sh ${type} ${loop} ${string} ${count} ${DIAG_SUFFIX:-}.nc4" >> cmdfile
+            echo "diag_${type}_${string}.${PDY}${cyc}${DIAG_SUFFIX:-}.nc4${COMPRESS_SUFFIX:-}" >> "${diaglist[n]}"
+            numfile[n]=$((numfile[n] + 1))
         done
-    fi
+    done
+    echo "END loop ${string}"
+done
 
-    # Now exit if compression failed
+ncmd=$(wc -l < cmdfile)
+if [[ ${ncmd} -eq 0 ]]; then
+    echo "WARNING: No diagnostic files found to process!"
+    exit 0
+fi
+
+# MPMD can only be executed on a single node,
+# so break up cmdfile into parts of tasks_per_node size files
+# and run them sequentially
+split -l "${tasks_per_node}" ./cmdfile cmdfile_part_
+cmdfile_parts=$(ls cmdfile_part_*)
+for partfile in ${cmdfile_parts}; do
+    "${USHgfs}/run_mpmd.sh" "${partfile}" && true
+    export err=$?
     if [[ ${err} -ne 0 ]]; then
-        err_exit "Failed to compress one or more observation diagnostic files!"
+        err_exit "Failed to create one or more observation diagnostic files for ${partfile}!"
     fi
-
-    # If requested, create diagnostic file tarballs
-    if [[ "${DIAG_TARBALL}" == "YES" ]]; then
-        # shellcheck disable=SC2312
-        echo "$(date) START tar diagnostic files" >&2
-        for ((n = 0; n < ${#diagtype[@]}; n++)); do
-            TAROPTS="-uvf"
-            if [[ ! -s "${diagfile[n]}" ]]; then
-                TAROPTS="-cvf"
-            fi
-            if [[ -s "${diaglist[n]}" ]]; then
-                tar "${TAROPTS}" "${diagfile[n]}" -T "${diaglist[n]}"
-                export err=$?
-                if [[ ${err} -ne 0 ]]; then
-                    # Delay err_exit to avoid rstprod leakage
-                    err_msg="Unable to create ${diagfile[n]}!"
-                    break
-                fi
+done
+
+# Restrict diagnostic files containing rstprod data
+if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
+    rlist="conv_gps conv_ps conv_pw conv_q conv_sst conv_t conv_uv saphir"
+    for rtype in ${rlist}; do
+        for rfile in *"${rtype}"*; do
+            if [[ -s "${rfile}" ]]; then
+                ${CHGRP_CMD} "${rfile}"
             fi
         done
+    done
+fi
 
-        # Restrict CNVSTAT
-        chmod 750 "${CNVSTAT}"
-        if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
-            ${CHGRP_CMD} "${CNVSTAT}"
+# If requested, create diagnostic file tarballs
+if [[ "${DIAG_TARBALL}" == "YES" ]]; then
+    echo "START tar diagnostic files"
+    n=-1
+    while [[ ${n} -lt ${ntype} ]]; do
+        n=$((n + 1))
+        TAROPTS="-uvf"
+        if [[ ! -s "${diagfile[n]}" ]]; then
+            TAROPTS="-cvf"
         fi
-
-        # Restrict RADSTAT
-        if [[ -s "${RADSTAT}" ]]; then
-            chmod 750 "${RADSTAT}"
-            if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
-                ${CHGRP_CMD} "${RADSTAT}"
+        if [[ ${numfile[n]} -gt 0 ]]; then
+            tar "${TAROPTS}" "${diagfile[n]}" -T "${diaglist[n]}"
+            export err=$?
+            if [[ ${err} -ne 0 ]]; then
+                err_exit "Unable to create ${diagfile[n]}!"
             fi
         fi
+    done
+    echo "END tar diagnostic files"
 
-        # Now exit if there was an error
-        if [[ ${err} -ne 0 ]]; then
-            err_exit "${err_msg}"
-        fi
+    # Restrict CNVSTAT
+    chmod 750 "${CNVSTAT}"
+    if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
+        ${CHGRP_CMD} "${CNVSTAT}"
+    fi
 
-        # shellcheck disable=SC2312
-        echo "$(date) END tar diagnostic files" >&2
+    # Restrict RADSTAT
+    if [[ -s "${RADSTAT}" ]]; then
+        chmod 750 "${RADSTAT}"
+        if [[ "${CHGRP_RSTPROD}" == "YES" ]]; then
+            ${CHGRP_CMD} "${RADSTAT}"
+        fi
     fi
-fi # End diagnostic file generation block - if [[ "${GENDIAG}" == "YES" ]]
+fi
 
