Issue #527: update workflow generator, env, resources, jobs, and scri…

…pts to execute global_cycle as a standalone job
NOAA-EMC · Dec 14, 2021 · 50b53b5 · 50b53b5
1 parent 512ae81
commit 50b53b5
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Showing 7 changed files with 61 additions and 75 deletions.
diff --git a/env/WCOSS_DELL_P3.env b/env/WCOSS_DELL_P3.env
@@ -4,7 +4,7 @@ if [ $# -ne 1 ]; then
 
     echo "Must specify an input argument to set runtime environment variables!"
     echo "argument can be any one of the following:"
-    echo "anal fcst post vrfy metp"
+    echo "anal sfcanl fcst post vrfy metp"
     echo "eobs eupd ecen esfc efcs epos"
     echo "postsnd awips gempak"
     exit 1
@@ -80,6 +80,14 @@ elif [ $step = "anal" ]; then
     export USE_CFP=${USE_CFP:-"YES"}
     export APRUNCFP="$launcher \$ncmd $mpmd"
 
+elif [ $step = "sfcanl" ]; then
+    nth_max=$(($npe_node_max / $npe_node_sfcanl))
+
+    export NTHREADS_CYCLE=${nth_sfcanl:-14}
+    [[ $NTHREADS_CYCLE -gt $npe_node_max ]] && export NTHREADS_CYCLE=$npe_node_max
+    npe_sfcanl=${ntiles:-6}
+    export APRUN_CYCLE="$launcher $npe_sfcanl"
+
 elif [ $step = "gldas" ]; then
 
     nth_max=$(($npe_node_max / $npe_node_gldas))

diff --git a/jobs/JGLOBAL_ATMOS_SFCANL b/jobs/JGLOBAL_ATMOS_SFCANL
@@ -10,7 +10,7 @@ date
 # Source relevant config files
 #############################
 export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
-configs="base anal analcalc"
+configs="base sfcanl"
 config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
 for config in $configs; do
     . $config_path/config.$config
@@ -22,7 +22,7 @@ done
 ##########################################
 # Source machine runtime environment
 ##########################################
-. $HOMEgfs/env/${machine}.env anal
+. $HOMEgfs/env/${machine}.env sfcanl
 status=$?
 [[ $status -ne 0 ]] && exit $status
 
@@ -140,10 +140,6 @@ export TCVITL="${COMOUT}/${OPREFIX}syndata.tcvitals.tm00"
 export DOGCYCLE=${DOGCYCLE:-"YES"}
 
 
-# Generate Gaussian surface analysis
-export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
-
-
 ###############################################################
 # Run relevant script
 env

diff --git a/jobs/rocoto/sfcanl.sh b/jobs/rocoto/sfcanl.sh
@@ -0,0 +1,13 @@
+#!/bin/ksh -x
+
+###############################################################
+# Source FV3GFS workflow modules
+. $HOMEgfs/ush/load_fv3gfs_modules.sh
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Execute the JJOB
+$HOMEgfs/jobs/JGLOBAL_ATMOS_SFCANL
+status=$?
+exit $status
diff --git a/parm/config/config.resources b/parm/config/config.resources
@@ -9,7 +9,7 @@ if [ $# -ne 1 ]; then
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
     echo "getic init coupled_ic"
-    echo "anal analcalc analdiag gldas fcst post vrfy metp arch echgres"
+    echo "anal sfcanl analcalc analdiag gldas fcst post vrfy metp arch echgres"
     echo "eobs ediag eomg eupd ecen esfc efcs epos earc"
     echo "init_chem mom6ic ocnpost"
     echo "waveinit waveprep wavepostsbs wavepostbndpnt wavepostbndpntbll wavepostpnt"
@@ -147,6 +147,13 @@ elif [ $step = "anal" ]; then
     export nth_cycle=$nth_anal
     if [[ "$machine" == "WCOSS_C" ]]; then export memory_anal="3072M"; fi
 
+elif [ $step = "sfcanl" ]; then
+
+    export wtime_sfcanl="00:10:00"
+    export npe_sfcanl=6
+    export nth_sfcanl=$npe_node_max
+    export npe_node_sfcanl=$(echo "$npe_node_max / $nth_sfcanl" | bc)
+
 elif [ $step = "analcalc" ]; then
 
     export wtime_analcalc="00:10:00"

diff --git a/scripts/exglobal_atmos_sfcanl.sh b/scripts/exglobal_atmos_sfcanl.sh
@@ -68,12 +68,6 @@ export DELTSFC=${DELTSFC:-6}
 export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
 export FIXfv3=${FIXfv3:-$HOMEgfs/fix/fix_fv3_gmted2010}
 
