Remove nemsio support (#1255)

Removes remaining nemsio support from scripts. Now-unnecessary variables will be removed in a follow-up PR. Refs: #601
NOAA-EMC · Jan 19, 2023 · 78509d6 · 78509d6
1 parent 62944fb
commit 78509d6
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diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS b/jobs/JGLOBAL_ATMOS_ANALYSIS
@@ -55,13 +55,8 @@ fi
 
 
 # Get LEVS
-if [ ${GSUFFIX} = ".nc" ]; then
-    export LEVS=$(${NCLEN} ${ATMGES} pfull)
-    status=$?
-else
-    export LEVS=$(${NEMSIOGET} ${ATMGES} dimz | awk '{print $2}')
-    status=$?
-fi
+export LEVS=$(${NCLEN} ${ATMGES} pfull)
+status=$?
 [[ ${status} -ne 0 ]] && exit ${status}
 
 

diff --git a/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC b/jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
@@ -53,13 +53,8 @@ fi
 
 
 # Get LEVS
-if [ ${GSUFFIX} = ".nc" ]; then
-    export LEVS=$(${NCLEN} ${ATMGES} pfull)
-    status=$?
-else
-    export LEVS=$(${NEMSIOGET} ${ATMGES} dimz | awk '{print $2}')
-    status=$?
-fi
+export LEVS=$(${NCLEN} ${ATMGES} pfull)
+status=$?
 [[ ${status} -ne 0 ]] && exit ${status}
 
 

diff --git a/parm/config/config.anal b/parm/config/config.anal
@@ -40,11 +40,6 @@ fi
 export lobsdiag_forenkf=".false."  # anal does not need to write out jacobians
 								   # set to .true. in config.eobs and config.eupd
 
-if [ $OUTPUT_FILE = "nemsio" ]; then
-	export DO_CALC_INCREMENT="YES"
-	export DO_CALC_ANALYSIS="NO"
-fi
-
 # Do not process the following datasets
 export GSNDBF=${GSNDBF:-/dev/null}
 export AMSREBF=${AMSREBF:-/dev/null}

diff --git a/parm/config/config.base.emc.dyn b/parm/config/config.base.emc.dyn
@@ -87,7 +87,6 @@ export VERBOSE="YES"
 export KEEPDATA="NO"
 export CHGRP_RSTPROD="@CHGRP_RSTPROD@"
 export CHGRP_CMD="@CHGRP_CMD@"
-export NEMSIOGET="$HOMEgfs/exec/nemsio_get"
 export NCDUMP="$NETCDF/bin/ncdump"
 export NCLEN="$HOMEgfs/ush/getncdimlen"
 
@@ -271,8 +270,8 @@ export ILPOST=1           # gempak output frequency up to F120
 export restart_interval_gfs=0
 
 # 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
-# if gaussian_grid, set OUTPUT_FILE for nemsio or netcdf
+# if quilting=true, choose OUTPUT_GRID as cubed_sphere_grid in netcdf
+# if gaussian_grid, set OUTPUT_FILE for netcdf
 # WRITE_DOPOST=true, use inline POST
 export QUILTING=".true."
 export OUTPUT_GRID="gaussian_grid"
@@ -281,15 +280,9 @@ export WRITE_DOPOST=".true."
 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
+export SUFFIX=".nc"
+export NEMSIO_IN=".false."
+export NETCDF_IN=".true."
 
 # IAU related parameters
 export DOIAU="YES"        # Enable 4DIAU for control with 3 increments
@@ -378,11 +371,6 @@ export MAKE_ACFTBUFR="@MAKE_ACFTBUFR@"
 # 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.post b/parm/config/config.post
@@ -8,16 +8,10 @@ echo "BEGIN: config.post"
 # Get task specific resources
 . $EXPDIR/config.resources post
 
-# Convert nemsio files to grib files using post job
-#-------------------------------------------
-
 # No. of concurrent post jobs [0 implies sequential]
 export NPOSTGRP=42
 export OUTTYP=4
-export MODEL_OUT_FORM=binarynemsiompiio
-if [ $OUTPUT_FILE = "netcdf" ]; then
-    export MODEL_OUT_FORM=netcdfpara
-fi
+export MODEL_OUT_FORM=netcdfpara
 
 # Post driver job that calls gfs_post.sh and downstream jobs
 export POSTJJOBSH="$HOMEpost/jobs/JGLOBAL_POST"

diff --git a/parm/config/config.resources b/parm/config/config.resources
@@ -764,10 +764,6 @@ elif [ ${step} = "postsnd" ]; then
     export npe_node_postsnd=10
     export npe_postsndcfp=9
     export npe_node_postsndcfp=1
-    if [ ${OUTPUT_FILE} == "nemsio" ]; then
-        export npe_postsnd=13
-        export npe_node_postsnd=4
-    fi
     if [[ "$(echo "${npe_node_postsnd} * ${nth_postsnd}" | bc)" -gt "${npe_node_max}" ]]; then
         export npe_node_postsnd=$(echo "${npe_node_max} / ${nth_postsnd}" | bc)
     fi

diff --git a/scripts/exgdas_atmos_post.sh b/scripts/exgdas_atmos_post.sh
@@ -49,15 +49,11 @@ export JO=${LATB:-721}
 # specify default model output format: 3 for sigio and 4
 # for nemsio
 export OUTTYP=${OUTTYP:-4}
-export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export TCYC=${TCYC:-".t${cyc}z."}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
 if (( OUTTYP == 4 )) ; then
-  if [[ "${OUTPUT_FILE}" = "netcdf" ]]; then
-    export SUFFIX=".nc"
-  else
-    export SUFFIX=".nemsio"
-  fi
+  export SUFFIX=".nc"
 else
   export SUFFIX=
 fi
@@ -202,7 +198,7 @@ else   ## not_anl if_stimes
       # period and error exit
       ###############################
       if (( ic == SLEEP_LOOP_MAX )); then
-        echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
+        echo " *** FATAL ERROR: No model output for f${fhr} "
         export err=9
         err_chk
       fi

diff --git a/scripts/exgdas_enkf_sfc.sh b/scripts/exgdas_enkf_sfc.sh
@@ -32,7 +32,6 @@ ntiles=${ntiles:-6}
 # Utilities
 NCP=${NCP:-"/bin/cp -p"}
 NLN=${NLN:-"/bin/ln -sf"}
-NEMSIOGET=${NEMSIOGET:-${NWPROD}/exec/nemsio_get}
 NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
 
 # Scripts

diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
@@ -25,7 +25,6 @@ pwd=$(pwd)
 # Utilities
 NCP=${NCP:-"/bin/cp -p"}
 NLN=${NLN:-"/bin/ln -sf"}
-NEMSIOGET=${NEMSIOGET:-$NWPROD/utils/exec/nemsio_get}
 NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
 USE_CFP=${USE_CFP:-"NO"}
 CFP_MP=${CFP_MP:-"NO"}
@@ -89,30 +88,20 @@ INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
 
 ################################################################################
 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 $ATMGES_ENSMEAN pfull)} # get LEVS_ENFK
-   use_gfs_ncio=".true."
-   use_gfs_nemsio=".false."
-   paranc=${paranc:-".true."}
-   if [ $DO_CALC_INCREMENT = "YES" ]; then
-      write_fv3_incr=".false."
-   else
-      write_fv3_incr=".true."
-      WRITE_INCR_ZERO="incvars_to_zero= $INCREMENTS_TO_ZERO,"
-   fi
+LONB_ENKF=${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."}
+if [ $DO_CALC_INCREMENT = "YES" ]; then
+   write_fv3_incr=".false." 
 else
-   LEVS_ENKF=${LEVS_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimz | awk '{print $2}')}
-   LATB_ENKF=${LATB_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimy | awk '{print $2}')}
-   LONB_ENKF=${LONB_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimx | awk '{print $2}')}
-   use_gfs_ncio=".false."
-   use_gfs_nemsio=".true."
-   paranc=${paranc:-".false."}
+   write_fv3_incr=".true."
+   WRITE_INCR_ZERO="incvars_to_zero= $INCREMENTS_TO_ZERO,"
 fi
 LATA_ENKF=${LATA_ENKF:-$LATB_ENKF}
 LONA_ENKF=${LONA_ENKF:-$LONB_ENKF}
-
 SATANGL=${SATANGL:-${FIXgsi}/global_satangbias.txt}
 SATINFO=${SATINFO:-${FIXgsi}/global_satinfo.txt}
 CONVINFO=${CONVINFO:-${FIXgsi}/global_convinfo.txt}
@@ -121,7 +110,6 @@ SCANINFO=${SCANINFO:-${FIXgsi}/global_scaninfo.txt}
 HYBENSINFO=${HYBENSINFO:-${FIXgsi}/global_hybens_info.l${LEVS_ENKF}.txt}
 ANAVINFO=${ANAVINFO:-${FIXgsi}/global_anavinfo.l${LEVS_ENKF}.txt}
 VLOCALEIG=${VLOCALEIG:-${FIXgsi}/vlocal_eig_l${LEVS_ENKF}.dat}
-
 ENKF_SUFFIX="s"
 [[ $SMOOTH_ENKF = "NO" ]] && ENKF_SUFFIX=""
 

diff --git a/scripts/exgfs_atmos_post.sh b/scripts/exgfs_atmos_post.sh
@@ -40,7 +40,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 
 cd "${DATA}" || exit 1
 
-# specify model output format type: 4 for nemsio, 3 for sigio
 export POSTGPSH=${POSTGPSH:-${USHgfs}/gfs_post.sh}
 export GFSDOWNSH=${GFSDOWNSH:-${USHgfs}/fv3gfs_downstream_nems.sh}
 export GFSDOWNSHF=${GFSDOWNSHF:-${USHgfs}/inter_flux.sh}
@@ -66,14 +65,10 @@ export GOESF=${GOESF:-"YES"}
 export WAFSF=${WAFSF:-"NO"}
 export PGBF=${PGBF:-"YES"}
 export TCYC=${TCYC:-".t${cyc}z."}
-export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export PREFIX=${PREFIX:-${RUN}${TCYC}}
 if (( OUTTYP == 4 )); then
-  if [[ "${OUTPUT_FILE}" = "netcdf" ]]; then
-    export SUFFIX=".nc"
-  else
-    export SUFFIX=".nemsio"
-  fi
+  export SUFFIX=".nc"
 else
   export SUFFIX=
 fi
@@ -256,7 +251,7 @@ else   ## not_anl if_stime
       # period and error exit
       ###############################
       if (( ic == SLEEP_LOOP_MAX )); then
-        echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
+        echo " *** FATAL ERROR: No model output for f${fhr} "
         export err=9
         err_chk
       fi

diff --git a/scripts/exgfs_atmos_postsnd.sh b/scripts/exgfs_atmos_postsnd.sh
@@ -36,38 +36,20 @@ export INCREMENT=12
 export MAKEBUFR=NO
 export F00FLAG=YES
 export fformat=${OUTPUT_FILE:-netcdf}
-if [ $fformat == "netcdf" ]
- then
 export atmfm="nc"
 export logfm="txt"
-else 
-export atmfm="nemsio"
-export logfm="nemsio"
-fi
-
-    export NINT1=${FHOUT_HF_GFS:-1}
-    export NEND1=${FHMAX_HF_GFS:-120}
-    export NINT3=${FHOUT_GFS:-3}
+export NINT1=${FHOUT_HF_GFS:-1}
+export NEND1=${FHMAX_HF_GFS:-120}
+export NINT3=${FHOUT_GFS:-3}
 
 rm -f -r ${COMOUT}/bufr.${cycle}
 mkdir -p ${COMOUT}/bufr.${cycle}
-
-    if [ -f $HOMEgfs/ush/getncdimlen ]
-	then
-	GETDIM=$HOMEgfs/ush/getncdimlen
-	else
-	GETDIM=$EXECbufrsnd/getncdimlen
-	fi
-if [ $fformat == "netcdf" ]
- then
-export LEVS=$($GETDIM $COMIN/${RUN}.${cycle}.atmf000.${atmfm} pfull)
+if [ -f $HOMEgfs/ush/getncdimlen ]; then
+  GETDIM=$HOMEgfs/ush/getncdimlen
 else
-# Extract number of vertical levels from $STARTHOUR atmospheric file
-export NEMSIOGET=${NEMSIOGET:-$EXECbufrsnd/nemsio_get}
-fhr3=$(printf %03i $STARTHOUR)
-ATMFCS=$COMIN/${RUN}.${cycle}.atmf${fhr3}.nemsio
-export LEVS=$($NEMSIOGET $ATMFCS dimz | awk '{print $2}')
+  GETDIM=$EXECbufrsnd/getncdimlen
 fi
+export LEVS=$($GETDIM $COMIN/${RUN}.${cycle}.atmf000.${atmfm} pfull)
 
 ### Loop for the hour and wait for the sigma and surface flux file:
 export FSTART=$STARTHOUR

diff --git a/scripts/exglobal_archive.sh b/scripts/exglobal_archive.sh
@@ -16,12 +16,7 @@ fi
 # CURRENT CYCLE
 APREFIX="${CDUMP}.t${cyc}z."
 ASUFFIX=${ASUFFIX:-${SUFFIX}}
-
-if [ "${ASUFFIX}" = ".nc" ]; then
-   format="netcdf"
-else
-   format="nemsio"
-fi
+format="netcdf"
 
 # Realtime parallels run GFS MOS on 1 day delay
 # If realtime parallel, back up CDATE_MOS one day

diff --git a/scripts/exglobal_atmos_analysis_calc.sh b/scripts/exglobal_atmos_analysis_calc.sh
@@ -43,7 +43,6 @@ export NCP=${NCP:-"/bin/cp"}
 export NMV=${NMV:-"/bin/mv"}
 export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
-export NEMSIOGET=${NEMSIOGET:-${NWPROD}/exec/nemsio_get}
 export NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
 COMPRESS=${COMPRESS:-gzip}
 UNCOMPRESS=${UNCOMPRESS:-gunzip}

diff --git a/scripts/exglobal_diag.sh b/scripts/exglobal_diag.sh
@@ -42,7 +42,6 @@ export NCP=${NCP:-"/bin/cp"}
 export NMV=${NMV:-"/bin/mv"}
 export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
-export NEMSIOGET=${NEMSIOGET:-${NWPROD}/exec/nemsio_get}
 export NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
 export CATEXEC=${CATEXEC:-$ncdiag_ROOT/bin/ncdiag_cat_serial.x}
 COMPRESS=${COMPRESS:-gzip}

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -501,14 +501,8 @@ EOF
   JCAP_STP=${JCAP_STP:-$JCAP_CASE}
   LONB_STP=${LONB_STP:-$LONB_CASE}
   LATB_STP=${LATB_STP:-$LATB_CASE}
-
   cd $DATA
-
   affix="nc"
-  if [ "$OUTPUT_FILE" = "nemsio" ]; then
-    affix="nemsio"
-  fi
-
   if [ $QUILTING = ".true." -a $OUTPUT_GRID = "gaussian_grid" ]; then
     fhr=$FHMIN
     for fhr in $OUTPUT_FH; do

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
@@ -133,11 +133,10 @@ FV3_GFS_predet(){
 
   QUILTING=${QUILTING:-".true."}
   OUTPUT_GRID=${OUTPUT_GRID:-"gaussian_grid"}
-  OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+  OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
   WRITE_NEMSIOFLIP=${WRITE_NEMSIOFLIP:-".true."}
   WRITE_FSYNCFLAG=${WRITE_FSYNCFLAG:-".true."}
-  affix="nemsio"
-  [[ "$OUTPUT_FILE" = "netcdf" ]] && affix="nc"
+  affix="nc"
 
   rCDUMP=${rCDUMP:-$CDUMP}
 

diff --git a/ush/gaussian_sfcanl.sh b/ush/gaussian_sfcanl.sh
@@ -121,13 +121,8 @@ LATB_SFC=${LATB_SFC:-$LATB_CASE}
 DONST=${DONST:-"NO"}
 LEVS=${LEVS:-64}
 LEVSP1=$(($LEVS+1))
-OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
-if [ $OUTPUT_FILE = "netcdf" ]; then
-    export NETCDF_OUT=".true."
-else
-    export NETCDF_OUT=".false."
-fi
-
+OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
+export NETCDF_OUT=".true."
 #  Directories.
 gfs_ver=${gfs_ver:-v16.3.0}
 BASEDIR=${BASEDIR:-${PACKAGEROOT:-/lfs/h1/ops/prod/packages}}

diff --git a/ush/gfs_post.sh b/ush/gfs_post.sh
@@ -222,8 +222,7 @@ export LOGSCRIPT=${LOGSCRIPT:-}
 export ENDSCRIPT=${ENDSCRIPT:-}
 export GFSOUT=${GFSOUT:-gfsout}
 export CTLFILE=${CTLFILE:-${NWPROD}/parm/gfs_cntrl.parm}
-#export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-export OUTPUT_FILE=${OUTPUT_FILE:-"nemsio"}
+export OUTPUT_FILE=${OUTPUT_FILE:-"netcdf"}
 export GRIBVERSION=${GRIBVERSION:-'grib1'}
 #  Other variables.
 export POSTGPVARS=${POSTGPVARS}
@@ -260,16 +259,10 @@ fi
 export SIGHDR=${SIGHDR:-${NWPROD}/exec/global_sighdr} 
 export IDRT=${IDRT:-4}
 
-# run post to read nemsio file if OUTTYP=4
+# run post to read file if OUTTYP=4
 if (( OUTTYP == 4 )) ; then
-	if [ "${OUTPUT_FILE}" = "netcdf" ]; then
-		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-netcdfpara}
-	elif [ "${OUTPUT_FILE}" = "nemsio" ]; then
-		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-	else
-		export MODEL_OUT_FORM=${MODEL_OUT_FORM:-binarynemsiompiio}
-	fi
-	export GFSOUT=${NEMSINP}
+  export MODEL_OUT_FORM=${MODEL_OUT_FORM:-netcdfpara}
+  export GFSOUT=${NEMSINP}
 fi
 
 # allow threads to use threading in Jim's sp lib