Merge branch 'ufs-community:develop' into c5OSup

ufs-community · Nov 13, 2024 · 82f998c · 82f998c
2 parents b1d6712 + a7f882f
commit 82f998c
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diff --git a/docs/source/chgres_cube.rst b/docs/source/chgres_cube.rst
@@ -389,7 +389,7 @@ Namelist variables with “input” in their name refer to data input to chgres_
 Variable Mapping (VARMAP) table
 -------------------------------
 
-The VARMAP table, set in the chgres_cube namelist (variable varmap_file), controls how chgres_cube handles variables that might be missing from the GRIB2 files. Since there are so many different versions of GRIB2 files, it's often uncertain what fields are available even if you know what source model the data is coming from.  Each file contains the following:  (Note, only the GFS physics suite is currently supported.)
+The VARMAP table, set in the chgres_cube namelist (variable varmap_file), controls how chgres_cube handles variables that might be missing from the GRIB2 files. Since there are so many different versions of GRIB2 files, it's often uncertain what fields are available even if you know what source model the data is coming from.  Each file contains the following columns:
 
 Column 1: Name the code searches for in the table. Do not change.  Some definitions:
 
@@ -417,6 +417,7 @@ Column 1: Name the code searches for in the table. Do not change.  Some definiti
       * hice - sea/lake ice thickness
       * weasd - snow liquid equivalent
       * snod - physical snow depth
+      * massden - smoke mass mixing ratio
 
 Column 2: Name of the variable in the output “coldstart” files. Unimplemented.
 

