Updates for GSL

 - changed if-statement for netcdf files in GSL archive script to look for a single file (atmf000 netcdf file) instead of multiple files since it now produces errors when running as bash script
 - added GSL archive script for archiving netcdf files only
 - changed getic script to look for atm file instead of sfc file in if-statements since atm file is much larger than sfc file
 - comment out if-statement to check if 0p25 grib2 file already exists in post.sh so post job will run if resubmitted when walltime is exceeded
 - change config.base.emc.dyn link to point to JET version
 # Please enter the commit message for your changes. Lines starting

jobs/rocoto/arch_gsl.sh

@@ -52,7 +52,7 @@ if [ $HPSSARCH = "YES" ]; then
       fi
 
       ## netcdf files ##
-      if [ -f *nc ]; then
+      if [ -f g*atmf000.nc ]; then
         # archive netcdf files (gfs.t00z.atmfHHH.nc, gfs.t00z.sfcfHHH.nc, gfs.t00z.logfHHH.txt )
         htar -P -cvf $ATARDIR/$YYYY/$CDATE/gfs_nc.tar gfs*.nc gfs.*log*.txt
         status=$?

jobs/rocoto/arch_gsl_nc.sh

@@ -0,0 +1,83 @@
+#!/bin/ksh -x
+
+###############################################################
+## Abstract:
+## Archive driver script
+## RUN_ENVIR : runtime environment (emc | nco)
+## HOMEgfs   : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE  : current analysis date (YYYYMMDDHH)
+## CDUMP  : cycle name (gdas / gfs)
+## PDY    : current date (YYYYMMDD)
+## cyc    : current cycle (HH)
+## ATCFNAME  : atcf track identifier
+## COMPONENT : component (atmos/wave)
+###############################################################
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Source relevant configs
+configs="base arch"
+for config in $configs; do
+    . $EXPDIR/config.${config}
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+COMIN="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+cd $COMIN
+
+YYYY=`echo $PDY|cut -c1-4`
+###############################################################
+# Archive data to HPSS
+if [ $HPSSARCH = "YES" ]; then
+###############################################################
+
+  if [ $CDUMP = "gfs" ]; then
+
+      ## nemsio files ##
+      if [ -f *nemsio ]; then
+        # archive nemsio files (gfs.t00z.atmfHHH.nemsio, gfs.t00z.sfcfHHH.nemsio, gfs.t00z.logfHHH.nemsio )
+        htar -P -cvf $ATARDIR/$YYYY/$CDATE/gfs_nemsio.tar gfs.*nemsio
+        status=$?
+        if [ $status -ne 0 ]; then
+          echo "HTAR $CDATE gfs_nemsio.tar failed"
+          exit $status
+        fi
+      fi
+
+      ## netcdf files ##
+#JKH      if [ -f *f???.nc ]; then
+      if [ -f g*atmf000.nc ]; then
+        # archive netcdf files (gfs.t00z.atmfHHH.nc, gfs.t00z.sfcfHHH.nc, gfs.t00z.logfHHH.txt )
+        htar -P -cvf $ATARDIR/$YYYY/$CDATE/gfs_nc.tar gfs*.nc gfs.*log*.txt
+        status=$?
+        if [ $status -ne 0 ]; then
+          echo "HTAR $CDATE gfs_nc.tar failed"
+          exit $status
+        fi
+      fi
+
+      # archive GRIB2 files (gfs.t00z.pgrb2.0p25.fHHH, gfs.t00z.pgrb2.0p50.fHHH) 
+      #   and tracker files (tctrk.atcf.YYYYMMDDHH.gcp1.txt)
+#JKH      if [ -f tctrk.atcf.${CDATE}.${ATCFNAME}.txt ]; then
+#JKH        htar -P -cvf $ATARDIR/$YYYY/$CDATE/gfs_pgrb2.tar gfs.*pgrb2.0p25* gfs.*pgrb2.0p5* tctrk.atcf.${CDATE}.${ATCFNAME}.txt
+#JKH      else
+#JKH        htar -P -cvf $ATARDIR/$YYYY/$CDATE/gfs_pgrb2.tar gfs.*pgrb2.0p25* gfs.*pgrb2.0p5* 
+#JKH      fi
+#JKH      status=$?
+#JKH      if [ $status -ne 0 ]; then
+#JKH        echo "HTAR $CDATE gfs_pgrb2.tar failed"
+#JKH        exit $status
+#JKH      fi
+
+  fi
+
+###############################################################
+fi  ##end of HPSS archive
+###############################################################

jobs/rocoto/getic_gsl_fv3gfsv16.sh

@@ -37,17 +37,17 @@ atm_file=`echo $pubatm_file | cut -d. -f2-`
 echo "pubsfc_file:  $pubsfc_file"
 echo "pubatm_file:  $pubatm_file"
 
-if [[ -f $PUBDIR/${pubsfc_file} ]]; then
-  echo "linking $PUBDIR...."
-  ln -fs $PUBDIR/${pubsfc_file} $sfc_file
-  ln -fs $PUBDIR/${pubatm_file} $atm_file
-elif  [[ -f $RETRODIR/${pubsfc_file} ]]; then
+if  [[ -f $RETRODIR/${pubatm_file} ]]; then
   echo "linking $RETRODIR...."
   echo "pubsfc_file:  $pubsfc_file"
   echo "pubatm_file:  $pubatm_file"
   ln -fs $RETRODIR/${pubsfc_file} $sfc_file
   ln -fs $RETRODIR/${pubatm_file} $atm_file 
-elif  [[ -f $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${sfc_file} ]]; then
+elif [[ -f $PUBDIR/${pubatm_file} ]]; then
+  echo "linking $PUBDIR...."
+  ln -fs $PUBDIR/${pubsfc_file} $sfc_file
+  ln -fs $PUBDIR/${pubatm_file} $atm_file
+elif  [[ -f $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
   echo "linking $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
   echo "sfc_file:  $sfc_file"
   echo "atm_file:  $atm_file"

jobs/rocoto/post.sh

@@ -36,12 +36,12 @@ for fhr in $fhrlst; do
 
     #master=$ROTDIR/${CDUMP}.${PDY}/${cyc}/$COMPONENT/${CDUMP}.t${cyc}z.master.grb2f${fhr}
     pgb0p25=$ROTDIR/${CDUMP}.${PDY}/${cyc}/$COMPONENT/${CDUMP}.t${cyc}z.pgrb2.0p25.f${fhr}
-    if [ ! -s $pgb0p25 ]; then
+#JKH    if [ ! -s $pgb0p25 ]; then
         export post_times=$fhr
         $HOMEgfs/jobs/JGLOBAL_ATMOS_NCEPPOST
         status=$?
         [[ $status -ne 0 ]] && exit $status
-    fi
+#JKH    fi
 
 done
 

parm/config/config.base.emc.dyn

@@ -1 +1 @@
-config.base.emc.dyn_hera
+config.base.emc.dyn_jet