diff --git a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
index f25da9b488..332ce23ff7 100755
--- a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
+++ b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
@@ -24,8 +24,6 @@ GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
@@ -44,7 +42,7 @@ export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
 export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
 
 
-export ATMGES="${COMIN_GES}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES="${COMIN_GES}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
@@ -52,7 +50,7 @@ fi
 
 
 if [ ${DOHYBVAR} = "YES" ]; then
-    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean${GSUFFIX}"
+    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
         echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
         exit 2
diff --git a/jobs/JGDAS_ATMOS_CHGRES_FORENKF b/jobs/JGDAS_ATMOS_CHGRES_FORENKF
index b1572e98cb..1e2e9ec2ac 100755
--- a/jobs/JGDAS_ATMOS_CHGRES_FORENKF
+++ b/jobs/JGDAS_ATMOS_CHGRES_FORENKF
@@ -25,9 +25,6 @@ GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
-
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
diff --git a/jobs/JGDAS_ENKF_DIAG b/jobs/JGDAS_ENKF_DIAG
index a9d65823c1..bc4c2eec49 100755
--- a/jobs/JGDAS_ENKF_DIAG
+++ b/jobs/JGDAS_ENKF_DIAG
@@ -29,8 +29,6 @@ export CDUMP_OBS=${CDUMP_OBS:-${CDUMP}}
 export OPREFIX="${CDUMP_OBS}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
-export GSUFFIX="${GSUFFIX:-".ensmean${SUFFIX}"}"
-export ASUFFIX="${ASUFFIX:-"${SUFFIX}"}"
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/${COMPONENT}}
@@ -48,7 +46,7 @@ export COMIN_GES=${COMIN_GES_ENS}
 export COMOUT="${ROTDIR}/enkf${CDUMP}.${PDY}/${cyc}"
 
 
-export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean.nc"
 if [ ! -f ${ATMGES_ENSMEAN} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
     exit 1
diff --git a/jobs/JGDAS_ENKF_ECEN b/jobs/JGDAS_ENKF_ECEN
index bf33ecc3f6..8a566a2b06 100755
--- a/jobs/JGDAS_ENKF_ECEN
+++ b/jobs/JGDAS_ENKF_ECEN
@@ -35,8 +35,6 @@ export OPREFIX="${CDUMP}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 export APREFIX_ENKF="${CDUMP_ENKF}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/atmos}
diff --git a/jobs/JGDAS_ENKF_SELECT_OBS b/jobs/JGDAS_ENKF_SELECT_OBS
index 7995a68093..e456cec892 100755
--- a/jobs/JGDAS_ENKF_SELECT_OBS
+++ b/jobs/JGDAS_ENKF_SELECT_OBS
@@ -29,8 +29,7 @@ export CDUMP_OBS=${CDUMP_OBS:-${CDUMP}}
 export OPREFIX="${CDUMP_OBS}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
-export GSUFFIX="${GSUFFIX:-".ensmean${SUFFIX}"}"
-export ASUFFIX="${ASUFFIX:-"${SUFFIX}"}"
+export GSUFFIX=".ensmean.nc"
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/${COMPONENT}}
diff --git a/jobs/JGDAS_ENKF_SFC b/jobs/JGDAS_ENKF_SFC
index 06c2c32391..dc5cff2b00 100755
--- a/jobs/JGDAS_ENKF_SFC
+++ b/jobs/JGDAS_ENKF_SFC
@@ -35,8 +35,6 @@ export OPREFIX="${CDUMP}.t${cyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 export APREFIX_ENKF="${CDUMP_ENKF}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/atmos}
diff --git a/jobs/JGDAS_ENKF_UPDATE b/jobs/JGDAS_ENKF_UPDATE
index ae3ddb0145..55ad4a05ae 100755
--- a/jobs/JGDAS_ENKF_UPDATE
+++ b/jobs/JGDAS_ENKF_UPDATE
@@ -22,9 +22,6 @@ gcyc=$(echo ${GDATE} | cut -c9-10)
 
 export APREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="gdas.t${gcyc}z."
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-
 
 # COMIN_GES_ENS and COMOUT_ANL_ENS are used in script
 export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
index 49dcd5f21c..e44e607581 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
index 9a21d032e2..093fccdd5a 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
index 32722f4ba3..876598ff7e 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
index 6022cc548a..e1d53b552e 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 export COMOUT_ENS=${COMOUT_ENS:-${ROTDIR}/enkf${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
index 48b4a5b99b..7b3ecee7ca 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 export COMOUT_ENS=${COMOUT_ENS:-${ROTDIR}/enkf${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
diff --git a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
index 2afbc9028e..45368d51ff 100755
--- a/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
+++ b/jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
@@ -23,8 +23,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
 export COMOUT_ENS=${COMOUT_ENS:-${ROTDIR}/enkf${CDUMP}.${PDY}/${cyc}/${COMPONENT}}
diff --git a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
index 6f4c4f29c3..8f51c2c1e1 100755
--- a/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
+++ b/jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
@@ -24,8 +24,6 @@ export GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
 
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS b/jobs/JGLOBAL_ATMOS_ANALYSIS
index ef504ba708..7c2a11b4be 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -27,8 +27,6 @@ GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
 
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
@@ -47,7 +45,7 @@ export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
 export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
 
 
-export ATMGES="${COMIN_GES}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES="${COMIN_GES}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
@@ -61,7 +59,7 @@ status=$?
 
 
 if [ ${DOHYBVAR} = "YES" ]; then
-    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean${GSUFFIX}"
+    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
         echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
         exit 2
diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
index b2f0fda786..801fc8f465 100755
--- a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
+++ b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -25,9 +25,6 @@ GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
-
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
@@ -45,7 +42,7 @@ export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
 export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
 
 
-export ATMGES="${COMIN_GES}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES="${COMIN_GES}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
@@ -59,7 +56,7 @@ status=$?
 
 
 if [ ${DOHYBVAR} = "YES" ]; then
-    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean${GSUFFIX}"
+    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
         echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
         exit 2
diff --git a/jobs/JGLOBAL_ATMOS_SFCANL b/jobs/JGLOBAL_ATMOS_SFCANL
index 151fd3d272..063438c9c7 100755
--- a/jobs/JGLOBAL_ATMOS_SFCANL
+++ b/jobs/JGLOBAL_ATMOS_SFCANL
@@ -27,9 +27,6 @@ GDUMP=${GDUMP:-"gdas"}
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
-export GSUFFIX=${GSUFFIX:-${SUFFIX}}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
-
 
 if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN=${COMIN:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
@@ -47,7 +44,7 @@ export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
 export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
 
 
-export ATMGES="${COMIN_GES}/${GPREFIX}atmf006${GSUFFIX}"
+export ATMGES="${COMIN_GES}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
     echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
     exit 1
diff --git a/jobs/rocoto/vrfy.sh b/jobs/rocoto/vrfy.sh
index 53806c66a2..6324eec568 100755
--- a/jobs/rocoto/vrfy.sh
+++ b/jobs/rocoto/vrfy.sh
@@ -69,7 +69,7 @@ if [ ${VRFYFITS} = "YES" -a ${CDUMP} = ${CDFNL} -a ${CDATE} != ${SDATE} ]; then
     xdate=$(${NDATE} -${VBACKUP_FITS} ${CDATE})
 
     export RUN_ENVIR_SAVE=${RUN_ENVIR}
-    export RUN_ENVIR=${OUTPUT_FILE}
+    export RUN_ENVIR="netcdf"
 
     ${PREPQFITSH} ${PSLOT} ${xdate} ${ROTDIR} ${ARCDIR} ${TMPDIR}
 
diff --git a/parm/config/config.aero b/parm/config/config.aero
old mode 100644
new mode 100755
diff --git a/parm/config/config.aerosol_init b/parm/config/config.aerosol_init
old mode 100644
new mode 100755
diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
index 348f6c1f84..42f86e0fa6 100755
--- a/parm/config/config.base.emc.dyn
+++ b/parm/config/config.base.emc.dyn
@@ -271,15 +271,9 @@ export restart_interval_gfs=0
 
 export QUILTING=".true."
 export OUTPUT_GRID="gaussian_grid"
-export OUTPUT_FILE="netcdf"
-export WRITE_DOPOST=".true."  # WRITE_DOPOST=true, use inline POST
+export WRITE_DOPOST=".true." # WRITE_DOPOST=true, use inline POST
 export WRITE_NSFLIP=".true."
 
-# suffix options depending on file format
-export SUFFIX=".nc"
-export NEMSIO_IN=".false."
-export NETCDF_IN=".true."
-
 # IAU related parameters
 export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
 export IAUFHRS="3,6,9"
diff --git a/parm/config/config.base.nco.static b/parm/config/config.base.nco.static
index 8d8301ced9..4e42a82863 100755
--- a/parm/config/config.base.nco.static
+++ b/parm/config/config.base.nco.static
@@ -162,23 +162,14 @@ export ILPOST=1           # gempak output frequency up to F120
 # frequency for saving restart files. set to 6,12,24,48 etc
 export restart_interval_gfs=12
 
+# I/O QUILTING, true--use Write Component; false--use GFDL FMS
+# if quilting=true, choose OUTPUT_GRID as cubed_sphere_grid in netcdf or gaussian_grid
+# WRITE_DOPOST=true, use inline POST
 export QUILTING=".true."
 export OUTPUT_GRID="gaussian_grid"
-export OUTPUT_FILE="netcdf"
-export WRITE_DOPOST=".true."  # WRITE_DOPOST=true, use inline POST
+export WRITE_DOPOST=".true." # WRITE_DOPOST=true, use inline POST
 export WRITE_NSFLIP=".true."
 
-# suffix options depending on file format
-if [ $OUTPUT_FILE = "netcdf" ]; then
-    export SUFFIX=".nc"
-    export NEMSIO_IN=".false."
-    export NETCDF_IN=".true."
-else
-    export SUFFIX=".nemsio"
-    export NEMSIO_IN=".true."
-    export NETCDF_IN=".false."
-fi
-
 # IAU related parameters
 export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
 export IAUFHRS="3,6,9"
@@ -239,11 +230,6 @@ export nst_anl=.true.
 # Analysis increments to zero in CALCINCEXEC
 export INCREMENTS_TO_ZERO="'liq_wat_inc','icmr_inc'"
 
-if [ $OUTPUT_FILE = "nemsio" ]; then
-    export DO_CALC_INCREMENT="YES"
-    export DO_CALC_ANALYSIS="NO"
-fi
-
 # Stratospheric increments to zero
 export INCVARS_ZERO_STRAT="'sphum_inc','liq_wat_inc','icmr_inc'"
 export INCVARS_EFOLD="5"
diff --git a/parm/config/config.defaults.s2sw b/parm/config/config.defaults.s2sw
old mode 100644
new mode 100755
diff --git a/parm/config/config.ice b/parm/config/config.ice
old mode 100644
new mode 100755
diff --git a/parm/config/config.ocn b/parm/config/config.ocn
old mode 100644
new mode 100755
diff --git a/parm/config/config.ocnanal b/parm/config/config.ocnanal
old mode 100644
new mode 100755
diff --git a/parm/config/config.ocnanalpost b/parm/config/config.ocnanalpost
old mode 100644
new mode 100755
diff --git a/parm/config/config.ocnanalrun b/parm/config/config.ocnanalrun
old mode 100644
new mode 100755
diff --git a/parm/config/config.sfcanl b/parm/config/config.sfcanl
old mode 100644
new mode 100755
diff --git a/scripts/exgdas_atmos_chgres_forenkf.sh b/scripts/exgdas_atmos_chgres_forenkf.sh
index 254ab206f6..0662720c42 100755
--- a/scripts/exgdas_atmos_chgres_forenkf.sh
+++ b/scripts/exgdas_atmos_chgres_forenkf.sh
@@ -63,24 +63,23 @@ SIGLEVEL=${SIGLEVEL:-${FIXgsm}/global_hyblev.l${LEVS}.txt}
 
