NOAA-EMC · WalterKolczynski-NOAA · Dec 10, 2021 · Jul 19, 2021 · Jul 19, 2021 · Jul 20, 2021
diff --git a/.gitignore b/.gitignore
@@ -30,7 +30,7 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-sorc/fv3gfs.fd
+sorc/ufs_model.fd
 sorc/gfs_post.fd
 sorc/gfs_wafs.fd
 sorc/gldas.fd

diff --git a/README.md b/README.md
@@ -12,6 +12,9 @@ The global-workflow current supports the following machines:
 * WCOSS-Dell
 * WCOSS-Cray
 * Hera
+* Orion
+
+Quick-start instructions are below. Full instructions are available in the [wiki](https://github.com/NOAA-EMC/global-workflow/wiki/Run-Global-Workflow)
 
 ## Build global-workflow:
 
@@ -25,15 +28,26 @@ $ sh checkout.sh
 ### 2. Build components
 
 While in /sorc folder:
+
+Uncoupled
 ```
 $ sh build_all.sh
 ```
+Coupled
+```
+$ sh build_all.sh -c
+```
 
 ### 3. Link components
 
 While in /sorc folder:
+
+Uncoupled
 ```
-$ sh link_fv3gfs.sh emc $MACHINE
+$ sh link_workflow.sh emc $MACHINE
 ```
-
-...where $MACHINE is "dell", "cray", or "hera".
+Coupled
+```
+$ sh link_workflow.sh emc $MACHINE coupled
+```
+...where $MACHINE is "dell", "cray", "hera", or "orion".
diff --git a/env/HERA.env b/env/HERA.env
@@ -135,7 +135,10 @@ elif [ $step = "fcst" ]; then
     export NTHREADS_FV3=${nth_fv3:-$nth_max}
     [[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
     export cores_per_node=$npe_node_max
-    export APRUN_FV3="$launcher"
+    if [[ $CDUMP == "gfs" ]]; then
+        npe_fcst=$npe_fcst_gfs
+    fi
+    export APRUN_FV3="$launcher -n $npe_fcst"
 
     export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
     [[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max
@@ -152,7 +155,7 @@ elif [ $step = "efcs" ]; then
     export NTHREADS_FV3=${nth_efcs:-$nth_max}
     [[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
     export cores_per_node=$npe_node_max
-    export APRUN_FV3="$launcher"
+    export APRUN_FV3="$launcher -n $npe_efcs"
 
     export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
     [[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max

diff --git a/env/ORION.env b/env/ORION.env
@@ -131,7 +131,10 @@ elif [ $step = "fcst" ]; then
     export NTHREADS_FV3=${nth_fv3:-$nth_max}
     [[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
     export cores_per_node=$npe_node_max
-    export APRUN_FV3="$launcher"
+    if [[ $CDUMP == "gfs" ]]; then
+        npe_fcst=$npe_fcst_gfs
+    fi
+    export APRUN_FV3="$launcher -n $npe_fcst"
 
     export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
     [[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max
@@ -148,7 +151,7 @@ elif [ $step = "efcs" ]; then
     export NTHREADS_FV3=${nth_efcs:-$nth_max}
     [[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
     export cores_per_node=$npe_node_max
-    export APRUN_FV3="$launcher"
+    export APRUN_FV3="$launcher -n $npe_efcs"
 
     export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
     [[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max

@@ -9,6 +9,12 @@ date
 if [ $RUN_ENVIR = "emc" ]; then
 #--------------------------------
 
+##############################################
+# Set variables used in the exglobal script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
 #############################
 # Source relevant config files
 #############################
@@ -20,15 +26,6 @@ for config in $configs; do
     status=$?
     [[ $status -ne 0 ]] && exit $status
 done
-# Source additional configs
-if [ ${DO_WAVE:-"NO"} = "YES" ]; then
-  configs="wave"
-  for config in $configs; do
-    . $config_path/config.$config
-    status=$?
-    [[ $status -ne 0 ]] && exit $status
-  done
-fi
 
 ##########################################
 # Source machine runtime environment
@@ -65,12 +62,6 @@ export pgmout="OUTPUT.${pid}"
 export pgmerr=errfile
 
 
-##############################################
-# Set variables used in the exglobal script
-##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-
 if [ $RUN_ENVIR = "nco" ]; then
     export ROTDIR=${COMROOT:?}/$NET/$envir
     export RSTDIR=${GESROOT:?}/$envir

@@ -73,19 +73,23 @@ if [ $RUN_ENVIR = "nco" ]; then
   export COMIN_WAV_ICE=${COMIN_WAV_ICE:-$(compath.py gfs/prod)}/${CDUMP}.${PDY}/${cyc}/atmos
   export COMIN_WAV_RTOFS=${COMIN_WAV_RTOFS:-$(compath.py ${WAVECUR_DID}/prod)}
 else
-  if [ ! -d $DMPDIR/${WAVECUR_DID}.${RPDY} ]; then export RPDY=`$NDATE -24 ${PDY}00 | cut -c1-8`; fi 
-  if [ ! -L $ROTDIR/${WAVECUR_DID}.${RPDY} ]; then # Check if symlink already exists in ROTDIR
-    $NLN $DMPDIR/${WAVECUR_DID}.${RPDY} $ROTDIR/${WAVECUR_DID}.${RPDY}
-  fi
-  BRPDY=`$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 [ $WW3CURINP = "YES" ]; then
+    if [ ! -d $DMPDIR/${WAVECUR_DID}.${RPDY} ]; then export RPDY=`$NDATE -24 ${PDY}00 | cut -c1-8`; fi 
+    if [ ! -L $ROTDIR/${WAVECUR_DID}.${RPDY} ]; then # Check if symlink already exists in ROTDIR
+      $NLN $DMPDIR/${WAVECUR_DID}.${RPDY} $ROTDIR/${WAVECUR_DID}.${RPDY}
+    fi
+    BRPDY=`$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}.${BRPDY}
+    fi
+    export COMIN_WAV_RTOFS=${COMIN_WAV_RTOFS:-$ROTDIR}
+  fi 
+  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
 