 ################################################################################
 # Postprocessing
-# Remove $DIAG_DIR
-if [[ "${REMOVE_DIAG_DIR}" == "YES" ]]; then
-    rm -rf "${DIAG_DIR}"
-fi
 
 exit 0
diff --git a/sorc/build_gdas.sh b/sorc/build_gdas.sh
index 32213153423..e49cc00429c 100755
--- a/sorc/build_gdas.sh
+++ b/sorc/build_gdas.sh
@@ -13,11 +13,9 @@ while getopts ":j:dv" option; do
     v) _opts+="-v ";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
-      usage
       ;;
     *)
       echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
       ;;
   esac
 done
diff --git a/sorc/build_gsi_enkf.sh b/sorc/build_gsi_enkf.sh
index 09cf250acf2..badba6c332d 100755
--- a/sorc/build_gsi_enkf.sh
+++ b/sorc/build_gsi_enkf.sh
@@ -9,11 +9,9 @@ while getopts ":j:dv" option; do
     v) BUILD_VERBOSE="YES";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
-      usage
       ;;
     *)
       echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
       ;;
   esac
 done
@@ -33,4 +31,3 @@ REGRESSION_TESTS=NO \
 "${HOMEgfs_}/sorc/gsi_enkf.fd/ush/build.sh"
 
 exit
-
diff --git a/sorc/build_gsi_monitor.sh b/sorc/build_gsi_monitor.sh
index d355067f127..e982f14f703 100755
--- a/sorc/build_gsi_monitor.sh
+++ b/sorc/build_gsi_monitor.sh
@@ -12,11 +12,9 @@ while getopts ":j:dv" option; do
     v) BUILD_VERBOSE="YES";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
-      usage
       ;;
     *)
       echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
       ;;
   esac
 done
diff --git a/sorc/build_ufs_utils.sh b/sorc/build_ufs_utils.sh
index 2284b151343..e6698bb5008 100755
--- a/sorc/build_ufs_utils.sh
+++ b/sorc/build_ufs_utils.sh
@@ -12,11 +12,9 @@ while getopts ":j:dv" option; do
     v) BUILD_VERBOSE="YES";;
     :)
       echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
-      usage
       ;;
     *)
       echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-      usage
       ;;
   esac
 done
@@ -31,4 +29,3 @@ BUILD_VERBOSE=${BUILD_VERBOSE:-} \
 "${HOMEgfs_}/sorc/ufs_utils.fd/build_all.sh"
 