 # forecast files
 APREFIX=${APREFIX:-""}
-ASUFFIX=${ASUFFIX:-$SUFFIX}
 # at full resolution
-ATMF03=${ATMF03:-${COMOUT}/${APREFIX}atmf003${ASUFFIX}}
-ATMF04=${ATMF04:-${COMOUT}/${APREFIX}atmf004${ASUFFIX}}
-ATMF05=${ATMF05:-${COMOUT}/${APREFIX}atmf005${ASUFFIX}}
-ATMF06=${ATMF06:-${COMOUT}/${APREFIX}atmf006${ASUFFIX}}
-ATMF07=${ATMF07:-${COMOUT}/${APREFIX}atmf007${ASUFFIX}}
-ATMF08=${ATMF08:-${COMOUT}/${APREFIX}atmf008${ASUFFIX}}
-ATMF09=${ATMF09:-${COMOUT}/${APREFIX}atmf009${ASUFFIX}}
+ATMF03=${ATMF03:-${COMOUT}/${APREFIX}atmf003.nc}
+ATMF04=${ATMF04:-${COMOUT}/${APREFIX}atmf004.nc}
+ATMF05=${ATMF05:-${COMOUT}/${APREFIX}atmf005.nc}
+ATMF06=${ATMF06:-${COMOUT}/${APREFIX}atmf006.nc}
+ATMF07=${ATMF07:-${COMOUT}/${APREFIX}atmf007.nc}
+ATMF08=${ATMF08:-${COMOUT}/${APREFIX}atmf008.nc}
+ATMF09=${ATMF09:-${COMOUT}/${APREFIX}atmf009.nc}
 # at ensemble resolution
-ATMF03ENS=${ATMF03ENS:-${COMOUT}/${APREFIX}atmf003.ensres${ASUFFIX}}
-ATMF04ENS=${ATMF04ENS:-${COMOUT}/${APREFIX}atmf004.ensres${ASUFFIX}}
-ATMF05ENS=${ATMF05ENS:-${COMOUT}/${APREFIX}atmf005.ensres${ASUFFIX}}
-ATMF06ENS=${ATMF06ENS:-${COMOUT}/${APREFIX}atmf006.ensres${ASUFFIX}}
-ATMF07ENS=${ATMF07ENS:-${COMOUT}/${APREFIX}atmf007.ensres${ASUFFIX}}
-ATMF08ENS=${ATMF08ENS:-${COMOUT}/${APREFIX}atmf008.ensres${ASUFFIX}}
-ATMF09ENS=${ATMF09ENS:-${COMOUT}/${APREFIX}atmf009.ensres${ASUFFIX}}
-ATMFCST_ENSRES=${ATMFCST_ENSRES:-${COMOUT_ENS}/mem001/atmos/${APREFIX}atmf006${ASUFFIX}}
+ATMF03ENS=${ATMF03ENS:-${COMOUT}/${APREFIX}atmf003.ensres.nc}
+ATMF04ENS=${ATMF04ENS:-${COMOUT}/${APREFIX}atmf004.ensres.nc}
+ATMF05ENS=${ATMF05ENS:-${COMOUT}/${APREFIX}atmf005.ensres.nc}
+ATMF06ENS=${ATMF06ENS:-${COMOUT}/${APREFIX}atmf006.ensres.nc}
+ATMF07ENS=${ATMF07ENS:-${COMOUT}/${APREFIX}atmf007.ensres.nc}
+ATMF08ENS=${ATMF08ENS:-${COMOUT}/${APREFIX}atmf008.ensres.nc}
+ATMF09ENS=${ATMF09ENS:-${COMOUT}/${APREFIX}atmf009.ensres.nc}
+ATMFCST_ENSRES=${ATMFCST_ENSRES:-${COMOUT_ENS}/mem001/atmos/${APREFIX}atmf006.nc}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
index 441f8a92ab..895765c970 100755
--- a/scripts/exgdas_atmos_post.sh
+++ b/scripts/exgdas_atmos_post.sh
@@ -49,14 +49,8 @@ export JO=${LATB:-721}
 # specify default model output format: 3 for sigio and 4
 # for nemsio
 export OUTTYP=${OUTTYP:-4}
-export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export TCYC=${TCYC:-".t${cyc}z."}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
-if (( OUTTYP == 4 )) ; then
-  export SUFFIX=".nc"
-else
-  export SUFFIX=
-fi
 export machine=${machine:-WCOSS2}
 
 ###########################
@@ -75,11 +69,7 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Chuang: modify to process analysis when post_times is 00
 stime="$(echo "${post_times}" | cut -c1-3)"
 export stime
-if (( OUTTYP == 4 )) ; then
-  export loganl="${COMIN}/${PREFIX}atmanl${SUFFIX}"
-else
-  export loganl="${COMIN}/${PREFIX}sanl"
-fi
+export loganl="${COMIN}/${PREFIX}atmanl.nc"
 
 if [[ "${stime}" = "anl" ]]; then
   if [[ -f "${loganl}" ]]; then
@@ -109,12 +99,11 @@ if [[ "${stime}" = "anl" ]]; then
     fi
 
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if (( OUTTYP == 4 )) ; then
-      ln -fs "${COMIN}/${PREFIX}atmanl${SUFFIX}" nemsfile
-      export NEMSINP=nemsfile
-      ln -fs "${COMIN}/${PREFIX}sfcanl${SUFFIX}" flxfile
-      export FLXINP=flxfile
-    fi
+    
+    ln -fs "${COMIN}/${PREFIX}atmanl.nc" nemsfile
+    export NEMSINP=nemsfile
+    ln -fs "${COMIN}/${PREFIX}sfcanl.nc" flxfile
+    export FLXINP=flxfile
     export PGBOUT=pgbfile
     export PGIOUT=pgifile
     export PGBOUT2=pgbfile.grib2
@@ -155,8 +144,8 @@ if [[ "${stime}" = "anl" ]]; then
       if [[ "${SENDDBN}" = 'YES' ]]; then
         run="$(echo "${RUN}" | tr '[:lower:]' '[:upper:]')"
         if [[ "${GRIBVERSION}" = 'grib2' ]]; then
-          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job}" "${COMOUT}/${PREFIX}sfc${fhr3}${SUFFIX}"
-          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SA" "${job}" "${COMIN}/${PREFIX}atm${fhr3}${SUFFIX}"
+          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_MSC_sfcanl" "${job}" "${COMOUT}/${PREFIX}sfc${fhr3}.nc"
+          "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SA" "${job}" "${COMIN}/${PREFIX}atm${fhr3}.nc"
           "${DBNROOT}/bin/dbn_alert" MODEL "GDAS_PGA_GB2" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}"
           "${DBNROOT}/bin/dbn_alert" MODEL "GDAS_PGA_GB2_WIDX" "${job}" "${COMOUT}/${PREFIX}pgrb2.1p00.${fhr3}.idx"
         fi
@@ -210,12 +199,10 @@ else   ## not_anl if_stimes
     ###############################
     [[ -f flxfile ]] && rm flxfile
     [[ -f nemsfile ]] && rm nemsfile
-    if (( OUTTYP == 4 )) ; then
-      ln -sf "${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}" nemsfile
-      export NEMSINP=nemsfile
-      ln -sf "${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}" flxfile
-      export FLXINP=flxfile
-    fi
+    ln -sf "${COMIN}/${PREFIX}atmf${fhr}.nc" nemsfile
+    export NEMSINP=nemsfile
+    ln -sf "${COMIN}/${PREFIX}sfcf${fhr}.nc" flxfile
+    export FLXINP=flxfile
 
     if (( d_fhr > 0 )); then
       export IGEN=${IGEN_FCST}
@@ -313,8 +300,8 @@ else   ## not_anl if_stimes
       # use post to generate Grib2 flux files
 
       if (( OUTTYP == 4 )) ; then
-        export NEMSINP=${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}
-        export FLXINP=${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}
+        export NEMSINP=${COMIN}/${PREFIX}atmf${fhr}.nc
+        export FLXINP=${COMIN}/${PREFIX}sfcf${fhr}.nc
         if (( d_fhr == 0 )); then
           export PostFlatFile=${PARMpost}/postxconfig-NT-GFS-FLUX-F00.txt
           export CTLFILE=${PARMpost}/postcntrl_gfs_flux_f00.xml
@@ -336,8 +323,8 @@ else   ## not_anl if_stimes
       fi
 
       if [[ "${SENDDBN}" = 'YES' ]] && [[ "${RUN}" = 'gdas' ]] && (( d_fhr % 3 == 0 )); then
-        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SF" "${job}" "${COMOUT}/${PREFIX}atmf${fhr}${SUFFIX}"
-        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_BF" "${job}" "${COMOUT}/${PREFIX}sfcf${fhr}${SUFFIX}"
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SF" "${job}" "${COMOUT}/${PREFIX}atmf${fhr}.nc"
+        "${DBNROOT}/bin/dbn_alert" MODEL "${run}_BF" "${job}" "${COMOUT}/${PREFIX}sfcf${fhr}.nc"
         "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SGB_GB2" "${job}" "${COMOUT}/${PREFIX}sfluxgrbf${fhr}.grib2"
         "${DBNROOT}/bin/dbn_alert" MODEL "${run}_SGB_GB2_WIDX ""${job}" "${COMOUT}/${PREFIX}sfluxgrbf${fhr}.grib2.idx"
       fi
diff --git a/scripts/exgdas_enkf_ecen.sh b/scripts/exgdas_enkf_ecen.sh
index 32aed709c5..41467324b2 100755
--- a/scripts/exgdas_enkf_ecen.sh
+++ b/scripts/exgdas_enkf_ecen.sh
@@ -48,9 +48,7 @@ OPREFIX=${OPREFIX:-""}
 OSUFFIX=${OSUFFIX:-""}
 APREFIX=${APREFIX:-""}
 APREFIX_ENKF=${APREFIX_ENKF:-$APREFIX}
-ASUFFIX=${ASUFFIX:-$SUFFIX}
 GPREFIX=${GPREFIX:-""}
-GSUFFIX=${GSUFFIX:-$SUFFIX}
 
 # Variables
 NMEM_ENKF=${NMEM_ENKF:-80}
@@ -111,12 +109,12 @@ for FHR in $(seq $FHMIN $FHOUT $FHMAX); do
 
 for imem in $(seq 1 $NMEM_ENKF); do
    memchar="mem"$(printf %03i $imem)
-   $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}atmf00${FHR}${ENKF_SUFFIX}$GSUFFIX ./atmges_$memchar
+   $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}atmf00${FHR}${ENKF_SUFFIX}.nc ./atmges_$memchar
    if [ $DO_CALC_INCREMENT = "YES" ]; then
       if [ $FHR -eq 6 ]; then
-         $NLN $COMIN_ENS/$memchar/atmos/${APREFIX_ENKF}atmanl$ASUFFIX ./atmanl_$memchar
+         $NLN $COMIN_ENS/$memchar/atmos/${APREFIX_ENKF}atmanl.nc ./atmanl_$memchar
       else
-         $NLN $COMIN_ENS/$memchar/atmos/${APREFIX_ENKF}atma00${FHR}$ASUFFIX ./atmanl_$memchar
+         $NLN $COMIN_ENS/$memchar/atmos/${APREFIX_ENKF}atma00${FHR}.nc ./atmanl_$memchar
       fi
    fi
    mkdir -p $COMOUT_ENS/$memchar
@@ -128,15 +126,15 @@ for imem in $(seq 1 $NMEM_ENKF); do
    if [[ $RECENTER_ENKF = "YES" ]]; then
       if [ $DO_CALC_INCREMENT = "YES" ]; then
          if [ $FHR -eq 6 ]; then
-            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratmanl$ASUFFIX ./ratmanl_$memchar
+            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratmanl.nc ./ratmanl_$memchar
          else
-            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratma00${FHR}$ASUFFIX ./ratmanl_$memchar
+            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratma00${FHR}.nc ./ratmanl_$memchar
          fi
      else
          if [ $FHR -eq 6 ]; then
-            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratminc$ASUFFIX ./ratminc_$memchar
+            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratminc.nc ./ratminc_$memchar
          else
-            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratmi00${FHR}$ASUFFIX ./ratminc_$memchar
+            $NLN $COMOUT_ENS/$memchar/atmos/${APREFIX}ratmi00${FHR}.nc ./ratminc_$memchar
          fi
      fi
    fi
@@ -145,9 +143,9 @@ done
 if [ $DO_CALC_INCREMENT = "YES" ]; then
    # Link ensemble mean analysis
    if [ $FHR -eq 6 ]; then
-      $NLN $COMIN_ENS/${APREFIX_ENKF}atmanl.ensmean$ASUFFIX ./atmanl_ensmean
+      $NLN $COMIN_ENS/${APREFIX_ENKF}atmanl.ensmean.nc ./atmanl_ensmean
    else
-      $NLN $COMIN_ENS/${APREFIX_ENKF}atma00${FHR}.ensmean$ASUFFIX ./atmanl_ensmean
+      $NLN $COMIN_ENS/${APREFIX_ENKF}atma00${FHR}.ensmean.nc ./atmanl_ensmean
    fi
 
    # Compute ensemble mean analysis
@@ -165,9 +163,9 @@ if [ $DO_CALC_INCREMENT = "YES" ]; then
 else
    # Link ensemble mean increment
    if [ $FHR -eq 6 ]; then
-      $NLN $COMIN_ENS/${APREFIX_ENKF}atminc.ensmean$ASUFFIX ./atminc_ensmean
+      $NLN $COMIN_ENS/${APREFIX_ENKF}atminc.ensmean.nc ./atminc_ensmean
    else
-      $NLN $COMIN_ENS/${APREFIX_ENKF}atmi00${FHR}.ensmean$ASUFFIX ./atminc_ensmean
+      $NLN $COMIN_ENS/${APREFIX_ENKF}atmi00${FHR}.ensmean.nc ./atminc_ensmean
    fi
 
