Combine setup_workflows scripts (#859)

`setup_workflow.py` and `setup_workflow_fcstonly.py` are used for setting up the XML for cycled and forecast only configurations.
They share large parts of the tasks and dependencies.

This PR unifies the ones listed above and makes room for extending for incoming applications.
The above two scripts are being replaced by `setup_xml.py`.
The usage is:

```
$> setup_xml.py /path/to/experiment_directory
```

This PR also removes the handicap of defining hundreds of entities for task resources.  Instead the task resources are placed with the task itself.

This PR also does the following:
- moves the declaration of `DOBNDPNT_WAVE="NO"` from `config.wave` to `config.base`
- reduces timestep at `C48` from `1200s` to `450s` in `config.fv3`.  Several ensemble members failed.  Inspecting `config.fv3.nco.static`, the value there is `450s`
- `eobs` job times out with a wallclock time of `15m`.  It is increased to `45m` to play it safe.

.gitignore

@@ -5,6 +5,7 @@ __pycache__
 *.[aox]
 *.mod
 *.sw[a-p]
+.idea/
 
 # Ignore folders
 #-------------------

parm/config/config.base.emc.dyn

@@ -159,6 +159,7 @@ export DO_ICE="NO"
 export DO_AERO="NO"
 export CCPP_SUITE="FV3_GFS_v17_p8"
 export WAVE_CDUMP="" # When to include wave suite: gdas, gfs, or both
+export DOBNDPNT_WAVE="NO"
 export cplwav2atm=".false."
 
 case "${APP}" in
@@ -190,7 +191,7 @@ case "${APP}" in
 
     if [[ "$APP" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
-        export WAVE_CDUMP="both"    
+        export WAVE_CDUMP="both"
         export cplwav2atm=".true."
         export confignamevarfornems="${confignamevarfornems}_wave"
     fi

parm/config/config.base.nco.static

@@ -161,7 +161,7 @@ export FHMAX_HF_GFS=120
 export FHOUT_HF_GFS=1
 export ILPOST=1           # gempak output frequency up to F120
 
-# frequency for saving restart files. set to 6,12,24,48 etc 
+# 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
@@ -209,6 +209,7 @@ export gldas_cyc=00
 # run wave component
 export DO_WAVE=YES
 export WAVE_CDUMP="both"
+export DOBNDPNT_WAVE="YES"
 
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
 export imp_physics=8

parm/config/config.fv3

@@ -41,7 +41,7 @@ fi
 # (Standard) Model resolution dependent variables
 case $case_in in
     "C48")
-        export DELTIM=1200
+        export DELTIM=450
         export layout_x=3
         export layout_y=2
         export layout_x_gfs=3

parm/config/config.resources

@@ -184,12 +184,12 @@ elif [ $step = "sfcanl" ]; then
 elif [ $step = "gldas" ]; then
 
     export wtime_gldas="00:10:00"
-    export npe_gldas=96  
-    export nth_gldas=1 
+    export npe_gldas=96
+    export nth_gldas=1
     export npe_node_gldas=$npe_node_max
-    export npe_gaussian=96  
-    export nth_gaussian=1 
-    export npe_node_gaussian=24           
+    export npe_gaussian=96
+    export nth_gaussian=1
+    export npe_node_gaussian=24
     if [[ "$machine" = "WCOSS_DELL_P3" ]]; then export npe_gldas=112 ; fi
     if [[ "$machine" == "WCOSS_C" ]]; then export memory_gldas="3072M"; fi
 
@@ -360,13 +360,13 @@ elif [ $step = "vrfy" ]; then
     export npe_vrfy_gfs=1
     export npe_node_vrfy_gfs=1
     if [[ "$machine" == "WCOSS_C" ]]; then
-	    export memory_vrfy="3072M"
+      export memory_vrfy="3072M"
     elif [[ "$machine" == "HERA" ]]; then
-	    export memory_vrfy="16384M"
+      export memory_vrfy="16384M"
     fi
 
 elif [ $step = "metp" ]; then
-    
+
     export nth_metp=1
     export wtime_metp="03:00:00"
     export npe_metp=4
@@ -375,9 +375,9 @@ elif [ $step = "metp" ]; then
     export npe_metp_gfs=4
     export npe_node_metp_gfs=4
     if [[ "$machine" == "WCOSS_C" ]]; then
-            export memory_metp="3072M"
+      export memory_metp="3072M"
     elif [[ "$machine" == "THEIA" ]]; then
-            export memory_metp="16384M"
+      export memory_metp="16384M"
     fi
 