 exit
-
diff --git a/sorc/build_ww3prepost.sh b/sorc/build_ww3prepost.sh
index 19133b12972..5408a5c390c 100755
--- a/sorc/build_ww3prepost.sh
+++ b/sorc/build_ww3prepost.sh
@@ -16,11 +16,9 @@ while getopts ":j:a:dvw" option; do
   w) PDLIB="OFF" ;;
   :)
     echo "[${BASH_SOURCE[0]}]: ${option} requires an argument"
-    usage
     ;;
   *)
     echo "[${BASH_SOURCE[0]}]: Unrecognized option: ${option}"
-    usage
     ;;
   esac
 done
diff --git a/ush/gaussian_sfcanl.sh b/ush/gaussian_sfcanl.sh
index 70780e63a8a..0652c0117c5 100755
--- a/ush/gaussian_sfcanl.sh
+++ b/ush/gaussian_sfcanl.sh
@@ -23,35 +23,12 @@
 #     CASE          Forecast model and restart resolution.  Defaults to C768.
 #     CASE_HIST     History file output resolution.  Defaults to $CASE.
 #     DONST         Process NST fields when 'yes'.  Default is 'no'.
-#     OUTPUT_FILE   Output gaussian analysis file format.  Default is "nemsio"
-#                   Set to "netcdf" for netcdf output file
-#                   Otherwise, output in nemsio.
 #     FIXWGTS       Weight file to use for interpolation
-#     DATA          Working directory
-#                   (if nonexistent will be made, used and deleted)
-#                   Defaults to current working directory
 #     COMOUT        Output directory
 #                   (if nonexistent will be made)
 #                   defaults to current working directory
-#     XC            Suffix to add to executables. Defaults to none.
 #     GAUSFCANLEXE  Program executable.
 #                   Defaults to $EXECgfs/gaussian_sfcanl.x
-#     INISCRIPT     Preprocessing script.  Defaults to none.
-#     LOGSCRIPT     Log posting script.  Defaults to none.
-#     ENDSCRIPT     Postprocessing script
-#                   defaults to none
-#     PGMOUT        Executable standard output
-#                   defaults to $pgmout, then to '&1'
-#     PGMERR        Executable standard error
-#                   defaults to $pgmerr, then to '&1'
-#     pgmout        Executable standard output default
-#     pgmerr        Executable standard error default
-#     REDOUT        standard output redirect ('1>' or '1>>')
-#                   defaults to '1>', or to '1>>' to append if $PGMOUT is a file
-#     REDERR        standard error redirect ('2>' or '2>>')
-#                   defaults to '2>', or to '2>>' to append if $PGMERR is a file
-#     VERBOSE       Verbose flag (YES or NO)
-#                   defaults to NO
 #     gfs_ver       Version number of gfs directory.  Default is
 #                   v15.0.0.
 #     OMP_NUM_
@@ -60,15 +37,11 @@
 #                   Default is none.
 #
 #   Exported Shell Variables:
-#     PGM           Current program name
 #     pgm
-#     ERR           Last return code
 #     err
 #
 #   Modules and files referenced:
-#     scripts    : $INISCRIPT
-#                  $LOGSCRIPT
-#                  $ENDSCRIPT
+#     scripts    :
 #
 #     programs   : $GAUSFCANLEXE
 #
@@ -77,10 +50,9 @@
 #                  ${FIXgfs}/am/global_hyblev.l65.txt
 #
 #     input data : ${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile*.nc
+#                  ${COMIN_ATMOS_ANALYSIS}/increment.sfc.i006.tile${i}.nc"
 #
-#     output data: $PGMOUT
-#                  $PGMERR
-#                  $COMOUT/${APREFIX}analysis.sfc.a006.nc
+#     output data: $COMOUT/${APREFIX}analysis.sfc.a006.nc
 #
 # Remarks:
 #
@@ -95,7 +67,6 @@
 #
 # Attributes:
 #   Language: POSIX shell
-#   Machine: IBM SP
 #
 ################################################################################
 
@@ -104,94 +75,69 @@ CASE_HIST=${CASE_HIST:-${CASE}}
 resh=${CASE_HIST:1}
 LONB_CASE=$((resh*4))
 LATB_CASE=$((resh*2))
-LONB_SFC=${LONB_SFC:-$LONB_CASE}
-LATB_SFC=${LATB_SFC:-$LATB_CASE}
+LONB_SFC=${LONB_SFC:-${LONB_CASE}}
+LATB_SFC=${LATB_SFC:-${LATB_CASE}}
 DONST=${DONST:-"NO"}
 LEVS=${LEVS:-64}
-LEVSP1=$(($LEVS+1))
+LEVSP1=$(( LEVS + 1 ))
 FIXWGTS=${FIXWGTS:-${FIXorog}/${CASE}/fv3_SCRIP_${CASE}_GRIDSPEC_lon${LONB_SFC}_lat${LATB_SFC}.gaussian.neareststod.nc}
 
 #  Filenames.
-XC=${XC:-}
-GAUSFCANLEXE=${GAUSFCANLEXE:-$EXECgfs/gaussian_sfcanl.x}
+GAUSFCANLEXE=${GAUSFCANLEXE:-${EXECgfs}/gaussian_sfcanl.x}
 SIGLEVEL=${SIGLEVEL:-${FIXgfs}/am/global_hyblev.l${LEVSP1}.txt}
 
 #  Other variables.
-export PGMOUT=${PGMOUT:-${pgmout:-'&1'}}
-export PGMERR=${PGMERR:-${pgmerr:-'&2'}}
-export REDOUT=${REDOUT:-'1>'}
-export REDERR=${REDERR:-'2>'}
 
 # Set defaults
 ################################################################################
 #  Preprocessing
-${INISCRIPT:-}
-pwd=$(pwd)
-if [[ ! -d "${COMOUT_ATMOS_ANALYSIS}" ]]; then
-   mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
-fi
 