    # Compute ensemble mean increment
@@ -184,8 +182,8 @@ else
    export err=$?; err_chk
 
    # If available, link to ensemble mean guess.  Otherwise, compute ensemble mean guess
-   if [ -s $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean$GSUFFIX ]; then
-       $NLN $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean$GSUFFIX ./atmges_ensmean
+   if [ -s $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean.nc ]; then
+       $NLN $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean.nc ./atmges_ensmean
    else
        DATAPATH="./"
        ATMGESNAME="atmges"
@@ -220,11 +218,11 @@ if [ $RECENTER_ENKF = "YES" ]; then
 
    # GSI EnVar analysis
    if [ $FHR -eq 6 ]; then
-     ATMANL_GSI=$COMIN/${APREFIX}atmanl$ASUFFIX
-     ATMANL_GSI_ENSRES=$COMIN/${APREFIX}atmanl.ensres$ASUFFIX
+     ATMANL_GSI=$COMIN/${APREFIX}atmanl.nc
+     ATMANL_GSI_ENSRES=$COMIN/${APREFIX}atmanl.ensres.nc
    else
-     ATMANL_GSI=$COMIN/${APREFIX}atma00${FHR}$ASUFFIX
-     ATMANL_GSI_ENSRES=$COMIN/${APREFIX}atma00${FHR}.ensres$ASUFFIX
+     ATMANL_GSI=$COMIN/${APREFIX}atma00${FHR}.nc
+     ATMANL_GSI_ENSRES=$COMIN/${APREFIX}atma00${FHR}.ensres.nc
    fi
 
    # if we already have a ensemble resolution GSI analysis then just link to it
@@ -237,15 +235,9 @@ if [ $RECENTER_ENKF = "YES" ]; then
       $NLN $ATMANL_GSI        atmanl_gsi
       $NLN $ATMANL_GSI_ENSRES atmanl_gsi_ensres
       SIGLEVEL=${SIGLEVEL:-${FIXgsm}/global_hyblev.l${LEVS}.txt}
-      if [ ${SUFFIX} = ".nc" ]; then
-         $NLN $CHGRESNC chgres.x
-         chgresnml=chgres_nc_gauss.nml
-         nmltitle=chgres
-      else
-         $NLN $CHGRESNEMS chgres.x
-         chgresnml=fort.43
-         nmltitle=nam
-      fi
+      $NLN $CHGRESNC chgres.x
+      chgresnml=chgres_nc_gauss.nml
+      nmltitle=chgres
 
       export OMP_NUM_THREADS=$NTHREADS_CHGRES
 
@@ -322,11 +314,7 @@ if [ $DO_CALC_INCREMENT = "YES" ]; then
    fi
 
    export OMP_NUM_THREADS=$NTHREADS_CALCINC
-   if [ ${SUFFIX} = ".nc" ]; then
-      CALCINCEXEC=$CALCINCNCEXEC
-   else
-      CALCINCEXEC=$CALCINCNEMSEXEC
-   fi
+   CALCINCEXEC=$CALCINCNCEXEC
 
    export pgm=$CALCINCEXEC
    . prep_step
diff --git a/scripts/exgdas_enkf_fcst.sh b/scripts/exgdas_enkf_fcst.sh
index d75678a552..1c11decc26 100755
--- a/scripts/exgdas_enkf_fcst.sh
+++ b/scripts/exgdas_enkf_fcst.sh
@@ -60,7 +60,6 @@ export PREFIX_ATMINC=${PREFIX_ATMINC:-""}
 # Ops related stuff
 SENDECF=${SENDECF:-"NO"}
 SENDDBN=${SENDDBN:-"NO"}
-GSUFFIX=${GSUFFIX:-$SUFFIX}
 
 ################################################################################
 # Preprocessing
@@ -185,7 +184,7 @@ for imem in $(seq $ENSBEG $ENSEND); do
      while [ $fhr -le $FHMAX ]; do
        FH3=$(printf %03i $fhr)
        if [ $(expr $fhr % 3) -eq 0 ]; then
-         $DBNROOT/bin/dbn_alert MODEL GFS_ENKF $job $COMOUT/$memchar/atmos/${CDUMP}.t${cyc}z.sfcf${FH3}${GSUFFIX}
+         $DBNROOT/bin/dbn_alert MODEL GFS_ENKF $job $COMOUT/$memchar/atmos/${CDUMP}.t${cyc}z.sfcf${FH3}.nc
        fi
        fhr=$((fhr+FHOUT))
      done
diff --git a/scripts/exgdas_enkf_post.sh b/scripts/exgdas_enkf_post.sh
index 64447da841..1338b0ceef 100755
--- a/scripts/exgdas_enkf_post.sh
+++ b/scripts/exgdas_enkf_post.sh
@@ -42,7 +42,6 @@ GETSFCENSMEANEXEC=${GETSFCENSMEANEXEC:-$HOMEgfs/exec/getsfcensmeanp.x}
 
 # Other variables.
 PREFIX=${PREFIX:-""}
-SUFFIX=${SUFFIX:-""}
 FHMIN=${FHMIN_EPOS:-3}
 FHMAX=${FHMAX_EPOS:-9}
 FHOUT=${FHOUT_EPOS:-3}
@@ -79,23 +78,23 @@ for imem in $(seq 1 $NMEM_ENKF); do
    memchar="mem"$(printf %03i $imem)
    for fhr in $(seq $FHMIN $FHOUT $FHMAX); do
       fhrchar=$(printf %03i $fhr)
-      $NLN $COMIN/$memchar/atmos/${PREFIX}sfcf$fhrchar${SUFFIX} sfcf${fhrchar}_$memchar
-      $NLN $COMIN/$memchar/atmos/${PREFIX}atmf$fhrchar${SUFFIX} atmf${fhrchar}_$memchar
+      $NLN $COMIN/$memchar/atmos/${PREFIX}sfcf${fhrchar}.nc sfcf${fhrchar}_$memchar
+      $NLN $COMIN/$memchar/atmos/${PREFIX}atmf${fhrchar}.nc atmf${fhrchar}_$memchar
    done
 done
 
 # Forecast ensemble mean and smoothed files
 for fhr in $(seq $FHMIN $FHOUT $FHMAX); do
    fhrchar=$(printf %03i $fhr)
-   $NLN $COMOUT/${PREFIX}sfcf${fhrchar}.ensmean${SUFFIX} sfcf${fhrchar}.ensmean
-   $NLN $COMOUT/${PREFIX}atmf${fhrchar}.ensmean${SUFFIX} atmf${fhrchar}.ensmean
+   $NLN $COMOUT/${PREFIX}sfcf${fhrchar}.ensmean.nc sfcf${fhrchar}.ensmean
+   $NLN $COMOUT/${PREFIX}atmf${fhrchar}.ensmean.nc atmf${fhrchar}.ensmean
    if [ $SMOOTH_ENKF = "YES" ]; then
       for imem in $(seq 1 $NMEM_ENKF); do
          memchar="mem"$(printf %03i $imem)
-         $NLN $COMOUT/$memchar/atmos/${PREFIX}atmf${fhrchar}${ENKF_SUFFIX}${SUFFIX} atmf${fhrchar}${ENKF_SUFFIX}_$memchar
+         $NLN $COMOUT/$memchar/atmos/${PREFIX}atmf${fhrchar}${ENKF_SUFFIX}.nc atmf${fhrchar}${ENKF_SUFFIX}_$memchar
       done
    fi
-   [[ $ENKF_SPREAD = "YES" ]] && $NLN $COMOUT/${PREFIX}atmf${fhrchar}.ensspread${SUFFIX} atmf${fhrchar}.ensspread
+   [[ $ENKF_SPREAD = "YES" ]] && $NLN $COMOUT/${PREFIX}atmf${fhrchar}.ensspread.nc atmf${fhrchar}.ensspread
 done
 
 ################################################################################
@@ -150,7 +149,7 @@ if [ $SENDDBN = "YES" ]; then
       fhrchar=$(printf %03i $fhr)
       if [ $(expr $fhr % 3) -eq 0 ]; then
          if [ -s ./sfcf${fhrchar}.ensmean ]; then
-             $DBNROOT/bin/dbn_alert MODEL GFS_ENKF $job $COMOUT/${PREFIX}sfcf${fhrchar}.ensmean${SUFFIX}
+             $DBNROOT/bin/dbn_alert MODEL GFS_ENKF $job $COMOUT/${PREFIX}sfcf${fhrchar}.ensmean.nc
          fi
       fi
    done
diff --git a/scripts/exgdas_enkf_select_obs.sh b/scripts/exgdas_enkf_select_obs.sh
index 92e1fd8c60..7a6eec5535 100755
--- a/scripts/exgdas_enkf_select_obs.sh
+++ b/scripts/exgdas_enkf_select_obs.sh
@@ -30,7 +30,6 @@ ANALYSISSH=${ANALYSISSH:-$HOMEgfs/scripts/exglobal_atmos_analysis.sh}
 
 # Prefix and Suffix Variables.
 export APREFIX=${APREFIX:-""}
-export ASUFFIX=${ASUFFIX:-$SUFFIX}
 
 # Select obs
 export RUN_SELECT=${RUN_SELECT:-"YES"}
diff --git a/scripts/exgdas_enkf_sfc.sh b/scripts/exgdas_enkf_sfc.sh
index d3c1b96269..3fc99c1890 100755
--- a/scripts/exgdas_enkf_sfc.sh
+++ b/scripts/exgdas_enkf_sfc.sh
@@ -43,9 +43,7 @@ OPREFIX=${OPREFIX:-""}
 OSUFFIX=${OSUFFIX:-""}
 APREFIX=${APREFIX:-""}
 APREFIX_ENKF=${APREFIX_ENKF:-$APREFIX}
-ASUFFIX=${ASUFFIX:-$SUFFIX}
 GPREFIX=${GPREFIX:-""}
-GSUFFIX=${GSUFFIX:-$SUFFIX}
 
 # Variables
 NMEM_ENKF=${NMEM_ENKF:-80}
diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
index b22dcbfea8..ff8422548c 100755
--- a/scripts/exgdas_enkf_update.sh
+++ b/scripts/exgdas_enkf_update.sh
@@ -45,9 +45,7 @@ CDUMP=${CDUMP:-"gdas"}
 
 # Filenames.
 GPREFIX=${GPREFIX:-""}
-GSUFFIX=${GSUFFIX:-$SUFFIX}
 APREFIX=${APREFIX:-""}
-ASUFFIX=${ASUFFIX:-$SUFFIX}
 
 SMOOTH_ENKF=${SMOOTH_ENKF:-"YES"}
 
@@ -92,7 +90,7 @@ fi
 INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
 
 ################################################################################
-ATMGES_ENSMEAN=$COMIN_GES_ENS/${GPREFIX}atmf006.ensmean${GSUFFIX}
+ATMGES_ENSMEAN=$COMIN_GES_ENS/${GPREFIX}atmf006.ensmean.nc
 LONB_ENKF=${LONB_ENKF:-$($NCLEN $ATMGES_ENSMEAN grid_xt)} # get LONB_ENKF
 LATB_ENKF=${LATB_ENKF:-$($NCLEN $ATMGES_ENSMEAN grid_yt)} # get LATB_ENFK
 LEVS_ENKF=${LEVS_ENKF:-$($NCLEN $ATMGES_ENSMEAN pfull)} # get LEVS_ENFK
@@ -195,21 +193,21 @@ for imem in $(seq 1 $NMEM_ENKF); do
    fi
    mkdir -p $COMOUT_ANL_ENS/$memchar/atmos
    for FHR in $nfhrs; do
-      $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}atmf00${FHR}${ENKF_SUFFIX}${GSUFFIX}  sfg_${CDATE}_fhr0${FHR}_${memchar}
+      $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}atmf00${FHR}${ENKF_SUFFIX}.nc  sfg_${CDATE}_fhr0${FHR}_${memchar}
       if [ $cnvw_option = ".true." ]; then
-         $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}sfcf00${FHR}${GSUFFIX} sfgsfc_${CDATE}_fhr0${FHR}_${memchar}
+         $NLN $COMIN_GES_ENS/$memchar/atmos/${GPREFIX}sfcf00${FHR}.nc sfgsfc_${CDATE}_fhr0${FHR}_${memchar}
       fi
       if [ $FHR -eq 6 ]; then
          if [ $DO_CALC_INCREMENT = "YES" ]; then
-            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atmanl${ASUFFIX}             sanl_${CDATE}_fhr0${FHR}_${memchar}
+            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atmanl.nc             sanl_${CDATE}_fhr0${FHR}_${memchar}
          else
-            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atminc${ASUFFIX}             incr_${CDATE}_fhr0${FHR}_${memchar}
+            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atminc.nc             incr_${CDATE}_fhr0${FHR}_${memchar}
          fi
       else
          if [ $DO_CALC_INCREMENT = "YES" ]; then
-            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atma00${FHR}${ASUFFIX}             sanl_${CDATE}_fhr0${FHR}_${memchar}
+            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atma00${FHR}.nc             sanl_${CDATE}_fhr0${FHR}_${memchar}
          else
-            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atmi00${FHR}${ASUFFIX}             incr_${CDATE}_fhr0${FHR}_${memchar}
+            $NLN $COMOUT_ANL_ENS/$memchar/atmos/${APREFIX}atmi00${FHR}.nc             incr_${CDATE}_fhr0${FHR}_${memchar}
          fi
       fi
    done
@@ -217,9 +215,9 @@ done
 