 # Execute the Script  

@@ -175,59 +175,35 @@ cd $ROTDIR
 
 if [ $CDUMP = "gfs" ]; then
 
-    #for targrp in gfsa gfsb - NOTE - do not check htar error status
-    for targrp in gfsa gfsb; do
-        htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
-    done
+    targrp_list="gfsa gfsb"
 
-    #for targrp in gfs_flux gfs_netcdf/nemsio gfs_pgrb2b; do
-    if [ ${SAVEFCSTNEMSIO:-"YES"} = "YES" ]; then
+    if [ ${ARCH_GAUSSIAN:-"NO"} = "YES" ]; then
+        targrp_list="$targrp_list gfs_flux gfs_${format}b gfs_pgrb2b"
         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`
+          targrp_list="$targrp_list gfs_${format}a"
         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
-                echo "HTAR $CDATE ${targrp}.tar failed"
-                exit $status
-            fi
-        done
     fi
 
-    #for targrp in gfswave
     if [ $DO_WAVE = "YES" -a "$WAVE_CDUMP" != "gdas" ]; then
-        for targrp in gfswave; do
-            htar -P -cvf $ATARDIR/$CDATE/${targrp}.tar `cat $ARCH_LIST/${targrp}.txt`
-            status=$?
-            if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-                echo "HTAR $CDATE ${targrp}.tar failed"
-                exit $status
-            fi
-        done
+        targrp_list="$targrp_list gfswave"
+    fi
+
+    if [ $DO_OCN = "YES" ]; then
+        targrp_list="$targrp_list ocn_ice_grib2_0p5 ocn_ice_grib2_0p25 ocn_2D ocn_3D ocn_xsect ocn_daily wavocn gfs_flux_1p00"
+    fi
+
+    if [ $DO_ICE = "YES" ]; then
+        targrp_list="$targrp_list ice"
     fi
 
     #for restarts    
     if [ $SAVEFCSTIC = "YES" ]; then
-        htar -P -cvf $ATARDIR/$CDATE/gfs_restarta.tar `cat $ARCH_LIST/gfs_restarta.txt`
-        status=$?
-        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-            echo "HTAR $CDATE gfs_restarta.tar failed"
-            exit $status
-        fi
+        targrp_list="$targrp_list gfs_restarta"
     fi
 
     #for downstream products
     if [ $DO_BUFRSND = "YES" -o $WAFSF = "YES" ]; then
-        htar -P -cvf $ATARDIR/$CDATE/gfs_downstream.tar `cat $ARCH_LIST/gfs_downstream.txt`
-        status=$?
-        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-            echo "HTAR $CDATE gfs_downstream.tar failed"
-            exit $status
-        fi
+        targrp_list="$targrp_list gfs_downstream"  
     fi
 
     #--save mdl gfsmos output from all cycles in the 18Z archive directory
@@ -239,57 +215,37 @@ if [ $CDUMP = "gfs" ]; then
             exit $status
         fi
     fi
+elif [ $CDUMP = "gdas" ]; then
 
-fi
-
-
-if [ $CDUMP = "gdas" ]; then
-
-    htar -P -cvf $ATARDIR/$CDATE/gdas.tar `cat $ARCH_LIST/gdas.txt`
-    status=$?
-    if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-        echo "HTAR $CDATE gdas.tar failed"
-        exit $status
-    fi
+    targrp_list="gdas"
 
     #gdaswave
     if [ $DO_WAVE = "YES" ]; then
-        htar -P -cvf $ATARDIR/$CDATE/gdaswave.tar `cat $ARCH_LIST/gdaswave.txt`
-        status=$?
-        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-            echo "HTAR $CDATE gdaswave.tar failed"
-            exit $status
-        fi
+        targrp_list="$targrp_list gdaswave"
     fi
 
     if [ $SAVEWARMICA = "YES" -o $SAVEFCSTIC = "YES" ]; then
-        htar -P -cvf $ATARDIR/$CDATE/gdas_restarta.tar `cat $ARCH_LIST/gdas_restarta.txt`
-        status=$?
-        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-            echo "HTAR $CDATE gdas_restarta.tar failed"
-            exit $status
-        fi
+        targrp_list="$targrp_list gdas_restarta"
+
         if [ $DO_WAVE = "YES" ]; then
-            htar -P -cvf $ATARDIR/$CDATE/gdaswave_restart.tar `cat $ARCH_LIST/gdaswave_restart.txt`
-            status=$?
-            if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-                echo "HTAR $CDATE gdaswave_restart.tar failed"
-                exit $status
-            fi
+            targrp_list="$targrp_list gdaswave_restart"
         fi
     fi
 
     if [ $SAVEWARMICB = "YES" -o $SAVEFCSTIC = "YES" ]; then
-        htar -P -cvf $ATARDIR/$CDATE/gdas_restartb.tar `cat $ARCH_LIST/gdas_restartb.txt`
-        status=$?
-        if [ $status -ne 0  -a $CDATE -ge $firstday ]; then
-            echo "HTAR $CDATE gdas_restartb.tar failed"
-            exit $status
-        fi
+        targrp_list="$targrp_list gdas_restartb"
     fi
-
 fi
 
+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
+        echo "HTAR $CDATE ${targrp}.tar failed"
+        exit $status
+    fi
+done
+
 ###############################################################
 fi  ##end of HPSS archive
 ###############################################################