 ################################################################################
 #  Make surface analysis
-export PGM=$GAUSFCANLEXE
-export pgm=$PGM
-$LOGSCRIPT
-
-iy=${PDY:0:4}
-im=${PDY:4:2}
-id=${PDY:6:2}
-ih=${cyc}
-
-export OMP_NUM_THREADS=${OMP_NUM_THREADS_SFC:-1}
-
 # input interpolation weights
-${NLN} "${FIXWGTS}" "./weights.nc"
+cpreq "${FIXWGTS}" "./weights.nc"
 
 # input analysis tiles (with nst records)
-${NLN} "${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"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile1.nc" "./anal.tile1.nc"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile2.nc" "./anal.tile2.nc"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile3.nc" "./anal.tile3.nc"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile4.nc" "./anal.tile4.nc"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile5.nc" "./anal.tile5.nc"
+cpreq "${COMIN_ATMOS_RESTART}/${PDY}.${cyc}0000.sfcanl_data.tile6.nc" "./anal.tile6.nc"
 
 # input orography tiles
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile1.nc" "./orog.tile1.nc"
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile2.nc" "./orog.tile2.nc"
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile3.nc" "./orog.tile3.nc"
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile4.nc" "./orog.tile4.nc"
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile5.nc" "./orog.tile5.nc"
-${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile6.nc" "./orog.tile6.nc"
-
-${NLN} "${SIGLEVEL}" "./vcoord.txt"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile1.nc" "./orog.tile1.nc"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile2.nc" "./orog.tile2.nc"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile3.nc" "./orog.tile3.nc"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile4.nc" "./orog.tile4.nc"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile5.nc" "./orog.tile5.nc"
+cpreq "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile6.nc" "./orog.tile6.nc"
 
-# output gaussian global surface analysis files
-${NLN} "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}analysis.sfc.a006.nc" "./sfc.gaussian.analysis.file"
+cpreq "${SIGLEVEL}" "./vcoord.txt"
 
 # Namelist uses booleans now
-if [[ ${DONST} == "YES" ]]; then do_nst='.true.'; else do_nst='.false.'; fi
+if [[ "${DONST}" == "YES" ]]; then
+    do_nst=".true."
+else
+    do_nst=".false."
+fi
 
-#Add soil increments to gdas gaussian sfcanal if they are not added by gcycle (i.e., when landiau=true)
+# Add soil increments to gdas gaussian sfcanal if they are not added by gcycle (i.e., when landiau=true)
 LSOIL_INCR=${LSOIL_INCR:-2}
-if [[ "${DO_LAND_IAU:-.false.}" == ".true." ]]; then   
+if [[ "${DO_LAND_IAU:-.false.}" == ".true." ]]; then
     for i in $(seq 1 6); do
-	sfc_inc="${COMOUT_ATMOS_ANALYSIS}/increment.sfc.i006.tile${i}.nc"
-        if [[ ! -f "${sfc_inc}" ]]; then
-            echo "Error! gaussian sfc analysis missing increment file ${sfc_inc}"
-            exit 1
-        else
-            ${NLN} "${sfc_inc}" "./sfc_inc.tile${i}.nc"
-        fi
+        sfc_inc="${COMIN_ATMOS_ANALYSIS}/increment.sfc.i006.tile${i}.nc"
+        cpreq "${sfc_inc}" "./sfc_inc.tile${i}.nc"
     done
 fi
 
 # Executable namelist
 cat <<EOF > fort.41
- &setup
-  yy=${iy},
-  mm=${im},
-  dd=${id},
-  hh=${ih},
+&setup
+  yy=${PDY:0:4},
+  mm=${PDY:4:2},
+  dd=${PDY:6:2},
+  hh=${cyc},
   igaus=${LONB_SFC},
   jgaus=${LATB_SFC},
   donst=${do_nst},
@@ -200,19 +146,25 @@ cat <<EOF > fort.41
   add_soil_inc=${DO_LAND_IAU},
   lsoil_incr=${LSOIL_INCR},
   sfc_inc_file="./sfc_inc",
- /
+/
 EOF
+cat fort.41
 
+export pgm="${GAUSFCANLEXE}"
+export OMP_NUM_THREADS=${OMP_NUM_THREADS_SFC:-1}
 ${APRUNSFC} "${GAUSFCANLEXE}"
-
 export err=$?
 if [[ ${err} -ne 0 ]]; then
    echo "FATAL ERROR: ${GAUSFCANLEXE} returned non-zero exit status!"
    exit "${err}"
 fi
 