 # Ensemble mean guess
 for FHR in $nfhrs; do
-   $NLN $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean${GSUFFIX} sfg_${CDATE}_fhr0${FHR}_ensmean
+   $NLN $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean.nc sfg_${CDATE}_fhr0${FHR}_ensmean
    if [ $cnvw_option = ".true." ]; then
-      $NLN $COMIN_GES_ENS/${GPREFIX}sfcf00${FHR}.ensmean${GSUFFIX} sfgsfc_${CDATE}_fhr0${FHR}_ensmean
+      $NLN $COMIN_GES_ENS/${GPREFIX}sfcf00${FHR}.ensmean.nc sfgsfc_${CDATE}_fhr0${FHR}_ensmean
    fi
 done
 
diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
index f8478b2662..aa266c1721 100755
--- a/scripts/exgfs_atmos_post.sh
+++ b/scripts/exgfs_atmos_post.sh
@@ -65,13 +65,7 @@ export GOESF=${GOESF:-"YES"}
 export WAFSF=${WAFSF:-"NO"}
 export PGBF=${PGBF:-"YES"}
 export TCYC=${TCYC:-".t${cyc}z."}
-export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
-if (( OUTTYP == 4 )); then
-  export SUFFIX=".nc"
-else
-  export SUFFIX=
-fi
 export machine=${machine:-WCOSS2}
 
 ###########################
@@ -90,11 +84,7 @@ export IDRT=${IDRT:-0} # IDRT=0 is setting for outputting grib files on lat/lon
 # Process analysis when post_times is 00
 stime="$(echo "${post_times}" | cut -c1-3)"
 export stime
-if (( OUTTYP == 4 )); then
-  export loganl="${COMIN}/${PREFIX}atmanl${SUFFIX}"
-else
-  export loganl="${COMIN}/${PREFIX}sanl"
-fi
+export loganl="${COMIN}/${PREFIX}atmanl.nc"
 
 if [[ "${stime}" = "anl" ]]; then
   if [[ -f "${loganl}" ]]; then
@@ -116,12 +106,10 @@ if [[ "${stime}" = "anl" ]]; then
     fi
 
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if (( OUTTYP == 4 )); then
-      ln -fs "${COMIN}/${PREFIX}atmanl${SUFFIX}" nemsfile
-      export NEMSINP=nemsfile
-      ln -fs "${COMIN}/${PREFIX}sfcanl${SUFFIX}" flxfile
-      export FLXINP=flxfile
-    fi
+    ln -fs "${COMIN}/${PREFIX}atmanl.nc" nemsfile
+    export NEMSINP=nemsfile
+    ln -fs "${COMIN}/${PREFIX}sfcanl.nc" flxfile
+    export FLXINP=flxfile
 
     export PGBOUT=pgbfile
     export PGIOUT=pgifile
@@ -155,8 +143,8 @@ if [[ "${stime}" = "anl" ]]; then
       fi
 
       if [[ "${SENDDBN}" = 'YES' ]]; then
-        "${DBNROOT}/bin/dbn_alert" MODEL GFS_MSC_sfcanl "${job}" "${COMOUT}/${PREFIX}sfcanl${SUFFIX}"
-        "${DBNROOT}/bin/dbn_alert" MODEL GFS_SA "${job}" "${COMOUT}/${PREFIX}atmanl${SUFFIX}"
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_MSC_sfcanl "${job}" "${COMOUT}/${PREFIX}sfcanl.nc"
+        "${DBNROOT}/bin/dbn_alert" MODEL GFS_SA "${job}" "${COMOUT}/${PREFIX}atmanl.nc"
         if [[ "${PGBF}" = 'YES' ]]; then
           "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25 "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl"
           "${DBNROOT}/bin/dbn_alert" MODEL GFS_PGB2_0P25_WIDX "${job}" "${COMOUT}/${PREFIX}pgrb2.0p25.anl.idx"
@@ -262,12 +250,10 @@ else   ## not_anl if_stime
     # for backup to start Model Fcst
     ###############################
     [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
-    if (( OUTTYP == 4 )); then
-      ln -fs "${COMIN}/${PREFIX}atmf${fhr}${SUFFIX}" nemsfile
-      export NEMSINP=nemsfile
-      ln -fs "${COMIN}/${PREFIX}sfcf${fhr}${SUFFIX}" flxfile
-      export FLXINP=flxfile
-    fi
+    ln -fs "${COMIN}/${PREFIX}atmf${fhr}.nc" nemsfile
+    export NEMSINP=nemsfile
+    ln -fs "${COMIN}/${PREFIX}sfcf${fhr}.nc" flxfile
+    export FLXINP=flxfile
 
     if (( fhr > 0 )); then
       export IGEN=${IGEN_FCST}
diff --git a/scripts/exgfs_atmos_postsnd.sh b/scripts/exgfs_atmos_postsnd.sh
index fd2ffe895f..c6d07bf9b9 100755
--- a/scripts/exgfs_atmos_postsnd.sh
+++ b/scripts/exgfs_atmos_postsnd.sh
@@ -35,7 +35,7 @@ export ENDHOUR=${ENDHOUR:-180}
 export INCREMENT=12
 export MAKEBUFR=NO
 export F00FLAG=YES
-export fformat=${OUTPUT_FILE:-netcdf}
+export fformat=netcdf
 export atmfm="nc"
 export logfm="txt"
 export NINT1=${FHOUT_HF_GFS:-1}
diff --git a/scripts/exglobal_archive.sh b/scripts/exglobal_archive.sh
index a3faea9f98..5bc76d896f 100755
--- a/scripts/exglobal_archive.sh
+++ b/scripts/exglobal_archive.sh
@@ -15,8 +15,6 @@ fi
 
 # CURRENT CYCLE
 APREFIX="${CDUMP}.t${cyc}z."
-ASUFFIX=${ASUFFIX:-${SUFFIX}}
-format="netcdf"
 
 # Realtime parallels run GFS MOS on 1 day delay
 # If realtime parallel, back up CDATE_MOS one day
@@ -95,8 +93,8 @@ if [ "${CDUMP}" = "gfs" ] && [ "${FITSARC}" = "YES" ]; then
     fhr=0
     while [[ ${fhr} -le ${fhmax} ]]; do
         fhr3=$(printf %03i "${fhr}")
-        sfcfile=${prefix}.sfcf${fhr3}${ASUFFIX}
-        sigfile=${prefix}.atmf${fhr3}${ASUFFIX}
+        sfcfile=${prefix}.sfcf${fhr3}.nc
+        sigfile=${prefix}.atmf${fhr3}.nc
         nb_copy "${sfcfile}" "${VFYARC}"/"${CDUMP}"."${PDY}"/"${cyc}"/
         nb_copy "${sigfile}" "${VFYARC}"/"${CDUMP}"."${PDY}"/"${cyc}"/
         (( fhr = 10#${fhr} + 6 ))
@@ -162,9 +160,9 @@ if [ "${CDUMP}" = "gfs" ]; then
     targrp_list="gfsa gfsb"
 
     if [ "${ARCH_GAUSSIAN:-"NO"}" = "YES" ]; then
-        targrp_list="${targrp_list} gfs_flux gfs_${format}b gfs_pgrb2b"
+        targrp_list="${targrp_list} gfs_flux gfs_netcdfb gfs_pgrb2b"
         if [ "${MODE}" = "cycled" ]; then
-          targrp_list="${targrp_list} gfs_${format}a"
+          targrp_list="${targrp_list} gfs_netcdfa"
         fi
     fi
 
diff --git a/scripts/exglobal_atmos_analysis.sh b/scripts/exglobal_atmos_analysis.sh
index 71c4e303bc..7b3fd5c381 100755
--- a/scripts/exglobal_atmos_analysis.sh
+++ b/scripts/exglobal_atmos_analysis.sh
@@ -156,7 +156,7 @@ HDOB=${HDOB:-${COMIN_OBS}/${OPREFIX}hdob.tm00.bufr_d${OSUFFIX}}
 
 # Guess files
 GPREFIX=${GPREFIX:-""}
-GSUFFIX=${GSUFFIX:-${SUFFIX}}
+GSUFFIX=${GSUFFIX:-".nc"}
 SFCG03=${SFCG03:-${COMIN_GES}/${GPREFIX}sfcf003${GSUFFIX}}
 SFCG04=${SFCG04:-${COMIN_GES}/${GPREFIX}sfcf004${GSUFFIX}}
 SFCG05=${SFCG05:-${COMIN_GES}/${GPREFIX}sfcf005${GSUFFIX}}
@@ -178,10 +178,9 @@ GRADSTAT=${GRADSTAT:-${COMIN_GES}/${GPREFIX}radstat}
 
 # Analysis files
 export APREFIX=${APREFIX:-""}
-export ASUFFIX=${ASUFFIX:-${SUFFIX}}
-SFCANL=${SFCANL:-${COMOUT}/${APREFIX}sfcanl${ASUFFIX}}
+SFCANL=${SFCANL:-${COMOUT}/${APREFIX}sfcanl.nc}
 DTFANL=${DTFANL:-${COMOUT}/${APREFIX}dtfanl.nc}
-ATMANL=${ATMANL:-${COMOUT}/${APREFIX}atmanl${ASUFFIX}}
+ATMANL=${ATMANL:-${COMOUT}/${APREFIX}atmanl.nc}
 ABIAS=${ABIAS:-${COMOUT}/${APREFIX}abias}
 ABIASPC=${ABIASPC:-${COMOUT}/${APREFIX}abias_pc}
 ABIASAIR=${ABIASAIR:-${COMOUT}/${APREFIX}abias_air}
@@ -244,14 +243,12 @@ JCAP=${JCAP:--9999} # there is no jcap in these files
 
 # Get header information from Ensemble Guess files
 if [ ${DOHYBVAR} = "YES" ]; then
-   SFCGES_ENSMEAN=${SFCGES_ENSMEAN:-${COMIN_GES_ENS}/${GPREFIX}sfcf006.ensmean${GSUFFIX}}
-   export ATMGES_ENSMEAN=${ATMGES_ENSMEAN:-${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean${GSUFFIX}}
-   if [ ${SUFFIX} = ".nc" ]; then
-      LONB_ENKF=${LONB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_xt)} # get LONB_ENKF
-      LATB_ENKF=${LATB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_yt)} # get LATB_ENFK
-      LEVS_ENKF=${LEVS_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} pfull)} # get LATB_ENFK
-      JCAP_ENKF=${JCAP_ENKF:--9999} # again, no jcap in the netcdf files
-   fi
+   SFCGES_ENSMEAN=${SFCGES_ENSMEAN:-${COMIN_GES_ENS}/${GPREFIX}sfcf006.ensmean.nc}
+   export ATMGES_ENSMEAN=${ATMGES_ENSMEAN:-${COMIN_GES_ENS}/${GPREFIX}atmf006.ensmean.nc}
+   LONB_ENKF=${LONB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_xt)} # get LONB_ENKF
+   LATB_ENKF=${LATB_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} grid_yt)} # get LATB_ENFK
+   LEVS_ENKF=${LEVS_ENKF:-$(${NCLEN} ${ATMGES_ENSMEAN} pfull)} # get LATB_ENFK
+   JCAP_ENKF=${JCAP_ENKF:--9999} # again, no jcap in the netcdf files
    NLON_ENKF=${NLON_ENKF:-${LONB_ENKF}}
    NLAT_ENKF=${NLAT_ENKF:-$((${LATB_ENKF}+2))}
    [ ${JCAP_ENKF} -eq -9999 -a ${LATB_ENKF} -ne -9999 ] && JCAP_ENKF=$((LATB_ENKF-2))
@@ -340,17 +337,17 @@ fi
 
 # Set 4D-EnVar specific variables
 if [ ${DOHYBVAR} = "YES" -a ${l4densvar} = ".true." -a ${lwrite4danl} = ".true." ]; then
-   ATMA03=${ATMA03:-${COMOUT}/${APREFIX}atma003${ASUFFIX}}
+   ATMA03=${ATMA03:-${COMOUT}/${APREFIX}atma003.nc}
    ATMI03=${ATMI03:-${COMOUT}/${APREFIX}atmi003.nc}
-   ATMA04=${ATMA04:-${COMOUT}/${APREFIX}atma004${ASUFFIX}}
+   ATMA04=${ATMA04:-${COMOUT}/${APREFIX}atma004.nc}
    ATMI04=${ATMI04:-${COMOUT}/${APREFIX}atmi004.nc}
-   ATMA05=${ATMA05:-${COMOUT}/${APREFIX}atma005${ASUFFIX}}
+   ATMA05=${ATMA05:-${COMOUT}/${APREFIX}atma005.nc}
    ATMI05=${ATMI05:-${COMOUT}/${APREFIX}atmi005.nc}
-   ATMA07=${ATMA07:-${COMOUT}/${APREFIX}atma007${ASUFFIX}}
+   ATMA07=${ATMA07:-${COMOUT}/${APREFIX}atma007.nc}
    ATMI07=${ATMI07:-${COMOUT}/${APREFIX}atmi007.nc}
-   ATMA08=${ATMA08:-${COMOUT}/${APREFIX}atma008${ASUFFIX}}
+   ATMA08=${ATMA08:-${COMOUT}/${APREFIX}atma008.nc}
    ATMI08=${ATMI08:-${COMOUT}/${APREFIX}atmi008.nc}
-   ATMA09=${ATMA09:-${COMOUT}/${APREFIX}atma009${ASUFFIX}}
+   ATMA09=${ATMA09:-${COMOUT}/${APREFIX}atma009.nc}
    ATMI09=${ATMI09:-${COMOUT}/${APREFIX}atmi009.nc}
 fi
 