-DOGAUSFCANL=${DOGAUSFCANL-"NO"}
-GAUSFCANLSH=${GAUSFCANLSH:-$HOMEgfs/ush/gaussian_sfcanl.sh}
-export GAUSFCANLEXE=${GAUSFCANLEXE:-$HOMEgfs/exec/gaussian_sfcanl.exe}
-NTHREADS_GAUSFCANL=${NTHREADS_GAUSFCANL:-1}
-APRUN_GAUSFCANL=${APRUN_GAUSFCANL:-${APRUN:-""}}
-
 # FV3 specific info (required for global_cycle)
 export CASE=${CASE:-"C384"}
 ntiles=${ntiles:-6}
@@ -292,60 +286,6 @@ if [ $DOGCYCLE = "YES" ]; then
 fi
 
 
-##############################################################
-# If analysis increment is written by GSI, produce an analysis file here
-if [ $DO_CALC_ANALYSIS == "YES" ]; then 
-   # link analysis and increment files
-   $NLN $ATMANL siganl
-   $NLN $ATMINC siginc.nc
-   if [ $DOHYBVAR = "YES" -a $l4densvar = ".true." -a $lwrite4danl = ".true." ]; then
-      $NLN $ATMA03   siga03
-      $NLN $ATMI03   sigi03.nc
-      $NLN $ATMA04   siga04
-      $NLN $ATMI04   sigi04.nc
-      $NLN $ATMA05   siga05
-      $NLN $ATMI05   sigi05.nc
-      $NLN $ATMA07   siga07
-      $NLN $ATMI07   sigi07.nc
-      $NLN $ATMA08   siga08
-      $NLN $ATMI08   sigi08.nc
-      $NLN $ATMA09   siga09
-      $NLN $ATMI09   sigi09.nc
-   fi
-   # link guess files
-   $NLN $ATMG03 sigf03
-   $NLN $ATMGES sigf06
-   $NLN $ATMG09 sigf09
-
-   [[ -f $ATMG04 ]] && $NLN $ATMG04 sigf04
-   [[ -f $ATMG05 ]] && $NLN $ATMG05 sigf05
-   [[ -f $ATMG07 ]] && $NLN $ATMG07 sigf07
-   [[ -f $ATMG08 ]] && $NLN $ATMG08 sigf08
-
-   # Link hourly backgrounds (if present)
-   if [ -f $ATMG04 -a -f $ATMG05 -a -f $ATMG07 -a -f $ATMG08 ]; then
-      nhr_obsbin=1
-   fi
-
-   $CALCANLPY
-   export err=$?; err_chk
-else
-   echo "Neither increment nor analysis are generated by external utils"
-fi
-
-##############################################################
-# Create gaussian grid surface analysis file at middle of window
-if [ $DOGAUSFCANL = "YES" ]; then
-    export APRUNSFC=$APRUN_GAUSFCANL
-    export OMP_NUM_THREADS_SFC=$NTHREADS_GAUSFCANL
-
-    $GAUSFCANLSH
-    export err=$?; err_chk
-fi
-
-echo "$CDUMP $CDATE atmanl and sfcanl done at `date`" > $COMOUT/${APREFIX}loganl.txt
-
-
 ################################################################################
 # Postprocessing
 cd $pwd

diff --git a/sorc/checkout.sh b/sorc/checkout.sh
@@ -41,9 +41,11 @@ fi
 echo gsi checkout ...
 if [[ ! -d gsi.fd ]] ; then
     rm -f ${topdir}/checkout-gsi.log
-    git clone --recursive https://github.com/NOAA-EMC/GSI.git gsi.fd >> ${logdir}/checkout-gsi.log 2>&1
+##  git clone --recursive https://github.com/NOAA-EMC/GSI.git gsi.fd >> ${logdir}/checkout-gsi.log 2>&1
+    git clone --recursive https://github.com/RussTreadon-NOAA/GSI.git gsi.fd >> ${logdir}/checkout-gsi.log 2>&1
     cd gsi.fd
-    git checkout 9c1fc15d42573b398037319bbf8d5143ad126fb6
+##  git checkout 9c1fc15d42573b398037319bbf8d5143ad126fb6
+    git checkout feature/rm_sfcanl
     git submodule update
     cd ${topdir}
 else

diff --git a/ush/rocoto/setup_workflow.py b/ush/rocoto/setup_workflow.py
@@ -42,7 +42,7 @@ def main():
         print(f'input arg:     --expdir = {repr(args.expdir)}')
         sys.exit(1)
 