+# output gaussian global surface analysis files
+if [[ -f "sfc.gaussian.analysis.file" ]]; then
+    cpfs "./sfc.gaussian.analysis.file" "${COMOUT_ATMOS_ANALYSIS}/${APREFIX}analysis.sfc.a006.nc"
+fi
+
 ################################################################################
 #  Postprocessing
-cd "${pwd}"
 
 exit 0
diff --git a/ush/python/pygfs/task/stage_ic.py b/ush/python/pygfs/task/stage_ic.py
index cbec76c78f0..873d4346593 100644
--- a/ush/python/pygfs/task/stage_ic.py
+++ b/ush/python/pygfs/task/stage_ic.py
@@ -220,6 +220,16 @@ def execute_stage(self, stage_dict: AttrDict) -> None:
 
         stage_set = parse_j2yaml(stage_dict.STAGE_IC_YAML_TMPL, stage_dict, allow_missing=False)
 
+        # Parse staging yaml to get list of files to stage
+        stage_set = parse_j2yaml(self.task_config.STAGE_IC_YAML_TMPL, stage_dict, allow_missing=False)
+        logger.info(stage_set)
+
+        # Write stage_set to a file in DATA for debugging
+        stage_yaml = f"./stage{stage_dict.member:03}.yaml"
+        stage_set.save(stage_yaml)
+        logger.debug(f"Staging yaml written to '{stage_yaml}' for debugging purposes.")
+
+        # stage files to ROTDIR
         for key in stage_set.keys():
             FileHandler(stage_set[key]).sync()
 
diff --git a/ush/regrid_gsiSfcIncr_to_tile.sh b/ush/regrid_gsiSfcIncr_to_tile.sh
index aa922229f6c..5e2fe1cf59f 100755
--- a/ush/regrid_gsiSfcIncr_to_tile.sh
+++ b/ush/regrid_gsiSfcIncr_to_tile.sh
@@ -9,12 +9,6 @@ source "${HOMEgfs}/ush/atparse.bash"
 # David New, Nov 2025 (parallelization updates)
 #-------------------------------------------------------------------------------------------------
 
-export PGMOUT=${PGMOUT:-${pgmout:-'&1'}}
-export PGMERR=${PGMERR:-${pgmerr:-'&2'}}
-
-export PGM=${REGRID_EXEC}
-export pgm=${PGM}
-
 NMEM_REGRID=${NMEM_REGRID:-1}
 CASE_IN=${CASE_IN:-${CASE_ENS}}
 LFHR=${LFHR:-6}
@@ -31,13 +25,9 @@ LSOIL_INCR=${LSOIL_INCR:-2}
 
 export n_vars=$(( LSOIL_INCR*2 ))
 
-soil_incr_vars=""
-for vi in $( seq 1 "${LSOIL_INCR}" ); do
-    soil_incr_vars=${soil_incr_vars}'"soilt'${vi}'_inc"',
-done
-for vi in $( seq 1 "${LSOIL_INCR}" ); do
-    soil_incr_vars=${soil_incr_vars}'"slc'${vi}'_inc"',
-done
+soilt_incr_vars=$(seq -s ',' -f '"soilt%g_inc"' 1 "${LSOIL_INCR}")
+slc_incr_vars=$(seq -s ',' -f '"slc%g_inc"' 1 "${LSOIL_INCR}")
+export soil_incr_vars="${soilt_incr_vars},${slc_incr_vars}"
 
 if [[ "${DO_LAND_IAU}" = ".true." ]]; then
     IFS=',' read -ra landifhrs <<< "${IAUFHRS}"
@@ -52,9 +42,9 @@ export jres=${LATB_CASE_IN}
 export ireso=${CASE_OUT:1}
 export jreso=${CASE_OUT:1}
 
-regrid_nml_tmpl="${PARMgfs}/regrid_sfc/regrid.nml_tmpl" 
+regrid_nml_tmpl="${PARMgfs}/regrid_sfc/regrid.nml_tmpl"
 
-if (( LFHR >= 0 )); then
+if [[ "${LFHR}" -ge 0 ]]; then
     soilinc_fhrs=("${LFHR}")
 else # construct restart times for deterministic member
     soilinc_fhrs=("${assim_freq}") # increment file at middle of window
@@ -64,14 +54,14 @@ else # construct restart times for deterministic member
     fi
 fi
 