@@ -538,9 +535,9 @@ if [ ${DOHYBVAR} = "YES" ]; then
    for imem in $(seq 1 ${NMEM_ENKF}); do
       memchar="mem"$(printf %03i ${imem})
       for fhr in ${fhrs}; do
-         ${NLN} ${COMIN_GES_ENS}/${memchar}/atmos/${GPREFIX}atmf0${fhr}${ENKF_SUFFIX}${GSUFFIX} ./ensemble_data/sigf${fhr}_ens_${memchar}
+         ${NLN} ${COMIN_GES_ENS}/${memchar}/atmos/${GPREFIX}atmf0${fhr}${ENKF_SUFFIX}.nc ./ensemble_data/sigf${fhr}_ens_${memchar}
          if [ ${cnvw_option} = ".true." ]; then
-            ${NLN} ${COMIN_GES_ENS}/${memchar}/atmos/${GPREFIX}sfcf0${fhr}${GSUFFIX} ./ensemble_data/sfcf${fhr}_ens_${memchar}
+            ${NLN} ${COMIN_GES_ENS}/${memchar}/atmos/${GPREFIX}sfcf0${fhr}.nc ./ensemble_data/sfcf${fhr}_ens_${memchar}
          fi
       done
    done
diff --git a/scripts/exglobal_atmos_analysis_calc.sh b/scripts/exglobal_atmos_analysis_calc.sh
index 34d2425800..5c005ac892 100755
--- a/scripts/exglobal_atmos_analysis_calc.sh
+++ b/scripts/exglobal_atmos_analysis_calc.sh
@@ -82,21 +82,19 @@ SENDDBN=${SENDDBN:-"NO"}
 
 # Guess files
 GPREFIX=${GPREFIX:-""}
-GSUFFIX=${GSUFFIX:-$SUFFIX}
-ATMG03=${ATMG03:-${COMIN_GES}/${GPREFIX}atmf003${GSUFFIX}}
-ATMG04=${ATMG04:-${COMIN_GES}/${GPREFIX}atmf004${GSUFFIX}}
-ATMG05=${ATMG05:-${COMIN_GES}/${GPREFIX}atmf005${GSUFFIX}}
-ATMGES=${ATMGES:-${COMIN_GES}/${GPREFIX}atmf006${GSUFFIX}}
-ATMG07=${ATMG07:-${COMIN_GES}/${GPREFIX}atmf007${GSUFFIX}}
-ATMG08=${ATMG08:-${COMIN_GES}/${GPREFIX}atmf008${GSUFFIX}}
-ATMG09=${ATMG09:-${COMIN_GES}/${GPREFIX}atmf009${GSUFFIX}}
+ATMG03=${ATMG03:-${COMIN_GES}/${GPREFIX}atmf003.nc}
+ATMG04=${ATMG04:-${COMIN_GES}/${GPREFIX}atmf004.nc}
+ATMG05=${ATMG05:-${COMIN_GES}/${GPREFIX}atmf005.nc}
+ATMGES=${ATMGES:-${COMIN_GES}/${GPREFIX}atmf006.nc}
+ATMG07=${ATMG07:-${COMIN_GES}/${GPREFIX}atmf007.nc}
+ATMG08=${ATMG08:-${COMIN_GES}/${GPREFIX}atmf008.nc}
+ATMG09=${ATMG09:-${COMIN_GES}/${GPREFIX}atmf009.nc}
 
 # Analysis files
 export APREFIX=${APREFIX:-""}
-export ASUFFIX=${ASUFFIX:-$SUFFIX}
-SFCANL=${SFCANL:-${COMOUT}/${APREFIX}sfcanl${ASUFFIX}}
+SFCANL=${SFCANL:-${COMOUT}/${APREFIX}sfcanl.nc}
 DTFANL=${DTFANL:-${COMOUT}/${APREFIX}dtfanl.nc}
-ATMANL=${ATMANL:-${COMOUT}/${APREFIX}atmanl${ASUFFIX}}
+ATMANL=${ATMANL:-${COMOUT}/${APREFIX}atmanl.nc}
 
 # Increment files
 ATMINC=${ATMINC:-${COMOUT}/${APREFIX}atminc.nc}
@@ -116,17 +114,17 @@ fi
 
 # Set 4D-EnVar specific variables
 if [ $DOHYBVAR = "YES" -a $l4densvar = ".true." -a $lwrite4danl = ".true." ]; then
-   ATMA03=${ATMA03:-${COMOUT}/${APREFIX}atma003${ASUFFIX}}
+   ATMA03=${ATMA03:-${COMOUT}/${APREFIX}atma003.nc}
    ATMI03=${ATMI03:-${COMOUT}/${APREFIX}atmi003.nc}
-   ATMA04=${ATMA04:-${COMOUT}/${APREFIX}atma004${ASUFFIX}}
+   ATMA04=${ATMA04:-${COMOUT}/${APREFIX}atma004.nc}
    ATMI04=${ATMI04:-${COMOUT}/${APREFIX}atmi004.nc}
-   ATMA05=${ATMA05:-${COMOUT}/${APREFIX}atma005${ASUFFIX}}
+   ATMA05=${ATMA05:-${COMOUT}/${APREFIX}atma005.nc}
    ATMI05=${ATMI05:-${COMOUT}/${APREFIX}atmi005.nc}
-   ATMA07=${ATMA07:-${COMOUT}/${APREFIX}atma007${ASUFFIX}}
+   ATMA07=${ATMA07:-${COMOUT}/${APREFIX}atma007.nc}
    ATMI07=${ATMI07:-${COMOUT}/${APREFIX}atmi007.nc}
-   ATMA08=${ATMA08:-${COMOUT}/${APREFIX}atma008${ASUFFIX}}
+   ATMA08=${ATMA08:-${COMOUT}/${APREFIX}atma008.nc}
    ATMI08=${ATMI08:-${COMOUT}/${APREFIX}atmi008.nc}
-   ATMA09=${ATMA09:-${COMOUT}/${APREFIX}atma009${ASUFFIX}}
+   ATMA09=${ATMA09:-${COMOUT}/${APREFIX}atma009.nc}
    ATMI09=${ATMI09:-${COMOUT}/${APREFIX}atmi009.nc}
 fi
 
diff --git a/scripts/exglobal_diag.sh b/scripts/exglobal_diag.sh
index c913cdd132..3ff07d48f6 100755
--- a/scripts/exglobal_diag.sh
+++ b/scripts/exglobal_diag.sh
@@ -61,7 +61,6 @@ SENDDBN=${SENDDBN:-"NO"}
 
 # Analysis files
 export APREFIX=${APREFIX:-""}
-export ASUFFIX=${ASUFFIX:-$SUFFIX}
 RADSTAT=${RADSTAT:-${COMOUT}/${APREFIX}radstat}
 PCPSTAT=${PCPSTAT:-${COMOUT}/${APREFIX}pcpstat}
 CNVSTAT=${CNVSTAT:-${COMOUT}/${APREFIX}cnvstat}
diff --git a/ush/calcanl_gfs.py b/ush/calcanl_gfs.py
index 0243366241..fcf272b3ee 100755
--- a/ush/calcanl_gfs.py
+++ b/ush/calcanl_gfs.py
@@ -14,8 +14,8 @@
 
 
 # function to calculate analysis from a given increment file and background
-def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
-                ComIn_Ges, GPrefix, GSuffix,
+def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix,
+                ComIn_Ges, GPrefix,
                 FixDir, atmges_ens_mean, RunDir, NThreads, NEMSGet, IAUHrs,
                 ExecCMD, ExecCMDMPI, ExecAnl, ExecChgresInc, Cdump):
     print('calcanl_gfs beginning at: ', datetime.datetime.utcnow())
@@ -42,8 +42,8 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
                         gsi_utils.make_dir(CalcAnlDir)
                     gsi_utils.copy_file(ExecAnl, CalcAnlDir + '/calc_anl.x')
                     gsi_utils.link_file(RunDir + '/siginc.nc', CalcAnlDir + '/siginc.nc.06')
-                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atmanl.ensres' + ASuffix, CalcAnlDir + '/anl.ensres.06')
-                    gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf006.ensres' + GSuffix, CalcAnlDir + '/ges.ensres.06')
+                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atmanl.ensres.nc', CalcAnlDir + '/anl.ensres.06')
+                    gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf006.ensres.nc', CalcAnlDir + '/ges.ensres.06')
                     gsi_utils.link_file(RunDir + '/sigf06', CalcAnlDir + '/ges.06')
             else:
                 if os.path.isfile('sigi' + format(fh, '02') + '.nc'):
@@ -54,7 +54,7 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
                         gsi_utils.make_dir(CalcAnlDir)
                     if not os.path.exists(CalcAnlDir6):
                         gsi_utils.make_dir(CalcAnlDir6)
-                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atma' + format(fh, '03') + ASuffix,
+                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atma' + format(fh, '03') + '.nc',
                                         CalcAnlDir6 + '/anl.' + format(fh, '02'))
                     gsi_utils.link_file(RunDir + '/siga' + format(fh, '02'),
                                         CalcAnlDir6 + '/anl.' + format(fh, '02'))
@@ -74,11 +74,11 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
                         gsi_utils.make_dir(CalcAnlDir)
                     if not os.path.exists(CalcAnlDir6):
                         gsi_utils.make_dir(CalcAnlDir6)
-                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atma' + format(fh, '03') + '.ensres' + ASuffix,
+                    gsi_utils.link_file(ComOut + '/' + APrefix + 'atma' + format(fh, '03') + '.ensres.nc',
                                         CalcAnlDir6 + '/anl.ensres.' + format(fh, '02'))
                     gsi_utils.link_file(RunDir + '/sigi' + format(fh, '02') + '.nc',
                                         CalcAnlDir6 + '/siginc.nc.' + format(fh, '02'))
-                    gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf' + format(fh, '03') + '.ensres' + GSuffix,
+                    gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf' + format(fh, '03') + '.ensres.nc',
                                         CalcAnlDir6 + '/ges.ensres.' + format(fh, '02'))
 
     else:
@@ -97,15 +97,12 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
             gsi_utils.make_dir(CalcAnlDir)
         gsi_utils.copy_file(ExecAnl, CalcAnlDir + '/calc_anl.x')
         gsi_utils.link_file(RunDir + '/siginc.nc', CalcAnlDir + '/siginc.nc.06')
-        gsi_utils.link_file(ComOut + '/' + APrefix + 'atmanl.ensres' + ASuffix, CalcAnlDir + '/anl.ensres.06')
-        gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf006.ensres' + GSuffix, CalcAnlDir + '/ges.ensres.06')
+        gsi_utils.link_file(ComOut + '/' + APrefix + 'atmanl.ensres.nc', CalcAnlDir + '/anl.ensres.06')
+        gsi_utils.link_file(ComIn_Ges + '/' + GPrefix + 'atmf006.ensres.nc', CalcAnlDir + '/ges.ensres.06')
 
     # get dimension information from background and increment files
     AnlDims = gsi_utils.get_ncdims('siginc.nc')
-    if ASuffix == ".nc":
-        GesDims = gsi_utils.get_ncdims('sigf06')
-    else:
-        GesDims = gsi_utils.get_nemsdims('sigf06', NEMSGet)
+    GesDims = gsi_utils.get_ncdims('sigf06')
 
     levs = AnlDims['lev']
     LonA = AnlDims['lon']
@@ -346,10 +343,8 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
     Write4Danl = gsi_utils.isTrue(os.getenv('lwrite4danl', 'NO'))
     ComIn_Ges = os.getenv('COMIN_GES', './')
     GPrefix = os.getenv('GPREFIX', './')
-    GSuffix = os.getenv('GSUFFIX', './')
     ComOut = os.getenv('COMOUT', './')
     APrefix = os.getenv('APREFIX', '')
-    ASuffix = os.getenv('ASUFFIX', '')
     NThreads = os.getenv('NTHREADS_CHGRES', 1)
     FixDir = os.getenv('FIXgsm', './')
     atmges_ens_mean = os.getenv('ATMGES_ENSMEAN', './atmges_ensmean')
@@ -363,8 +358,8 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
     Cdump = os.getenv('CDUMP', 'gdas')
 
     print(locals())
-    calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix, ASuffix,
-                ComIn_Ges, GPrefix, GSuffix,
+    calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix,
+                ComIn_Ges, GPrefix,
                 FixDir, atmges_ens_mean, RunDir, NThreads, NEMSGet, IAUHrs,
                 ExecCMD, ExecCMDMPI, ExecAnl, ExecChgresInc,
                 Cdump)
diff --git a/ush/drive_makeprepbufr.sh b/ush/drive_makeprepbufr.sh
deleted file mode 100755
index 31154c10bb..0000000000
--- a/ush/drive_makeprepbufr.sh
+++ /dev/null
@@ -1,142 +0,0 @@
-#! /usr/bin/env bash
-
-###############################################################
-# < next few lines under version control, D O  N O T  E D I T >
-# $Date$
-# $Revision$
-# $Author$
-# $Id$
-###############################################################
-
-###############################################################
-## Author: Rahul Mahajan  Org: NCEP/EMC  Date: April 2017
-
-## Abstract:
-## Prepare for analysis driver script
-## EXPDIR : /full/path/to/config/files
-## CDATE  : current analysis date (YYYYMMDDHH)
-## CDUMP  : cycle name (gdas / gfs)
-###############################################################
-
-source "$HOMEgfs/ush/preamble.sh"
-
-###############################################################
-# Source relevant configs
-configs="base prep prepbufr"
-for config in $configs; do
-    . $EXPDIR/config.${config}
-    status=$?
-    [[ $status -ne 0 ]] && exit $status
-done
-
-###############################################################
-# Source machine runtime environment
-. $BASE_ENV/${machine}.env prepbufr
-status=$?
-[[ $status -ne 0 ]] && exit $status
-
-###############################################################
-KEEPDATA=${KEEPDATA:-"NO"}
-DO_RELOCATE=${DO_RELOCATE:-"NO"}
-DONST=${DONST:-"NO"}
-
-###############################################################
-# Set script and dependency variables
-COMPONENT=${COMPONENT:-atmos}
-
-GDATE=$($NDATE -$assim_freq $CDATE)
-
-cymd=$(echo $CDATE | cut -c1-8)
-chh=$(echo  $CDATE | cut -c9-10)
-gymd=$(echo $GDATE | cut -c1-8)
-ghh=$(echo  $GDATE | cut -c9-10)
-
-OPREFIX="${CDUMP}.t${chh}z."
-OSUFFIX=".bufr_d"
-GPREFIX="gdas.t${ghh}z."
-GSUFFIX=${GSUFFIX:-$SUFFIX}
-APREFIX="${CDUMP}.t${chh}z."
-ASUFFIX=${ASUFFIX:-$SUFFIX}
-
-COMIN_OBS=${COMIN_OBS:-"$DMPDIR/${CDUMP}${DUMP_SUFFIX}.${PDY}/${cyc}/${COMPONENT}"}
-COMIN_GES=${COMIN_GES:-"$ROTDIR/gdas.$gymd/$ghh/$COMPONENT"}
-COMOUT=${COMOUT:-"$ROTDIR/$CDUMP.$cymd/$chh/$COMPONENT"}
-[[ ! -d $COMOUT ]] && mkdir -p $COMOUT
-export DATA="$RUNDIR/$CDATE/$CDUMP/prepbufr"
-[[ -d $DATA ]] && rm -rf $DATA
-mkdir -p $DATA
-cd $DATA
-
-###############################################################
-# MAKEPREPBUFRSH environment specific variables
-export NEMSIO_IN=".true."
-export COMSP="$DATA/"
-export NET=$CDUMP
-
-###############################################################
-# Link observation files in BUFRLIST
-for bufrname in $BUFRLIST; do
-    $NLN $COMIN_OBS/${OPREFIX}${bufrname}.tm00$OSUFFIX ${bufrname}.tm00$OSUFFIX
-done
-
-# Link first guess files
-$NLN $COMIN_GES/${GPREFIX}atmf003${GSUFFIX} ./atmgm3$GSUFFIX
-$NLN $COMIN_GES/${GPREFIX}atmf006${GSUFFIX} ./atmges$GSUFFIX
-$NLN $COMIN_GES/${GPREFIX}atmf009${GSUFFIX} ./atmgp3$GSUFFIX
-
-[[ -f $COMIN_GES/${GPREFIX}atmf004${GSUFFIX} ]] && $NLN $COMIN_GES/${GPREFIX}atmf004${GSUFFIX} ./atmgm2$GSUFFIX
-[[ -f $COMIN_GES/${GPREFIX}atmf005${GSUFFIX} ]] && $NLN $COMIN_GES/${GPREFIX}atmf005${GSUFFIX} ./atmgm1$GSUFFIX
-[[ -f $COMIN_GES/${GPREFIX}atmf007${GSUFFIX} ]] && $NLN $COMIN_GES/${GPREFIX}atmf007${GSUFFIX} ./atmgp1$GSUFFIX
-[[ -f $COMIN_GES/${GPREFIX}atmf008${GSUFFIX} ]] && $NLN $COMIN_GES/${GPREFIX}atmf008${GSUFFIX} ./atmgp2$GSUFFIX
-
-# If relocation is turned off: these files don't exist, touch them
-if [ $DO_RELOCATE = "NO" ]; then
-    touch $DATA/tcvitals.relocate.tm00
-    touch $DATA/tropcy_relocation_status.tm00
-    echo "RECORDS PROCESSED" >> $DATA/tropcy_relocation_status.tm00
-fi
-
-###############################################################
-# if PREPDATA is YES and
-# 1. the aircft bufr file is not found, set PREPACQC to NO
-# 2. the ****** bufr file is not found, set ******** to NO
-if [ $PREPDATA = "YES" ]; then
-    [[ ! -s aircft.tm00$OSUFFIX ]] && export PREPACQC="NO"
-fi
-
-###############################################################
-# Execute MAKEPREPBUFRSH
-
-echo $(date) EXECUTING $MAKEPREPBUFRSH $CDATE >&2
-$MAKEPREPBUFRSH $CDATE
-status=$?
-echo $(date) EXITING $MAKEPREPBUFRSH with return code $status >&2
-[[ $status -ne 0 ]] && exit $status
-
-###############################################################
-# Create nsstbufr file
-if [ $DONST = "YES" ]; then
-    SFCSHPBF=${SFCSHPBF:-$COMIN_OBS/sfcshp.$CDUMP.$CDATE}
-    TESACBF=${TESACBF:-$COMIN_OBS/tesac.$CDUMP.$CDATE}
-    BATHYBF=${BATHYBF:-$COMIN_OBS/bathy.$CDUMP.$CDATE}
-    TRKOBBF=${TRKOBBF:-$COMIN_OBS/trkob.$CDUMP.$CDATE}
-    NSSTBF=${NSSTBF:-$COMOUT/${APREFIX}nsstbufr}
-
-    cat $SFCSHPBF $TESACBF $BATHYBF $TRKOBBF > $NSSTBF
-    status=$?
-    echo $(date) CREATE $NSSTBF with return code $status >&2
-
-    # NSST bufr file must be restricted since it contains unmasked ship ids
-    chmod 640  $NSSTBF
-    $CHGRP_CMD $NSSTBF
-fi
-###############################################################
-# Copy prepbufr and prepbufr.acft_profiles to COMOUT
-$NCP $DATA/prepda.t${chh}z        $COMOUT/${APREFIX}prepbufr
-$NCP $DATA/prepbufr.acft_profiles $COMOUT/${APREFIX}prepbufr.acft_profiles
-
-###############################################################
-# Exit out cleanly
-if [ $KEEPDATA = "NO" ] ; then rm -rf $DATA ; fi
-
-exit 0
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 4d26146e21..b2de7b1e43 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -502,19 +502,18 @@ EOF
   LONB_STP=${LONB_STP:-$LONB_CASE}
   LATB_STP=${LATB_STP:-$LATB_CASE}
   cd $DATA
-  affix="nc"
   if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
     fhr=$FHMIN
     for fhr in $OUTPUT_FH; do
       FH3=$(printf %03i $fhr)
       FH2=$(printf %02i $fhr)
-      atmi=atmf${FH3}.$affix
-      sfci=sfcf${FH3}.$affix
+      atmi=atmf${FH3}.nc
+      sfci=sfcf${FH3}.nc
       logi=logf${FH3}
       pgbi=GFSPRS.GrbF${FH2}
       flxi=GFSFLX.GrbF${FH2}
-      atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.$affix
-      sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.$affix
+      atmo=$memdir/${CDUMP}.t${cyc}z.atmf${FH3}.nc
+      sfco=$memdir/${CDUMP}.t${cyc}z.sfcf${FH3}.nc
       logo=$memdir/${CDUMP}.t${cyc}z.logf${FH3}.txt
       pgbo=$memdir/${CDUMP}.t${cyc}z.master.grb2f${FH3}
       flxo=$memdir/${CDUMP}.t${cyc}z.sfluxgrbf${FH3}.grib2
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 9ce8ebfcc6..00f2137a74 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -133,10 +133,8 @@ FV3_GFS_predet(){
 
   QUILTING=${QUILTING:-".true."}
   OUTPUT_GRID=${OUTPUT_GRID:-"gaussian_grid"}
-  OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
   WRITE_NEMSIOFLIP=${WRITE_NEMSIOFLIP:-".true."}
   WRITE_FSYNCFLAG=${WRITE_FSYNCFLAG:-".true."}
-  affix="nc"
 