 elif [ $step = "echgres" ]; then
@@ -394,9 +394,9 @@ elif [ $step = "init" ]; then
     export nth_init=1
     export npe_node_init=6
     if [ $machine = "WCOSS_DELL_P3" ]; then
-        export memory_init="10G"
+      export memory_init="10G"
     else
-        export memory_init="70G"
+      export memory_init="70G"
     fi
 
 elif [ $step = "init_chem" ]; then
@@ -428,7 +428,7 @@ elif [ $step = "coupled_ic" ]; then
 
 elif [ $step = "eobs" -o $step = "eomg" ]; then
 
-    export wtime_eobs="00:15:00"
+    export wtime_eobs="00:45:00"
     export wtime_eomg="01:00:00"
     if [ $CASE = "C768" ]; then
       export npe_eobs=200
@@ -439,10 +439,16 @@ elif [ $step = "eobs" -o $step = "eomg" ]; then
     elif [ $CASE = "C96" -o $CASE = "C48" ]; then
       export npe_eobs=20
     fi
+    export npe_eomg=$npe_eobs
     export nth_eobs=2
     if [[ "$machine" = "WCOSS_DELL_P3" ]]; then export nth_eobs=7; fi
+    export nth_eomg=$nth_eobs
     export npe_node_eobs=$(echo "$npe_node_max / $nth_eobs" | bc)
-    if [[ "$machine" == "WCOSS_C" ]]; then export memory_eobs="3072M"; fi
+    export npe_node_eomg=$npe_node_eobs
+    if [[ "$machine" == "WCOSS_C" ]]; then
+      export memory_eobs="3072M"
+      export memory_eomg=$memory_eobs
+    fi
 
 elif [ $step = "ediag" ]; then
 

parm/config/config.wave

@@ -30,7 +30,6 @@ export waveGRD=${waveGRD:-'gnh_10m aoc_9km gsh_15m'}
 export waveGRDN=${waveGRDN:-'1 2 3'} # gridnumber for ww3_multi
 export waveGRDG=${waveGRDG:-'10 20 30'} # gridgroup for ww3_multi
 export USE_WAV_RMP=${USE_WAV_RMP:-'YES'} #yes/no rmp grid remapping pre-processed coefficients
-export DOBNDPNT_WAVE=${DOBNDPNT_WAVE:-'YES'}
 export waveMULTIGRID=${waveMULTIGRID:-'.true.'}
 export MESH_WAV=${MESH_WAV:-'mesh.gwes_30m.nc'}
 
@@ -84,20 +83,20 @@ fi
 # Restart timing business
 
 export RSTTYPE_WAV='T'          # generate second tier of restart files
-if [ "${CDUMP}" != gfs ]; then    # Setting is valid for GDAS and GEFS 
+if [ "${CDUMP}" != gfs ]; then    # Setting is valid for GDAS and GEFS
   export DT_1_RST_WAV=10800       # time between restart files, set to DTRST=1 for a single restart file
   export DT_2_RST_WAV=43200       # restart stride for checkpointing restart
   export RSTIOFF_WAV=0            # first restart file offset relative to model start
 else                              # This is a GFS run
   rst_dt_gfs=$(( restart_interval_gfs * 3600 ))
-  if [ $rst_dt_gfs -gt 0 ]; then 
+  if [ $rst_dt_gfs -gt 0 ]; then
     export DT_1_RST_WAV=${rst_dt_gfs:-0}   # time between restart files, set to DTRST=1 for a single restart file
     export DT_2_RST_WAV=${rst_dt_gfs:-0}   # restart stride for checkpointing restart
-  else 
+  else
     rst_dt_fhmax=$(( FHMAX_WAV * 3600 ))
     export DT_1_RST_WAV=0                    # time between restart files, set to DTRST=1 for a single restart file
-    export DT_2_RST_WAV=${rst_dt_fhmax:-0}   # use checkpoint restart file name for creating restart at end of run 
-  fi 
+    export DT_2_RST_WAV=${rst_dt_fhmax:-0}   # use checkpoint restart file name for creating restart at end of run
+  fi
   export RSTIOFF_WAV=0                   # first restart file offset relative to model start
 fi
 #