diff --git a/parm/varmap_tables/GSDphys_smoke_var_map.txt b/parm/varmap_tables/GSDphys_smoke_var_map.txt
@@ -0,0 +1,28 @@
+dzdt                dzdt      set_to_fill   0         D
+delta_p             delp      skip          0         D
+sphum               sphum     intrp         1E-7      T
+liq_wat             liq_wat   intrp         0         T
+o3mr                o3mr      intrp         1E-7      T
+rainwat             rainwat   intrp         0         T
+ice_wat             ice_wat   intrp         0         T
+snowwat             snowwat   intrp         0         T
+graupel             graupel   intrp         0         T
+ice_nc              ice_nc    intrp         -1.0      T
+rain_nc             rain_nc   intrp         -1.0      T
+water_nc            water_nc  intrp         -1.0      T
+liq_aero            liq_aero  intrp         0         T
+ice_aero            ice_aero  intrp         0         T
+sgs_tke             sgs_tke   intrp         0         T
+vtype               vtype     skip          0         S
+sotype              stype     skip          0         S
+vfrac               vfrac     skip          0         S
+fricv               uustar    skip          0         S
+sfcr                zorl      set_to_fill   0.01      S
+soilw               smc       stop          0         S
+soilt               stc       stop          0         S
+cnwat               cnwat     set_to_fill   0.0       S
+icetk               icetk     set_to_fill   265.0     S
+weasd               weasd     set_to_fill   0.0       S
+snod                snod      set_to_fill   0.0       S
+tprcp               tprcp     set_to_fill   0.0       S
+massden             smoke     set_to_fill   1E-12     T	
diff --git a/parm/varmap_tables/GSDphys_var_map.txt b/parm/varmap_tables/GSDphys_var_map.txt
@@ -24,4 +24,4 @@ cnwat               cnwat     set_to_fill   0.0       S
 icetk               icetk     set_to_fill   265.0     S
 weasd               weasd     set_to_fill   0.0       S
 snod                snod      set_to_fill   0.0       S
-tprcp               tprcp     set_to_fill   0.0       S       	
+tprcp               tprcp     set_to_fill   0.0       S
diff --git a/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh b/reg_tests/chgres_cube/13km.conus.rap-smoke.grib2.sh
@@ -0,0 +1,103 @@
+#!/bin/bash
+
+#-----------------------------------------------------------------------------
+# Invoke chgres to create 13-km CONUS coldstart files using RAP-SMOKE GRIB2 data
+# as input. i.e., if one desires MASSDEN/SMOKE in the ICs/LBCS
+# The coldstart files are then compared to baseline files
+# using the 'nccmp' utility.  This script is run by the machine specific 
+# driver script.
+#-----------------------------------------------------------------------------
+
+set -x
+
+export DATA=$OUTDIR/13km_conus_rap-smoke_grib2
+rm -fr $DATA
+
+export CRES=778
+export KMRES=13km
+export FIXfv3=${HOMEreg}/fix/RRFS_CONUS_${KMRES}
+
+export COMIN=${HOMEreg}/input_data/rap.grib2
+
+export GRIB2_FILE_INPUT=1921221000900
+export VCOORD_FILE=${HOMEufs}/fix/am/global_hyblev.l64.txt
+export VARMAP_FILE=${HOMEufs}/parm/varmap_tables/GSDphys_smoke_var_map.txt
+export INPUT_TYPE='grib2'
+export CONVERT_NST=".false."
+export OROG_FILES_TARGET_GRID="C778_oro_data.tile7.nc"
+export REGIONAL=1
+export HALO_BLEND=0
+export HALO_BNDY=4 
+export CDATE=2019080100
+export EXTERNAL_MODEL="RAP"
+export NSOILL_OUT=9
+export TRACERS_TARGET='"NULL"'
+export TRACERS_INPUT='"NULL"'
+export SOTYP_FROM_CLIMO=.false.
+export VGTYP_FROM_CLIMO=.false.
+export VGFRC_FROM_CLIMO=.true.
+export MINMAX_VGFRC_FROM_CLIMO=.true.
+export TG3_FROM_SOIL=.true.
+export LAI_FROM_CLIMO=.true.
+export GEOGRID_FILE_INPUT=${HOMEufs}/fix/am/geo_em.d01.nc_RAPX
+
+export OMP_NUM_THREADS_CH=${OMP_NUM_THREADS:-1}
+
+NCCMP=${NCCMP:-$(which nccmp)}
+
+#-----------------------------------------------------------------------------
+# Invoke chgres program.
+#-----------------------------------------------------------------------------
+
+echo "Starting at: " `date`
+
+${HOMEufs}/ush/chgres_cube.sh
+
+iret=$?
+if [ $iret -ne 0 ]; then
+  set +x
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST FAILED. <<<"
+  exit $iret
+fi
+
+echo "Ending at: " `date`
+
+#-----------------------------------------------------------------------------
+# Compare output from chgres to baseline set of data.
+#
+# orion's nccmp utility does not work with the netcdf
+# required to run ufs_utils.  So swap it.
+#-----------------------------------------------------------------------------
+
+machine=${machine:-NULL}
+if [ $machine == 'orion' ]; then
+  module unload netcdfp/4.7.4.release
+  module load netcdf/4.7.2
+fi
+
+cd $DATA
+
+test_failed=0
+for files in *.nc
+do
+  if [ -f $files ]; then
+    echo CHECK $files
+    $NCCMP -dmfqS $files $HOMEreg/baseline_data/13km_conus_rap-smoke_grib2/$files
+    iret=$?
+    if [ $iret -ne 0 ]; then
+      test_failed=1
+    fi
+  fi
+done
+
+set +x
+if [ $test_failed -ne 0 ]; then
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST FAILED. >>>"
+  if [ "$UPDATE_BASELINE" = "TRUE" ]; then
+    $HOMEufs/reg_tests/update_baseline.sh $HOMEreg "13km_conus_rap-smoke_grib2" $commit_num
+  fi
+else
+  echo "<<< 13-km CONUS RAP-SMOKE W/ GSD PHYSICS AND SFC FROM FILE GRIB2 TEST PASSED. >>>"
+fi
+
+exit 0
diff --git a/reg_tests/chgres_cube/driver.hera.sh b/reg_tests/chgres_cube/driver.hera.sh
@@ -187,14 +187,25 @@ export OMP_NUM_THREADS=1   # should match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       -o $LOG_FILE -e $LOG_FILE ./c96.gefs.grib2.sh)
 
+
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS .
+#-----------------------------------------------------------------------------
+LOG_FILE=consistency.log14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
+      -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap-smoke.grib2.sh)
+
+
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 LOG_FILE=consistency.log
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
       --open-mode=append -q $QUEUE -d\
-     afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+     afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}??  > summary.log
 EOF

diff --git a/reg_tests/chgres_cube/driver.hercules.sh b/reg_tests/chgres_cube/driver.hercules.sh
@@ -188,13 +188,22 @@ export OMP_NUM_THREADS=1  # needs to match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 --mem=75G -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --open-mode=append -o $LOG_FILE13 -e $LOG_FILE13 ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE14=${LOG_FILE}14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 --mem=75G -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2 \
+      --open-mode=append -o $LOG_FILE14 -e $LOG_FILE14 ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE \
-       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > $SUM_FILE
 EOF

diff --git a/reg_tests/chgres_cube/driver.jet.sh b/reg_tests/chgres_cube/driver.jet.sh
@@ -183,14 +183,23 @@ export OMP_NUM_THREADS=1
 TEST13=$(sbatch --parsable --partition=xjet --nodes=1 --ntasks-per-node=6 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --exclusive -o $LOG_FILE -e $LOG_FILE ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS .
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --partition=xjet --ntasks-per-node=6 --nodes=1 -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2.conus \
+      --exclusive -o $LOG_FILE -e $LOG_FILE ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 LOG_FILE=consistency.log
 sbatch --partition=xjet --nodes=1  -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE -d\
-       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' $LOG_FILE*  > $SUM_FILE
 EOF

diff --git a/reg_tests/chgres_cube/driver.orion.sh b/reg_tests/chgres_cube/driver.orion.sh
@@ -186,13 +186,22 @@ export OMP_NUM_THREADS=1  # needs to match cpus-per-task
 TEST13=$(sbatch --parsable --ntasks-per-node=6 --nodes=1 --mem=75G -t 0:05:00 -A $PROJECT_CODE -q $QUEUE -J c96.gefs.grib2 \
       --open-mode=append -o $LOG_FILE13 -e $LOG_FILE13 ./c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE14=${LOG_FILE}14
+export OMP_NUM_THREADS=1   # should match cpus-per-task
+TEST14=$(sbatch --parsable --ntasks-per-node=12 --nodes=1 --mem=75G -t 0:10:00 -A $PROJECT_CODE -q $QUEUE -J 13km.conus.rap-smoke.grib2 \
+      --open-mode=append -o $LOG_FILE14 -e $LOG_FILE14 ./13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 sbatch --nodes=1 -t 0:01:00 -A $PROJECT_CODE -J chgres_summary -o $LOG_FILE -e $LOG_FILE \
        --open-mode=append -q $QUEUE \
-       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+       -d afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 grep -a '<<<' ${LOG_FILE}*  > $SUM_FILE
 EOF

diff --git a/reg_tests/chgres_cube/driver.wcoss2.sh b/reg_tests/chgres_cube/driver.wcoss2.sh
@@ -184,14 +184,23 @@ export APRUN="mpiexec -n 6 -ppn 6 --cpu-bind core"
 TEST13=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
         -N c96.gefs.grib2 -l select=1:ncpus=6:ompthreads=1:mem=15GB $PWD/c96.gefs.grib2.sh)
 
+#-----------------------------------------------------------------------------
+# Initialize CONUS 13-KM USING RAP-SMOKE GRIB2 file WITH GSD PHYSICS.
+#-----------------------------------------------------------------------------
+
+LOG_FILE=consistency.log14
+export APRUN="mpiexec -n 6 -ppn 6 --cpu-bind core"
+TEST14=$(qsub -V -o $LOG_FILE -e $LOG_FILE -q $QUEUE -A $PROJECT_CODE -l walltime=00:05:00 \
+        -N 13km.conus.rap-smoke.grib2.conus -l select=1:ncpus=6:ompthreads=1:mem=15GB $PWD/13km.conus.rap-smoke.grib2.sh)
+
 #-----------------------------------------------------------------------------
 # Create summary log.
 #-----------------------------------------------------------------------------
 
 LOG_FILE=consistency.log
 qsub -V -o ${LOG_FILE} -e ${LOG_FILE} -q $QUEUE -A $PROJECT_CODE -l walltime=00:01:00 \
         -N chgres_summary -l select=1:ncpus=1:mem=100MB \
-        -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13 << EOF
+        -W depend=afterok:$TEST1:$TEST2:$TEST3:$TEST4:$TEST5:$TEST6:$TEST7:$TEST8:$TEST9:$TEST10:$TEST11:$TEST12:$TEST13:$TEST14 << EOF
 #!/bin/bash
 cd ${this_dir}
 grep -a '<<<' ${LOG_FILE}?? | grep -v echo > $SUM_FILE