   rCDUMP=${rCDUMP:-$CDUMP}
 
diff --git a/ush/fv3gfs_nc2nemsio.sh b/ush/fv3gfs_nc2nemsio.sh
deleted file mode 100755
index 8bdd4c929a..0000000000
--- a/ush/fv3gfs_nc2nemsio.sh
+++ /dev/null
@@ -1,72 +0,0 @@
-#! /usr/bin/env bash
-
-#----------------------------------------------------------------------------
-#--Fanglin Yang, October 2016: convert FV3 NetCDF files to NEMSIO format.
-#    Note FV3 lat-lon grid is located at the center of each grid box,
-#    starting from south to north and from east to west.
-#    For example, for a 0.5-deg uniform grid, nlon=720, nlat=360
-#    X(1,1)=[0.25E,89.75S], X(nlon,nlat)=[359.75E,89.75N]
-#---------------------------------------------------------------------------
-
-source "$HOMEgfs/ush/preamble.sh"
-
-export CDATE=${CDATE:-"2016100300"}
-export GG=${master_grid:-"0p25deg"}         # 1deg 0p5deg 0p25deg 0p125deg
-export FHZER=${FHZER:-6}                    # accumulation bucket in hours
-export fdiag=${fdiag:-"none"}               # specified forecast output hours
-
-pwd=$(pwd)
-export DATA=${DATA:-$pwd}
-export HOMEgfs=${HOMEgfs:-$PACKAGEROOT}
-export NC2NEMSIOEXE=${NC2NEMSIOEXE:-$HOMEgfs/exec/fv3nc2nemsio.x}
-
-cycn=$(echo $CDATE | cut -c 9-10)
-export TCYC=${TCYC:-".t${cycn}z."}
-export CDUMP=${CDUMP:-gfs}
-
-export PREFIX=${PREFIX:-${CDUMP}${TCYC}}
-export SUFFIX=${SUFFIX:-".nemsio"}
-
-#--------------------------------------------------
-cd $DATA || exit 8
-
-input_dir=$DATA
-output_dir=$DATA
-
-in_3d=${PREFIX}nggps3d.${GG}.nc
-in_2d=${PREFIX}nggps2d.${GG}.nc
-if [ ! -s $in_3d -o ! -s $in_2d ]; then
-  echo "$in_3d and $in_2d are missing. exit"
-  exit 1
-fi
-
-#--check if the output is from non-hydrostatic case
-nhrun=$(ncdump -c $in_3d | grep nhpres)
-nhcase=$?
-
-# If no information on the time interval is given, deduce from the netCDF file
-[[ $fdiag = "none" ]] && fdiag=$(ncks -H -s "%g " -C -v time $in_3d)
-
-#---------------------------------------------------
-nt=0
-err=0
-for fhour in $(echo $fdiag | sed "s/,/ /g"); do
-   nt=$((nt+1))
-   ifhour=$(printf "%09d" $fhour)              # convert to integer
-   fhzh=$(( (ifhour/FHZER-1)*FHZER ))          # bucket accumulation starting hour
-   [[ $fhzh -lt 0 ]] && fhzh=0
-
-   fhr=$(printf "%03d" $fhour)
-   outfile=${PREFIX}atmf${fhr}${SUFFIX}
-
-   $NC2NEMSIOEXE $CDATE $nt $fhzh $fhour $input_dir $in_2d $in_3d $output_dir $outfile $nhcase
-   rc=$?
-   ((err+=rc))
-
-   [[ ! -f $outfile ]] && ((err+=1))
-
-done
-
-#---------------------------------------------------
-
-exit $err
diff --git a/ush/fv3gfs_regrid_nemsio.sh b/ush/fv3gfs_regrid_nemsio.sh
deleted file mode 100755
index d9bc11de19..0000000000
--- a/ush/fv3gfs_regrid_nemsio.sh
+++ /dev/null
@@ -1,118 +0,0 @@
-#! /usr/bin/env bash
-
-################################################################################
-# UNIX Script Documentation Block
-# Script name:         fv3gfs_regrid_nemsio.sh
-# Script description:  Remap FV3 forecasts on six tile in NetCDF to global Gaussian
-#                      grid with NEMSIO output
-#
-# $Id$
-#
-# Author:   Fanglin Yang       Org: NCEP/EMC       Date: 2016-12-01
-# Abstract: regrid_nemsio.fd provided by Jeffrey.S.Whitaker OAR/ESRL
-#
-# Script history log:
-# 2016-12-01  Fanglin Yang
-# 2017-02-13  Rahul Mahajan
-#
-# Attributes:
-#   Language: Portable Operating System Interface (POSIX) Shell
-################################################################################
-
-source "$HOMEgfs/ush/preamble.sh"
-
-#-------------------------------------------------------
-# Directories and paths
-pwd=$(pwd)
-DATA=${DATA:-$pwd}
-HOMEgfs=${HOMEgfs:-$PACKAGEROOT}
-FIX_DIR=${FIX_DIR:-$HOMEgfs/fix}
-FIX_AM=${FIX_AM:-$FIX_DIR/am}
-FIXfv3=${FIXfv3:-$FIX_DIR/orog}
-REGRID_NEMSIO_EXEC=${REGRID_NEMSIO_EXEC:-$HOMEgfs/exec/regrid_nemsio.x}
-REGRID_NEMSIO_TBL=${REGRID_NEMSIO_TBL:-$HOMEgfs/parm/parm_fv3diag/variable_table.txt}
-
-CDATE=${CDATE:-2017011500}
-CDUMP=${CDUMP:-"gdas"}
-CASE=${CASE:-C768}
-LEVS=${LEVS:-65}
-GG=${GG:-gaussian}              # gaussian or regular lat-lon
-res=$(echo $CASE | cut -c2-)
-JCAP=${JCAP:-$((res*2-2))}
-LATB=${LATB:-$((res*2))}
-LONB=${LONB:-$((res*4))}
-
-NEMSIO_OUT2DNAME=${NEMSIO_OUT2DNAME:-sfc.$CDATE}
-NEMSIO_OUT3DNAME=${NEMSIO_OUT3DNAME:-atm.$CDATE}
-DEBUG=${REGRID_NEMSIO_DEBUG:-".true."}
-
-APRUN_REGRID_NEMSIO=${APRUN_REGRID_NEMSIO:-${APRUN:-""}}
-NTHREADS_REGRID_NEMSIO=${NTHREADS_REGRID_NEMSIO:-${NTHREADS:-1}}
-
-NMV=${NMV:-"/bin/mv"}
-
-#-------------------------------------------------------
-# IO specific parameters and error traps
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
-
-#--------------------------------------------------
-# ESMF regrid weights and output variable table
-weight_bilinear=${weight_bilinear:-$FIXfv3/$CASE/fv3_SCRIP_${CASE}_GRIDSPEC_lon${LONB}_lat${LATB}.${GG}.bilinear.nc}
-weight_neareststod=${weight_neareststod:-$FIXfv3/$CASE/fv3_SCRIP_${CASE}_GRIDSPEC_lon${LONB}_lat${LATB}.${GG}.neareststod.nc}
-
-#-------------------------------------------------------
-# Go to the directory where the history files are
-cd $DATA || exit 8
-
-#-------------------------------------------------------
-# Create namelist
-rm -f regrid-nemsio.input
-
-cat > regrid-nemsio.input << EOF
-&share
-  debug=$DEBUG,
-  ntrunc=$JCAP,
-  nlons=$LONB,
-  nlats=$LATB,
-  datapathout2d='$NEMSIO_OUT2DNAME',
-  datapathout3d='$NEMSIO_OUT3DNAME',
-  analysis_filename='fv3_history.tile1.nc','fv3_history.tile2.nc','fv3_history.tile3.nc','fv3_history.tile4.nc','fv3_history.tile5.nc','fv3_history.tile6.nc',
-  analysis_filename2d='fv3_history2d.tile1.nc','fv3_history2d.tile2.nc','fv3_history2d.tile3.nc','fv3_history2d.tile4.nc','fv3_history2d.tile5.nc','fv3_history2d.tile6.nc',
-  forecast_timestamp='${CDATE}',
-  variable_table='$REGRID_NEMSIO_TBL',
-  nemsio_opt3d='bin4',
-  nemsio_opt2d='bin4'
-/
-
-&interpio
-  esmf_bilinear_filename='$weight_bilinear',
-  esmf_neareststod_filename='$weight_neareststod',
-  gfs_hyblevs_filename='$FIX_AM/global_hyblev.l$LEVS.txt'
-/
-EOF
-
-#------------------------------------------------------------------
-export OMP_NUM_THREADS=$NTHREADS_REGRID_NEMSIO
-$APRUN_REGRID_NEMSIO $REGRID_NEMSIO_EXEC
-
-export ERR=$?
-export err=$ERR
-$ERRSCRIPT || exit $err
-
-rm -f regrid-nemsio.input
-
-#------------------------------------------------------------------
-PDY=$(echo $CDATE | cut -c1-8)
-cyc=$(echo  $CDATE | cut -c9-10)
-PREFIX=${PREFIX:-"${CDUMP}.t${cyc}z."}
-SUFFIX=${SUFFIX:-".nemsio"}
-for ftype in atm sfc; do
-    for file in $(ls -1 ${ftype}.${CDATE}.fhr*); do
-        fhrchar=$(echo $file | cut -d. -f3 | cut -c4-)
-        $NMV $file ${PREFIX}${ftype}f${fhrchar}${SUFFIX}
-    done
-done
-
-#------------------------------------------------------------------
-
-exit $err
diff --git a/ush/gaussian_sfcanl.sh b/ush/gaussian_sfcanl.sh
index 48eff0d7c1..e7be2c034f 100755
--- a/ush/gaussian_sfcanl.sh
+++ b/ush/gaussian_sfcanl.sh
@@ -91,7 +91,7 @@
 #
 #     output data: $PGMOUT
 #                  $PGMERR
-#                  $COMOUT/${APREFIX}sfcanl${ASUFFIX}
+#                  $COMOUT/${APREFIX}sfcanl.nc
 #
 # Remarks:
 #
@@ -121,7 +121,6 @@ LATB_SFC=${LATB_SFC:-$LATB_CASE}
 DONST=${DONST:-"NO"}
 LEVS=${LEVS:-64}
 LEVSP1=$(($LEVS+1))
-OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export NETCDF_OUT=".true."
 #  Directories.
 gfs_ver=${gfs_ver:-v16.3.0}
@@ -201,7 +200,7 @@ $NLN $FIXfv3/$CASE/${CASE}_oro_data.tile6.nc   ./orog.tile6.nc
 $NLN $SIGLEVEL                                 ./vcoord.txt
 
 # output gaussian global surface analysis files
-$NLN $COMOUT/${APREFIX}sfcanl${ASUFFIX} ./sfc.gaussian.analysis.file
+$NLN $COMOUT/${APREFIX}sfcanl.nc ./sfc.gaussian.analysis.file
 
 # Executable namelist
 cat <<EOF > fort.41
diff --git a/ush/gfs_bufr_netcdf.sh b/ush/gfs_bufr_netcdf.sh
index d58d383307..b358c6b69a 100755
--- a/ush/gfs_bufr_netcdf.sh
+++ b/ush/gfs_bufr_netcdf.sh
@@ -48,10 +48,8 @@ else
    bufrflag=".false."
 fi
 
-fformat="nc"
-
- SFCF="sfc"
- CLASS="class1fv3"
+SFCF="sfc"
+CLASS="class1fv3"
 cat << EOF > gfsparm
  &NAMMET
   levs=$LEVS,makebufr=$bufrflag,
@@ -82,7 +80,7 @@ do
    ic=0
    while [ $ic -lt 1000 ]
    do
-      if [ ! -f $COMIN/${RUN}.${cycle}.logf${hh2}.${fformat} ]
+      if [ ! -f $COMIN/${RUN}.${cycle}.logf${hh2}.txt ]
       then
           sleep 10
           ic=$(expr $ic + 1)
@@ -96,8 +94,8 @@ do
       fi
    done
 #------------------------------------------------------------------
-   ln -sf $COMIN/${RUN}.${cycle}.atmf${hh2}.${fformat} sigf${hh} 
-   ln -sf $COMIN/${RUN}.${cycle}.${SFCF}f${hh2}.${fformat} flxf${hh}
+   ln -sf $COMIN/${RUN}.${cycle}.atmf${hh2}.nc sigf${hh} 
+   ln -sf $COMIN/${RUN}.${cycle}.${SFCF}f${hh2}.nc flxf${hh}
 
    hh=$( expr $hh + $FINT )
    if test $hh -lt 10
diff --git a/ush/gfs_post.sh b/ush/gfs_post.sh
index 6a0a808802..01161acf52 100755
--- a/ush/gfs_post.sh
+++ b/ush/gfs_post.sh
@@ -222,7 +222,6 @@ export LOGSCRIPT=${LOGSCRIPT:-}
 export ENDSCRIPT=${ENDSCRIPT:-}
 export GFSOUT=${GFSOUT:-gfsout}
 export CTLFILE=${CTLFILE:-${NWPROD}/parm/gfs_cntrl.parm}
-export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export GRIBVERSION=${GRIBVERSION:-'grib1'}
 #  Other variables.
 export POSTGPVARS=${POSTGPVARS}
diff --git a/ush/hpssarch_gen.sh b/ush/hpssarch_gen.sh
index 8283cc66b6..f88fc213e2 100755
--- a/ush/hpssarch_gen.sh
+++ b/ush/hpssarch_gen.sh
@@ -11,12 +11,9 @@ type=${1:-gfs}                ##gfs, gdas, enkfgdas or enkfggfs
 CDATE=${CDATE:-2018010100}
 PDY=$(echo $CDATE | cut -c 1-8)
 cyc=$(echo $CDATE | cut -c 9-10)
-OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 ARCH_GAUSSIAN=${ARCH_GAUSSIAN:-"YES"}
 ARCH_GAUSSIAN_FHMAX=${ARCH_GAUSSIAN_FHMAX:-36}
 ARCH_GAUSSIAN_FHINC=${ARCH_GAUSSIAN_FHINC:-6}
-SUFFIX=${SUFFIX:-".nc"}
-format="netcdf"
 
 # Set whether to archive downstream products
 DO_DOWN=${DO_DOWN:-"NO"}
@@ -42,15 +39,15 @@ if [ $type = "gfs" ]; then
 
   if [ $ARCH_GAUSSIAN = "YES" ]; then
     rm -f gfs_pgrb2b.txt
-    rm -f gfs_${format}b.txt
+    rm -f gfs_netcdfb.txt
     rm -f gfs_flux.txt
     touch gfs_pgrb2b.txt
-    touch gfs_${format}b.txt
+    touch gfs_netcdfb.txt
     touch gfs_flux.txt
 
     if [ $MODE = "cycled" ]; then
-      rm -f gfs_${format}a.txt
-      touch gfs_${format}a.txt
+      rm -f gfs_netcdfa.txt
+      touch gfs_netcdfa.txt
     fi
   fi
 
@@ -71,18 +68,18 @@ if [ $type = "gfs" ]; then
     echo  "${dirname}${head}pgrb2b.1p00.anl.idx              " >>gfs_pgrb2b.txt
 
     if [ $MODE = "cycled" ]; then
-      echo  "${dirname}${head}atmanl${SUFFIX}            " >>gfs_${format}a.txt
-      echo  "${dirname}${head}sfcanl${SUFFIX}            " >>gfs_${format}a.txt
-      echo  "${dirname}${head}atmi*.nc                   " >>gfs_${format}a.txt
-      echo  "${dirname}${head}dtfanl.nc                  " >>gfs_${format}a.txt
-      echo  "${dirname}${head}loginc.txt                 " >>gfs_${format}a.txt
+      echo  "${dirname}${head}atmanl.nc            " >>gfs_netcdfa.txt
+      echo  "${dirname}${head}sfcanl.nc            " >>gfs_netcdfa.txt
+      echo  "${dirname}${head}atmi*.nc                   " >>gfs_netcdfa.txt
+      echo  "${dirname}${head}dtfanl.nc                  " >>gfs_netcdfa.txt
+      echo  "${dirname}${head}loginc.txt                 " >>gfs_netcdfa.txt
     fi
 
     fh=0
     while [ $fh -le $ARCH_GAUSSIAN_FHMAX ]; do
       fhr=$(printf %03i $fh)
-      echo  "${dirname}${head}atmf${fhr}${SUFFIX}        " >>gfs_${format}b.txt
-      echo  "${dirname}${head}sfcf${fhr}${SUFFIX}        " >>gfs_${format}b.txt
+      echo  "${dirname}${head}atmf${fhr}.nc        " >>gfs_netcdfb.txt
+      echo  "${dirname}${head}sfcf${fhr}.nc        " >>gfs_netcdfb.txt
       fh=$((fh+ARCH_GAUSSIAN_FHINC))
     done
   fi
@@ -301,16 +298,16 @@ if [ $type = "gdas" ]; then
   echo  "${dirname}${head}pgrb2.0p25.anl.idx         " >>gdas.txt
   echo  "${dirname}${head}pgrb2.1p00.anl             " >>gdas.txt
   echo  "${dirname}${head}pgrb2.1p00.anl.idx         " >>gdas.txt
-  echo  "${dirname}${head}atmanl${SUFFIX}            " >>gdas.txt
-  echo  "${dirname}${head}sfcanl${SUFFIX}            " >>gdas.txt
-  if [ -s $ROTDIR/${dirpath}${head}atmanl.ensres${SUFFIX} ]; then
-     echo  "${dirname}${head}atmanl.ensres${SUFFIX}  " >>gdas.txt
+  echo  "${dirname}${head}atmanl.nc            " >>gdas.txt
+  echo  "${dirname}${head}sfcanl.nc            " >>gdas.txt
+  if [ -s $ROTDIR/${dirpath}${head}atmanl.ensres.nc ]; then
+     echo  "${dirname}${head}atmanl.ensres.nc  " >>gdas.txt
   fi
-  if [ -s $ROTDIR/${dirpath}${head}atma003.ensres${SUFFIX} ]; then
-     echo  "${dirname}${head}atma003.ensres${SUFFIX}  " >>gdas.txt
+  if [ -s $ROTDIR/${dirpath}${head}atma003.ensres.nc ]; then
+     echo  "${dirname}${head}atma003.ensres.nc  " >>gdas.txt
   fi
-  if [ -s $ROTDIR/${dirpath}${head}atma009.ensres${SUFFIX} ]; then
-     echo  "${dirname}${head}atma009.ensres${SUFFIX}  " >>gdas.txt
+  if [ -s $ROTDIR/${dirpath}${head}atma009.ensres.nc ]; then
+     echo  "${dirname}${head}atma009.ensres.nc  " >>gdas.txt
   fi
   if [ -s $ROTDIR/${dirpath}${head}cnvstat ]; then
      echo  "${dirname}${head}cnvstat                 " >>gdas.txt
@@ -338,8 +335,8 @@ if [ $type = "gdas" ]; then
     echo  "${dirname}${head}pgrb2.1p00.f${fhr}         " >>gdas.txt
     echo  "${dirname}${head}pgrb2.1p00.f${fhr}.idx     " >>gdas.txt
     echo  "${dirname}${head}logf${fhr}.txt             " >>gdas.txt
-    echo  "${dirname}${head}atmf${fhr}${SUFFIX}        " >>gdas.txt
-    echo  "${dirname}${head}sfcf${fhr}${SUFFIX}        " >>gdas.txt
+    echo  "${dirname}${head}atmf${fhr}.nc              " >>gdas.txt
+    echo  "${dirname}${head}sfcf${fhr}.nc              " >>gdas.txt
     fh=$((fh+3))
   done
   flist="001 002 004 005 007 008"
@@ -442,18 +439,18 @@ if [ $type = "enkfgdas" -o $type = "enkfgfs" ]; then
   fi
   for FHR in $nfhrs; do  # loop over analysis times in window
      if [ $FHR -eq 6 ]; then
-        if [ -s $ROTDIR/${dirpath}${head}atmanl.ensmean${SUFFIX} ]; then
-            echo  "${dirname}${head}atmanl.ensmean${SUFFIX}      " >>enkf${CDUMP}.txt
+        if [ -s $ROTDIR/${dirpath}${head}atmanl.ensmean.nc ]; then
+            echo  "${dirname}${head}atmanl.ensmean.nc      " >>enkf${CDUMP}.txt
 	fi
-        if [ -s $ROTDIR/${dirpath}${head}atminc.ensmean${SUFFIX} ]; then
-            echo  "${dirname}${head}atminc.ensmean${SUFFIX}      " >>enkf${CDUMP}.txt
+        if [ -s $ROTDIR/${dirpath}${head}atminc.ensmean.nc ]; then
+            echo  "${dirname}${head}atminc.ensmean.nc      " >>enkf${CDUMP}.txt
         fi
      else
-        if [ -s $ROTDIR/${dirpath}${head}atma00${FHR}.ensmean${SUFFIX} ]; then
-	    echo  "${dirname}${head}atma00${FHR}.ensmean${SUFFIX}      " >>enkf${CDUMP}.txt
+        if [ -s $ROTDIR/${dirpath}${head}atma00${FHR}.ensmean.nc ]; then
+	    echo  "${dirname}${head}atma00${FHR}.ensmean.nc      " >>enkf${CDUMP}.txt
         fi
-        if [ -s $ROTDIR/${dirpath}${head}atmi00${FHR}.ensmean${SUFFIX} ]; then
-            echo  "${dirname}${head}atmi00${FHR}.ensmean${SUFFIX}      " >>enkf${CDUMP}.txt
+        if [ -s $ROTDIR/${dirpath}${head}atmi00${FHR}.ensmean.nc ]; then
+            echo  "${dirname}${head}atmi00${FHR}.ensmean.nc      " >>enkf${CDUMP}.txt
         fi
      fi 
   done # loop over FHR
@@ -474,12 +471,10 @@ if [ $type = "enkfgdas" -o $type = "enkfgfs" ]; then
   fh=3
   while [ $fh -le 9 ]; do
       fhr=$(printf %03i $fh)
-      echo  "${dirname}${head}atmf${fhr}.ensmean${SUFFIX}       " >>enkf${CDUMP}.txt
-      echo  "${dirname}${head}sfcf${fhr}.ensmean${SUFFIX}       " >>enkf${CDUMP}.txt
-      if [ $OUTPUT_FILE = "netcdf" ]; then
-          if [ -s $ROTDIR/${dirpath}${head}atmf${fhr}.ensspread${SUFFIX} ]; then
-	     echo  "${dirname}${head}atmf${fhr}.ensspread${SUFFIX}     " >>enkf${CDUMP}.txt
-          fi
+      echo  "${dirname}${head}atmf${fhr}.ensmean.nc       " >>enkf${CDUMP}.txt
+      echo  "${dirname}${head}sfcf${fhr}.ensmean.nc       " >>enkf${CDUMP}.txt
+      if [ -s $ROTDIR/${dirpath}${head}atmf${fhr}.ensspread.nc ]; then
+          echo  "${dirname}${head}atmf${fhr}.ensspread.nc     " >>enkf${CDUMP}.txt
       fi
       fh=$((fh+3))
   done
@@ -508,34 +503,34 @@ if [ $type = "enkfgdas" -o $type = "enkfgfs" ]; then
     for FHR in $nfhrs; do  # loop over analysis times in window
       if [ $FHR -eq 6 ]; then
          if [ $n -le $NTARS2 ]; then
-            if [ -s $ROTDIR/${dirpath}${head}atmanl${SUFFIX} ] ; then
-                echo "${dirname}${head}atmanl${SUFFIX}      " >>enkf${CDUMP}_grp${n}.txt
+            if [ -s $ROTDIR/${dirpath}${head}atmanl.nc ] ; then
+                echo "${dirname}${head}atmanl.nc      " >>enkf${CDUMP}_grp${n}.txt
             fi
-	    if [ -s $ROTDIR/${dirpath}${head}ratminc${SUFFIX} ] ; then
-		echo "${dirname}${head}ratminc${SUFFIX}      " >>enkf${CDUMP}_grp${n}.txt
+	    if [ -s $ROTDIR/${dirpath}${head}ratminc.nc ] ; then
+		echo "${dirname}${head}ratminc.nc      " >>enkf${CDUMP}_grp${n}.txt
 	    fi
          fi
-         if [ -s $ROTDIR/${dirpath}${head}ratminc${SUFFIX} ] ; then
-             echo "${dirname}${head}ratminc${SUFFIX}      " >>enkf${CDUMP}_restarta_grp${n}.txt
+         if [ -s $ROTDIR/${dirpath}${head}ratminc.nc ] ; then
+             echo "${dirname}${head}ratminc.nc      " >>enkf${CDUMP}_restarta_grp${n}.txt
          fi
 
       else
          if [ $n -le $NTARS2 ]; then
-             if [ -s $ROTDIR/${dirpath}${head}atma00${FHR}${SUFFIX} ] ; then
-                 echo "${dirname}${head}atma00${FHR}${SUFFIX}      " >>enkf${CDUMP}_grp${n}.txt
+             if [ -s $ROTDIR/${dirpath}${head}atma00${FHR}.nc ] ; then
+                 echo "${dirname}${head}atma00${FHR}.nc      " >>enkf${CDUMP}_grp${n}.txt
              fi
-             if [ -s $ROTDIR/${dirpath}${head}ratmi00${FHR}${SUFFIX} ] ; then
-                 echo "${dirname}${head}ratmi00${FHR}${SUFFIX}      " >>enkf${CDUMP}_grp${n}.txt
+             if [ -s $ROTDIR/${dirpath}${head}ratmi00${FHR}.nc ] ; then
+                 echo "${dirname}${head}ratmi00${FHR}.nc      " >>enkf${CDUMP}_grp${n}.txt
              fi
          fi
-         if [ -s $ROTDIR/${dirpath}${head}ratmi00${FHR}${SUFFIX} ] ; then
-             echo "${dirname}${head}ratmi00${FHR}${SUFFIX}      " >>enkf${CDUMP}_restarta_grp${n}.txt
+         if [ -s $ROTDIR/${dirpath}${head}ratmi00${FHR}.nc ] ; then
+             echo "${dirname}${head}ratmi00${FHR}.nc      " >>enkf${CDUMP}_restarta_grp${n}.txt
          fi
 
       fi 
-      echo "${dirname}${head}atmf00${FHR}${SUFFIX}       " >>enkf${CDUMP}_grp${n}.txt
+      echo "${dirname}${head}atmf00${FHR}.nc       " >>enkf${CDUMP}_grp${n}.txt
       if [ $FHR -eq 6 ]; then
-	  echo "${dirname}${head}sfcf00${FHR}${SUFFIX}       " >>enkf${CDUMP}_grp${n}.txt
+	  echo "${dirname}${head}sfcf00${FHR}.nc       " >>enkf${CDUMP}_grp${n}.txt
       fi
     done # loop over FHR
 
diff --git a/workflow/rocoto/workflow_tasks.py b/workflow/rocoto/workflow_tasks.py
index c31397dd26..f07d26a3a8 100644
--- a/workflow/rocoto/workflow_tasks.py
+++ b/workflow/rocoto/workflow_tasks.py
@@ -242,7 +242,6 @@ def init(self):
 
     def prep(self):
 
-        suffix = self._base["SUFFIX"]
         dump_suffix = self._base["DUMP_SUFFIX"]
         gfs_cyc = self._base["gfs_cyc"]
         dmpdir = self._base["DMPDIR"]
@@ -251,7 +250,7 @@ def prep(self):
         deps = []
         dep_dict = {'type': 'metatask', 'name': f'{"gdas"}post', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009{suffix}'
+        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
         data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'
@@ -399,7 +398,6 @@ def analdiag(self):
 
     def atmanalprep(self):
 
-        suffix = self._base["SUFFIX"]
         dump_suffix = self._base["DUMP_SUFFIX"]
         gfs_cyc = self._base["gfs_cyc"]
         dmpdir = self._base["DMPDIR"]
@@ -408,7 +406,7 @@ def atmanalprep(self):
         deps = []
         dep_dict = {'type': 'metatask', 'name': 'gdaspost', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009{suffix}'
+        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
         data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'
@@ -456,14 +454,13 @@ def atmanalpost(self):
 
     def aeroanlinit(self):
 
-        suffix = self._base["SUFFIX"]
         dump_suffix = self._base["DUMP_SUFFIX"]
         dmpdir = self._base["DMPDIR"]
 
         deps = []
         dep_dict = {'type': 'metatask', 'name': 'gdaspost', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009{suffix}'
+        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
         data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'
@@ -501,12 +498,11 @@ def aeroanlfinal(self):
 
     def ocnanalprep(self):
 
-        suffix = self._base["SUFFIX"]
         dump_suffix = self._base["DUMP_SUFFIX"]
         dmpdir = self._base["DMPDIR"]
 
         deps = []
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/ocean/gdas.t@Hz.ocnf009{suffix}'
+        data = f'&ROTDIR;/gdas.@Y@m@d/@H/ocean/gdas.t@Hz.ocnf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
@@ -1087,7 +1083,6 @@ def eupd(self):
 
     def atmensanalprep(self):
 
-        suffix = self._base["SUFFIX"]
         dump_suffix = self._base["DUMP_SUFFIX"]
         gfs_cyc = self._base["gfs_cyc"]
         dmpdir = self._base["DMPDIR"]
@@ -1096,7 +1091,7 @@ def atmensanalprep(self):
         deps = []
         dep_dict = {'type': 'metatask', 'name': 'gdaspost', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
-        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009{suffix}'
+        data = f'&ROTDIR;/gdas.@Y@m@d/@H/atmos/gdas.t@Hz.atmf009.nc'
         dep_dict = {'type': 'data', 'data': data, 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
         data = f'{dmpdir}/{self.cdump}{dump_suffix}.@Y@m@d/@H/atmos/{self.cdump}.t@Hz.updated.status.tm00.bufr_d'