-    gfs_steps = ['prep', 'anal', 'analdiag', 'analcalc', 'gldas', 'fcst', 'postsnd', 'post', 'vrfy', 'arch']
+    gfs_steps = ['prep', 'anal', 'sfcanl', 'analdiag', 'analcalc', 'gldas', 'fcst', 'postsnd', 'post', 'vrfy', 'arch']
     gfs_steps_gempak = ['gempak']
     gfs_steps_awips = ['awips']
     gfs_steps_wafs = ['wafs', 'wafsgrib2', 'wafsblending', 'wafsgcip', 'wafsgrib20p25', 'wafsblending0p25']
@@ -244,7 +244,7 @@ def get_gdasgfs_resources(dict_configs, cdump='gdas'):
     reservation = base.get('RESERVATION', 'NONE').upper()
 
     #tasks = ['prep', 'anal', 'fcst', 'post', 'vrfy', 'arch']
-    tasks = ['prep', 'anal', 'analcalc']
+    tasks = ['prep', 'anal', 'sfcanl', 'analcalc']
 
     if cdump in ['gdas']:
         tasks += ['analdiag']
@@ -485,13 +485,27 @@ def get_gdasgfs_tasks(dict_configs, cdump='gdas'):
 
     dict_tasks[f'{cdump}anal'] = task
 
+    # sfcanl
+    deps = []
+    data = f'&ROTDIR;/{cdump}.@Y@m@d/@H/atmos/{cdump}.t@Hz.loginc.txt'
+    dep_dict = {'type': 'data', 'data': data}
+    deps.append(rocoto.add_dependency(dep_dict))
+    dep_dict = {'type': 'task', 'name': f'{cdump}anal'}
+    deps.append(rocoto.add_dependency(dep_dict))
+    dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
+    task = wfu.create_wf_task('sfcanl', cdump=cdump, envar=envars, dependency=dependencies)
+
+    dict_tasks[f'{cdump}sfcanl'] = task
+
     # analcalc
-    deps1 = []
+    deps = []
     data = f'&ROTDIR;/{cdump}.@Y@m@d/@H/atmos/{cdump}.t@Hz.loginc.txt'
     dep_dict = {'type': 'data', 'data': data}
-    deps1.append(rocoto.add_dependency(dep_dict))
+    deps.append(rocoto.add_dependency(dep_dict))
     dep_dict = {'type': 'task', 'name': f'{cdump}anal'}
     deps.append(rocoto.add_dependency(dep_dict))
+    dep_dict = {'type': 'task', 'name': f'{cdump}sfcanl'}
+    deps.append(rocoto.add_dependency(dep_dict))
     if dohybvar in ['y', 'Y', 'yes', 'YES'] and cdump == 'gdas':
         dep_dict = {'type': 'task', 'name': f'{"gdas"}echgres', 'offset': '-06:00:00'}
         deps.append(rocoto.add_dependency(dep_dict))
@@ -530,6 +544,8 @@ def get_gdasgfs_tasks(dict_configs, cdump='gdas'):
         deps1.append(rocoto.add_dependency(dep_dict))
         dep_dict = {'type': 'task', 'name': f'{cdump}anal'}
         deps1.append(rocoto.add_dependency(dep_dict))
+        dep_dict = {'type': 'task', 'name': f'{cdump}sfcanal'}
+        deps1.append(rocoto.add_dependency(dep_dict))
         dependencies1 = rocoto.create_dependency(dep_condition='or', dep=deps1)
 
         deps2 = []
@@ -553,11 +569,15 @@ def get_gdasgfs_tasks(dict_configs, cdump='gdas'):
             dep_dict = {'type': 'task', 'name': f'{cdump}gldas'}
             deps1.append(rocoto.add_dependency(dep_dict))
         else:
-            dep_dict = {'type': 'task', 'name': f'{cdump}analcalc'}
+            dep_dict = {'type': 'task', 'name': f'{cdump}anal'}
+            deps1.append(rocoto.add_dependency(dep_dict))
+            dep_dict = {'type': 'task', 'name': f'{cdump}sfcanl'}
             deps1.append(rocoto.add_dependency(dep_dict))
     elif cdump in ['gfs']:
         dep_dict = {'type': 'task', 'name': f'{cdump}anal'}
         deps1.append(rocoto.add_dependency(dep_dict))
+        dep_dict = {'type': 'task', 'name': f'{cdump}sfcanal'}
+        deps1.append(rocoto.add_dependency(dep_dict))
     dependencies1 = rocoto.create_dependency(dep_condition='or', dep=deps1)
 
     if do_wave in ['Y', 'YES'] and cdump in cdumps: