Update coupled with develop

.gitignore

@@ -33,6 +33,7 @@ sorc/logs
 sorc/fv3gfs.fd
 sorc/gfs_post.fd
 sorc/gfs_wafs.fd
+sorc/gldas.fd
 sorc/gsi.fd
 sorc/ufs_utils.fd
 sorc/verif-global.fd
@@ -61,7 +62,6 @@ sorc/checkout-verif-global.log
 sorc/chgres_cube.fd
 sorc/emcsfc_ice_blend.fd
 sorc/emcsfc_snow2mdl.fd
-sorc/filter_topo.fd
 sorc/fregrid.fd
 sorc/fv3gfs.fd/
 sorc/getsfcensmeanp.fd
@@ -104,13 +104,8 @@ sorc/global_gsi.fd
 sorc/interp_inc.fd
 sorc/make_hgrid.fd
 sorc/make_solo_mosaic.fd
-sorc/mkgfsnemsioctl.fd
 sorc/ncdiag_cat.fd
-sorc/nemsio_chgdate.fd
-sorc/nemsio_get.fd
-sorc/nemsio_read.fd
 sorc/nst_tf_chg.fd
-sorc/orog.fd
 sorc/oznmon_horiz.fd
 sorc/oznmon_time.fd
 sorc/radmon_angle.fd
@@ -191,10 +186,10 @@ scripts/exglobal_diag.sh
 # ush symlinks
 ush/calcanl_gfs.py
 ush/calcinc_gfs.py
+ush/chgres_cube.sh
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh
 ush/fix_precip.sh
-ush/fv3gfs_chgres.sh
 ush/fv3gfs_downstream_nems.sh
 ush/fv3gfs_driver_grid.sh
 ush/fv3gfs_dwn_nems.sh

Externals.cfg

@@ -1,35 +1,36 @@
 # External sub-modules of global-workflow
 
 [FV3GFS]
-tag = GFS.v16.0.16
+hash = 9350745855aebe0790813e0ed2ba5ad680e3f75c
 local_path = sorc/fv3gfs.fd
 repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
 [GSI]
-tag = gfsda.v16.1.0
+hash = 9c1fc15d42573b398037319bbf8d5143ad126fb6
 local_path = sorc/gsi.fd
 repo_url = https://github.com/NOAA-EMC/GSI.git
 protocol = git
 required = True
 
 [GLDAS]
-tag = gldas_gfsv16_release.v1.13.0
+tag = gldas_gfsv16_release.v1.15.0
 local_path = sorc/gldas.fd
 repo_url = https://github.com/NOAA-EMC/GLDAS.git
 protocol = git
 required = True
 
 [EMC_post]
-tag = upp_gfsv16_release.v1.1.3
+#No externals setting = .gitmodules will be invoked for CMakeModules and comupp/src/lib/crtm2 submodules
+hash = ff42e0227d6100285d4179a2572b700fd5a959cb
 local_path = sorc/gfs_post.fd
 repo_url = https://github.com/NOAA-EMC/EMC_post.git
 protocol = git
 required = True
 
 [UFS_UTILS]
-tag = ops-gfsv16.0.0
+tag = ufs_utils_1_4_0
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
 protocol = git
@@ -43,7 +44,7 @@ protocol = git
 required = True
 
 [EMC_gfs_wafs]
-tag = gfs_wafs.v6.0.22
+hash = c2a29a67d9432b4d6fba99eac7797b81d05202b6
 local_path = sorc/gfs_wafs.fd
 repo_url = https://github.com/NOAA-EMC/EMC_gfs_wafs.git
 protocol = git

env/HERA.env

@@ -160,14 +160,6 @@ elif [ $step = "efcs" ]; then
 
 elif [ $step = "post" ]; then
 
-    source /apps/lmod/lmod/init/sh
-    module unload esmf/8.0.1_ParallelNetCDF.release
-    module unload netcdf_parallel/4.7.4.release
-    module unload hdf5_parallel/1.10.6.release
-    module use -a /scratch2/NCEPDEV/nwprod/NCEPLIBS/modulefiles
-    module load hdf5_parallel/1.10.6
-    module load netcdf_parallel/4.7.4
-
     nth_max=$(($npe_node_max / $npe_node_post))
 
     export NTHREADS_NP=${nth_np:-1}
@@ -214,11 +206,9 @@ elif [ $step = "epos" ]; then
     [[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
     export APRUN_EPOS="$launcher"
 
-elif [ $step = "fv3ic" ]; then
+elif [ $step = "init" ]; then
 
-    export NTHREADS_CHGRES=${nth_chgres:-$npe_node_max}
-    [[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
-    export APRUN_CHGRES="time"
+    export APRUN="$launcher"
 
 elif [ $step = "postsnd" ]; then
 

env/JET.env

@@ -179,11 +179,9 @@ elif [ $step = "epos" ]; then
     [[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
     export APRUN_EPOS="$launcher ${npe_epos:-$PBS_NP}"
 
-elif [ $step = "fv3ic" ]; then
+elif [ $step = "init" ]; then
 
-    export NTHREADS_CHGRES=${nth_chgres:-$npe_node_max}
-    [[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
-    export APRUN_CHGRES="time"
+    export APRUN="$launcher"
 
 elif [ $step = "postsnd" ]; then
 

env/ORION.env

@@ -202,11 +202,9 @@ elif [ $step = "epos" ]; then
     [[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
     export APRUN_EPOS="$launcher"
 
-elif [ $step = "fv3ic" ]; then
+elif [ $step = "init" ]; then
 
-    export NTHREADS_CHGRES=${nth_chgres:-$npe_node_max}
-    [[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
-    export APRUN_CHGRES="time"
+    export APRUN="$launcher"
 
 elif [ $step = "postsnd" ]; then
 

env/WCOSS_C.env

@@ -198,11 +198,9 @@ elif [ $step = "epos" ]; then
     [[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
     export APRUN_EPOS="$launcher -j 1 -n $npe_epos -N $npe_node_epos -d $NTHREADS_EPOS -cc depth"
 
-elif [ $step = "fv3ic" ]; then
+elif [ $step = "init" ]; then
 
-    export NTHREADS_CHGRES=${nth_chgres:-$npe_node_max}
-    [[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
-    export APRUN_CHGRES="$launcher -j 1 -n 1 -N 1 -d $NTHREADS_CHGRES -cc depth"
+    export APRUN="$launcher"
 
 elif [ $step = "vrfy" ]; then
 

env/WCOSS_DELL_P3.env

@@ -204,11 +204,9 @@ elif [ $step = "epos" ]; then
     [[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
     export APRUN_EPOS="$launcher ${npe_epos:-$PBS_NP}"
 
-elif [ $step = "fv3ic" ]; then
+elif [ $step = "init" ]; then
 
-    export NTHREADS_CHGRES=${nth_chgres:-$npe_node_max}
-    [[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
-    export APRUN_CHGRES="time"
+    export APRUN="mpirun"
 
 elif [ $step = "postsnd" ]; then
 

jobs/JGLOBAL_WAVE_PREP

@@ -79,13 +79,24 @@ else
       $NLN $DMPDIR/${WAVECUR_DID}.${RPDY} $ROTDIR/${WAVECUR_DID}.${RPDY}
     fi
     export COMIN_WAV_RTOFS=${COMIN_WAV_RTOFS:-$ROTDIR}
-  fi 
+  fi
+
+  BRPDY=`$NDATE -24 ${RPDY}00 | cut -c1-8`
+  if [ ! -L $ROTDIR/${WAVECUR_DID}.${BRPDY} ]; then # Check if symlink already exists in ROTDIR
+    $NLN $DMPDIR/${WAVECUR_DID}.${BRPDY} $ROTDIR/${WAVECUR_DID}.${BRPDY}
+  fi
+  if [ ! -L $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/${WAVICEFILE} ]; then # Check if symlink already exists in ROTDIR
+    $NLN $DMPDIR/$CDUMP.${PDY}/$cyc/${WAVICEFILE} $ROTDIR/$CDUMP.${PDY}/$cyc/atmos/${WAVICEFILE}
+  fi
+  export COMIN_WAV_ICE=${COMIN_WAV_ICE:-$ROTDIR/$RUN.$PDY/$cyc/atmos}
+  export COMIN_WAV_RTOFS=${COMIN_WAV_RTOFS:-$ROTDIR}
+
   if [ $WW3ICEINP = "YES" ]; then 
     if [ ! -L $ROTDIR/${CDUMP}.${PDY}/${cyc}/atmos/${WAVICEFILE} ]; then # Check if symlink already exists in ROTDIR
       $NLN $DMPDIR/$CDUMP.${PDY}/$cyc/${WAVICEFILE} $ROTDIR/$CDUMP.${PDY}/$cyc/atmos/${WAVICEFILE}
     fi
     export COMIN_WAV_ICE=${COMIN_WAV_ICE:-$ROTDIR/$RUN.$PDY/$cyc/atmos}
-  fi 
+  fi
 fi
 
 # Execute the Script  

jobs/rocoto/arch.sh

@@ -204,7 +204,13 @@ if [ $CDUMP = "gfs" ]; then
 
     #for targrp in gfs_flux gfs_netcdf/nemsio gfs_pgrb2b; do
     if [ ${SAVEFCSTNEMSIO:-"YES"} = "YES" ]; then
-        for targrp in gfs_flux gfs_${format}a gfs_${format}b gfs_pgrb2b; do
+        if [ $MODE = "cycled" ]; then
+          targrp_list=`gfs_flux gfs_${format}a gfs_${format}b gfs_pgrb2b`
+        elif [ $MODE = "free" ]; then
+          targrp_list=`gfs_flux gfs_${format}b gfs_pgrb2b`
+        fi
+        #for targrp in gfs_flux gfs_${format}a gfs_${format}b gfs_pgrb2b; do
+        for targrp in $targrp_list; do
             htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
             status=$?
             if [ $status -ne 0  -a $CDATE -ge $firstday ]; then