-#
 # Stage input files
-#
+
+cd "${DATA}" || exit 1
 
 # Create MDMD command file for fixed files
-rm -f cmdfile.0
-touch cmdfile.0
-chmod 755 cmdfile.0
+rm -f cmdfile_in.0
+touch cmdfile_in.0
+chmod 755 cmdfile_in.0
 
 # Append fixed files command file to master command file
 {
@@ -91,80 +81,148 @@ for n in $(seq 1 "${ntiles}"); do
     echo "cpreq ${FIXorog}/${CASE_OUT}/${CASE_OUT}_grid.tile${n}.nc \
                 ${DATA}/${CASE_OUT}_grid.tile${n}.nc"
 done
-} > cmdfile.0
+} >> cmdfile_in.0
+
+if [[ "${NMEM_REGRID}" -gt 1 ]]; then
+
+    echo "INFO: Preparing to regrid surface increments for ${NMEM_REGRID} ensemble members."
+    for imem in $(seq 1 "${NMEM_REGRID}"); do
+
+        memdir=$(printf "mem%03i" "${imem}")
+
+        MEMDIR=${memdir} YMD=${PDY} HH=${cyc} declare_from_tmpl \
+            COMIN_SOIL_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL \
+            COMOUT_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
+
+        # Create MPMD command file for this member
+        rm -f "cmdfile_in.${imem}" "cmdfile_out.${imem}"
+        touch "cmdfile_in.${imem}" "cmdfile_out.${imem}"
+        chmod 755 "cmdfile_in.${imem}" "cmdfile_out.${imem}"
 
-for imem in $(seq 1 "${NMEM_REGRID}"); do
-    cmem=$(printf %03i "${imem}")
-    memchar="mem${cmem}"
+        # Create commands to stage input files
+        {
+        echo "#!/bin/bash"
 
-    # If deterministic job, COMOUT_ATMOS_ANALYSIS_MEM is just COMOUT_ATMOS_ANALYSIS
-    if (( NMEM_REGRID > 1 )); then
-        MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl \
-            COMIN_SOIL_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
+        echo "mkdir -p ${DATA}/${memdir}"
 
-        memdir="${DATA}/${memchar}"
-        mkdir -p "${memdir}"
+        for FHR in "${soilinc_fhrs[@]}"; do
+            echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}increment.sfc.i00${FHR}.nc \
+                        ${DATA}/${memdir}/sfci00${FHR}.nc"
+        done
 
-        if [[ "${imem}" -gt 1 ]]; then
-            in_dir+=", "
+        if [[ "${DO_LAND_IAU}" = ".true." ]]; then
+            for FHI in "${landifhrs[@]}"; do
+                echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}increment.sfc.i00${FHI}.nc \
+                            ${DATA}/${memdir}/sfci00${FHI}.nc"
+            done
+        fi
+        } >> "cmdfile_in.${imem}"
+
+        # Create commands to copy output files
+        {
+        echo "#!/bin/bash"
+
+        if [[ "${DO_LAND_IAU}" = ".false." || "${RUN}" == "gdas" || "${RUN}" == "gfs" ]]; then
+            for FHR in "${soilinc_fhrs[@]}"; do
+                for n in $(seq 1 "${ntiles}"); do
+                    echo "cpfs ${DATA}/${memdir}/sfci00${FHR}.mem${imem}.tile${n}.nc \
+                          ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.i00${FHR}.tile${n}.nc"
+                done
+            done
         fi
-        in_dir+="\"./${memchar}/\""        
-    else
-        # If deterministic job, memdir is just DATA
-        memdir="${DATA}"
 
-        in_dir="'./'"
-    fi
+        if [[ "${DO_LAND_IAU}" = ".true." ]]; then
+            for n in $(seq 1 "${ntiles}"); do
+                echo "cpfs ${DATA}/${memdir}/sfci.mem${imem}.tile${n}.nc \
+                      ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.tile${n}.nc"
+            done
+        fi
+        } >> "cmdfile_out.${imem}"
 
-    # Create MPMD command file for this member
-    rm -f "cmdfile.${imem}"
-    touch "cmdfile.${imem}"
-    chmod 755 "cmdfile.${imem}"
+    done  # for imem in $(seq 1 "${NMEM_REGRID}"); do
+    in_dir=$(seq -s ", " -f "'./mem%03g/'" 1 "${NMEM_REGRID}")
 
-    # Create commands to stage input files
-    {
-    echo "#!/bin/bash"
+else  # deterministic member only (NMEM_REGRID=1)
 
+    echo "INFO: Preparing to regrid surface increments for deterministic member."
+
+    # Create commands to stage input files and append to the cmdfile.0
+    {
     for FHR in "${soilinc_fhrs[@]}"; do
-        echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}increment.sfc.i00${FHR}.nc \
-                    ${memdir}/sfci00${FHR}.nc"
-    done 
+        echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}ensmean_increment.sfc.i00${FHR}.nc \
+                    ${DATA}/sfci00${FHR}.nc"
+    done
 
-    if [[ "${DO_LAND_IAU}" = ".true." ]]; then 
+    if [[ "${DO_LAND_IAU}" = ".true." ]]; then
         for FHI in "${landifhrs[@]}"; do
-            echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}increment.sfc.i00${FHI}.nc \
-                        ${memdir}/sfci00${FHI}.nc"
+            echo "cpreq ${COMIN_SOIL_ANALYSIS_MEM}/${APREFIX_ENS}ensmean_increment.sfc.i00${FHI}.nc \
+                        ${DATA}/sfci00${FHI}.nc"
         done
     fi
-    } > "cmdfile.${imem}"
-done
+    } >> "cmdfile_in.0"
+    in_dir="'./'"
 
-# Create master MPMD command file
-rm -f cmdfile
-touch cmdfile
-chmod 755 cmdfile
+    # Create commands to copy output files
+    rm -f cmdfile_out.0
+    touch cmdfile_out.0
+    chmod 755 cmdfile_out.0
+    {
+    echo "#!/bin/bash"
+
+    if [[ "${DO_LAND_IAU}" = ".false." || "${RUN}" == "gdas" || "${RUN}" == "gfs" ]]; then
+        for FHR in "${soilinc_fhrs[@]}"; do
+            for n in $(seq 1 "${ntiles}"); do
+                echo "cpfs ${DATA}/sfci00${FHR}.mem1.tile${n}.nc \
+                      ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.i00${FHR}.tile${n}.nc"
+            done
+        done
+    fi
+
+    if [[ "${DO_LAND_IAU}" = ".true." ]]; then
+        for n in $(seq 1 "${ntiles}"); do
+            echo "cpfs ${DATA}/sfci.mem1.tile${n}.nc \
+                  ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.tile${n}.nc"
+        done
+    fi
+    } >> "cmdfile_out.0"
+
+
+fi
+
+# Create master MPMD command files for input and output
+rm -f cmdfile_in cmdfile_out
+touch cmdfile_in cmdfile_out
 
 # Append all members' command files to master command file
-{
-echo "${DATA}/cmdfile.0" # fixed files
-for imem in $(seq 1 "${NMEM_REGRID}"); do
-    echo "${DATA}/cmdfile.${imem}"
-done
-} >> cmdfile
+if [[ -f cmdfile_in.0 ]]; then
+    echo "${DATA}/cmdfile_in.0" >> cmdfile_in
+fi
+if [[ -f cmdfile_out.0 ]]; then
+    echo "${DATA}/cmdfile_out.0" >> cmdfile_out
+fi
+if [[ "${NMEM_REGRID}" -gt 1 ]]; then
+    for imem in $(seq 1 "${NMEM_REGRID}"); do
+        if [[ -f "cmdfile_in.${imem}" ]]; then
+            echo "${DATA}/cmdfile_in.${imem}" >> cmdfile_in
+        fi
+        if [[ -f "cmdfile_out.${imem}" ]]; then
+            echo "${DATA}/cmdfile_out.${imem}" >> cmdfile_out
+        fi
+    done
+fi
 
 # Run MPMD to stage input files
-"${USHgfs}/run_mpmd.sh" "cmdfile" && true
+"${USHgfs}/run_mpmd.sh" "cmdfile_in" && true
 export err=$?
 if [[ ${err} -ne 0 ]]; then
-    err_exit "run_mpmd.sh failed!"
+    err_exit "run_mpmd.sh failed to copy input and fix data!"
 fi
+mv mpmd.out mpmd_in.out
 
 # Finish defining input/output directory list
 export out_dir="${in_dir}"
 
-#
-# Regrid soil increments and save to COMOUT
-#
+# Regrid soil increments
 
 # Increments for offline analysis
 # If land IAU --> deterministic only. If no land IAU --> both deterministic and ensemble
@@ -180,10 +238,11 @@ if [[ "${DO_LAND_IAU}" = ".false." || "${RUN}" == "gdas" || "${RUN}" == "gfs" ]]
         atparse < "${regrid_nml_tmpl}" >> "regrid.nml"
 
         # Run regrid executable
-        ${APRUN_REGRID} "${REGRID_EXEC}" 1>"${PGMOUT}" 2>"${PGMERR}"
+        export pgm="${REGRID_EXEC}"
+        ${APRUN_REGRID} "${REGRID_EXEC}"
     	export err=$?
 	    if [[ ${err} -ne 0 ]]; then
-	        err_exit "${REGRID_EXEC} failed, ABORT!"
+	        err_exit "${REGRID_EXEC} failed to regrid soil increments (without LANDIAU), ABORT!"
 	    fi
     done
 fi
@@ -202,75 +261,19 @@ if [[ "${DO_LAND_IAU}" = ".true." ]]; then
 
     # Run regrid executable
     export pgm="${REGRID_EXEC}"
-	${APRUN_REGRID} "${REGRID_EXEC}" 1>"${PGMOUT}" 2>"${PGMERR}"
+	${APRUN_REGRID} "${REGRID_EXEC}"
 	export err=$?
 	if [[ ${err} -ne 0 ]]; then
-	    err_exit "${pgm} failed, ABORT!"
+	    err_exit "${pgm} failed to regrid soil increments (with LANDIAU), ABORT!"
 	fi
 fi
 
-#
-# Save regridded files to COMOUT
-#
-
-for imem in $(seq 1 "${NMEM_REGRID}"); do
-    cmem=$(printf %03i "${imem}")
-    memchar="mem${cmem}"
-
-    # If deterministic job, COMOUT_ATMOS_ANALYSIS_MEM is just COMOUT_ATMOS_ANALYSIS
-    if (( NMEM_REGRID > 1 )); then
-        MEMDIR=${memchar} YMD=${PDY} HH=${cyc} declare_from_tmpl \
-            COMOUT_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
-
-        memdir="${DATA}/${memchar}"
-    else
-        # If deterministic job, memdir is just DATA
-        memdir="${DATA}"
-    fi
-
-    # Create MPMD command file for this member
-    rm -f "cmdfile.${imem}"
-    touch "cmdfile.${imem}"
-    chmod 755 "cmdfile.${imem}"
-
-    {
-    echo "#!/bin/bash"
-
-    if [[ "${DO_LAND_IAU}" = ".false." || "${RUN}" == "gdas" || "${RUN}" == "gfs" ]]; then
-        for FHR in "${soilinc_fhrs[@]}"; do
-            for n in $(seq 1 "${ntiles}"); do
-                echo "cpfs ${memdir}/sfci00${FHR}.mem${imem}.tile${n}.nc \
-                      ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.i00${FHR}.tile${n}.nc"
-            done
-        done
-    fi
-
-    if [[ "${DO_LAND_IAU}" = ".true." ]]; then
-        for n in $(seq 1 "${ntiles}"); do
-            echo "cpfs ${memdir}/sfci.mem${imem}.tile${n}.nc \
-                  ${COMOUT_ATMOS_ANALYSIS_MEM}/increment.sfc.tile${n}.nc"
-        done
-    fi
-    } > "cmdfile.${imem}"
-done
-
-# Create master MPMD command file
-rm -f cmdfile
-touch cmdfile
-chmod 755 cmdfile
-
-# Append all members' command files to master command file
-{
-for imem in $(seq 1 "${NMEM_REGRID}"); do
-    echo "${DATA}/cmdfile.${imem}"
-done
-} >> cmdfile
-
 # Run MPMD to save output files
-"${USHgfs}/run_mpmd.sh" "cmdfile" && true
+"${USHgfs}/run_mpmd.sh" "cmdfile_out" && true
 export err=$?
 if [[ ${err} -ne 0 ]]; then
-    err_exit "run_mpmd.sh failed!"
+    err_exit "run_mpmd.sh failed to copy output files to COMOUT, ABORT!"
 fi
+mv mpmd.out mpmd_out.out
 
 exit 0