code change for running RRFS_A on wcoss2 (NOAA-EMC#481)

* Tune v0.3.6 on wocss2 for speeding up ensemble DA to catch the control cycles.
Add grid and reource setup for NA 3km on wcoss2.

* Add configuration file for NA 3km control run and enkf DA run on WCOSS2
Add fix files for NA 3km smoke/dust
Add section to setup NA 3km resources fro WCOSS2.

---------

Co-authored-by: Shun Liu <Shun.Liu@noaa.gov>
Co-authored-by: ming hu <ming.hu@clogin04.cactus.wcoss2.ncep.noaa.gov>

fix/smoke_dust/RRFS_NA_3km/NA.nearest_weigt.nc

@@ -0,0 +1 @@
+../../.agent/smoke_dust/RRFS_NA_3km/NA.nearest_weigt.nc

fix/smoke_dust/RRFS_NA_3km/dust12m_data.nc_old

@@ -0,0 +1 @@
+../../.agent/smoke_dust/RRFS_NA_3km/dust12m_data.nc_old

scripts/exregional_nonvarcldanl.sh

@@ -82,6 +82,7 @@ case $MACHINE in
   APRUN="mpiexec -n ${IO_LAYOUT_Y} -ppn 16"
   ncores=$(( NNODES_RUN_NONVARCLDANL*PPN_RUN_NONVARCLDANL ))
   APRUN="mpiexec -n ${ncores} -ppn ${PPN_RUN_NONVARCLDANL}"
+  APRUN="mpiexec -n 1 -ppn 1"
   ;;
 #
 "HERA")

ush/config.sh.rrfs_a_c3

@@ -9,9 +9,12 @@ PREDEF_GRID_NAME=RRFS_CONUS_3km
 
 . set_rrfs_config_general.sh
 
+#DO_ENSEMBLE="TRUE"
+#DO_ENSFCST="TRUE"
 DO_DACYCLE="TRUE"
 DO_SURFACE_CYCLE="TRUE"
 DO_SPINUP="TRUE"
+#DO_SAVE_INPUT="TRUE"
 DO_POST_SPINUP="FALSE"
 DO_POST_PROD="TRUE"
 DO_RETRO="FALSE"
@@ -23,7 +26,7 @@ RADARREFL_TIMELEVEL=(0)
 FH_DFI_RADAR="0.0,0.25,0.5"
 DO_SOIL_ADJUST="TRUE"
 DO_RADDA="FALSE"
-DO_BUFRSND="FALSE"
+DO_BUFRSND="TRUE"
 USE_FVCOM="TRUE"
 PREP_FVCOM="TRUE"
 
@@ -35,13 +38,13 @@ BOUNDARY_PROC_GROUP_NUM="72"
 
 # avaialble retro period:
 # 20210511-20210531; 20210718-20210801
-DATE_FIRST_CYCL="20230120"
-DATE_LAST_CYCL="20230131"
+DATE_FIRST_CYCL="20230201"
+DATE_LAST_CYCL="20230331"
 CYCL_HRS=( "00" "12" )
 CYCL_HRS_SPINSTART=("03" "15")
 CYCL_HRS_PRODSTART=("09" "21")
-CYCLEMONTH="01"
-CYCLEDAY="20-31"
+CYCLEMONTH="02,03"
+CYCLEDAY="*"
 
 STARTYEAR=${DATE_FIRST_CYCL:0:4}
 STARTMONTH=${DATE_FIRST_CYCL:4:2}
@@ -70,8 +73,8 @@ POSTPROC_LONG_LEN_HRS="60"
 for i in {0..23}; do FCST_LEN_HRS_CYCLES[$i]=18; done
 for i in {0..23..6}; do FCST_LEN_HRS_CYCLES[$i]=60; done
 DA_CYCLE_INTERV="1"
-RESTART_INTERVAL="1 2 3"
-RESTART_INTERVAL_LONG="1 2 3"
+RESTART_INTERVAL="1 2"
+RESTART_INTERVAL_LONG="1 2"
 
 USE_RRFSE_ENS="TRUE"
 CYCL_HRS_HYB_FV3LAM_ENS=("00" "01" "02" "03" "04" "05" "06" "07" "08" "09" "10" "11" "12" "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23")
@@ -94,7 +97,7 @@ TAG="c3v36"
 
 ARCHIVEDIR="/NCEPDEV/emc-meso/1year/emc.lam"
 NCL_REGION="conus"
-MODEL="RRFS_A"
+MODEL="rrfs_a"
 
 #
 # In NCO mode, the following don't need to be explicitly set to "FALSE" 
@@ -110,12 +113,12 @@ COMINgfs=""
 
 . set_rrfs_config.sh
 
-STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/stmp"  # Path to directory STMP that mostly contains input files.
+STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains input files.
 PTMP="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains input files.
-NWGES="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges/${envir}/${NET}"  # Path to directory NWGES that save boundary, cold initial, restart files
+NWGES="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges"  # Path to directory NWGES that save boundary, cold initial, restart files
 if [[ ${regional_ensemble_option} == "5" ]]; then
-   RRFSE_NWGES=="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges"  # Path to RRFSE directory NWGES that mostly contains ensemble restart files for GSI hybrid.
+  RRFSE_NWGES="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges"  # Path to RRFSE directory NWGES that mostly contains ensemble restart files for GSI hybrid.
   NUM_ENS_MEMBERS=30     # FV3LAM ensemble size for GSI hybrid analysis
-  CYCL_HRS_PRODSTART_ENS=( "19" )
+  CYCL_HRS_PRODSTART_ENS=( "07" "19" )
   DO_ENVAR_RADAR_REF="TRUE"
 fi

ush/config.sh_rrfs_a_enkf_c3

@@ -20,12 +20,17 @@ DO_POST_SPINUP="FALSE"
 DO_POST_PROD="FALSE"
 #DO_RETRO="TRUE"
 DO_NONVAR_CLDANAL="TRUE"
+#DO_ENVAR_RADAR_REF="TRUE"
 DO_SMOKE_DUST="FALSE"
 #DO_REFL2TTEN="FALSE"
 #RADARREFL_TIMELEVEL=(0)
 #FH_DFI_RADAR="0.0,0.25,0.5"
 #DO_SOIL_ADJUST="TRUE"
 #DO_RADDA="FALSE"
+#DO_BUFRSND="TRUE"
+#USE_FVCOM="TRUE"
+#PREP_FVCOM="TRUE"
+
 if [[ ${DO_ENSFCST} == "TRUE" ]] ; then
   DO_SPINUP="FALSE"
   DO_SAVE_DA_OUTPUT="FALSE"
@@ -41,16 +46,16 @@ BOUNDARY_PROC_GROUP_NUM="4"
 
 # avaialble retro period:
 # 20210511-20210531; 20210718-20210801
-DATE_FIRST_CYCL="20230121"
-DATE_LAST_CYCL="20230131"
+DATE_FIRST_CYCL="20230201"
+DATE_LAST_CYCL="20230331"
 CYCL_HRS=( "00" "12" )
 CYCL_HRS=( "18" )
-CYCL_HRS_SPINSTART=("18")
-CYCL_HRS_PRODSTART=("19")
+CYCL_HRS_SPINSTART=("06" "18")
+CYCL_HRS_PRODSTART=("07" "19")
 #CYCL_HRS_STOCH=("00" "12")
 #CYCL_HRS_RECENTER=("19")
-CYCLEMONTH="01"
-CYCLEDAY="21-31"
+CYCLEMONTH="02,03"
+CYCLEDAY="*"
 
 STARTYEAR=${DATE_FIRST_CYCL:0:4}
 STARTMONTH=${DATE_FIRST_CYCL:4:2}
@@ -62,9 +67,9 @@ ENDDAY=${DATE_LAST_CYCL:6:2}
 ENDHOUR="23"
 
 PREEXISTING_DIR_METHOD="upgrade" # "rename"
-INITIAL_CYCLEDEF="${DATE_FIRST_CYCL}1800 ${DATE_LAST_CYCL}2300 24:00:00"
+INITIAL_CYCLEDEF="${DATE_FIRST_CYCL}1800 ${DATE_LAST_CYCL}2300 12:00:00"
 BOUNDARY_CYCLEDEF="${DATE_FIRST_CYCL}1800 ${DATE_LAST_CYCL}2300 06:00:00"
-PROD_CYCLEDEF="00 01-05,07-11,13-17,19-23 19-30 ${CYCLEMONTH} ${STARTYEAR} *"
+PROD_CYCLEDEF="00 01-05,07-11,13-17,19-23 ${CYCLEDAY} ${CYCLEMONTH} ${STARTYEAR} *"
 PRODLONG_CYCLEDEF="${DATE_FIRST_CYCL}0000 ${DATE_LAST_CYCL}2300 06:00:00"
 #RECENTER_CYCLEDEF="00 19 * 10 2022 *"
 ARCHIVE_CYCLEDEF="${DATE_FIRST_CYCL}1500 ${DATE_LAST_CYCL}2300 24:00:00"
@@ -77,7 +82,7 @@ if [[ ${DO_ENSFCST} == "TRUE" ]] ; then
   PRODLONG_CYCLEDEF="00 01 01 01 2100 *"
 fi
 if [[ $DO_SPINUP == "TRUE" ]] ; then
-  SPINUP_CYCLEDEF="${DATE_FIRST_CYCL}1800 ${DATE_LAST_CYCL}2300 24:00:00"
+  SPINUP_CYCLEDEF="${DATE_FIRST_CYCL}1800 ${DATE_LAST_CYCL}2300 12:00:00"
 fi
 if [[ $DO_SAVE_DA_OUTPUT == "TRUE" ]] ; then
   SAVEDA_CYCLEDEF="${DATE_FIRST_CYCL}1200 ${DATE_LAST_CYCL}2300 12:00:00"
@@ -88,15 +93,15 @@ FCST_LEN_HRS_SPINUP="1"
 POSTPROC_LEN_HRS="1"
 #FCST_LEN_HRS_CYCLES=(48 18 18 18 18 18 48 18 18 18 18 18 48 18 18 18 18 18 48 18 18 18 18 18)
 for i in {0..23}; do FCST_LEN_HRS_CYCLES[$i]=1; done
-for i in {0..23..6}; do FCST_LEN_HRS_CYCLES[$i]=2; done 
+for i in {0..23..6}; do FCST_LEN_HRS_CYCLES[$i]=1; done 
 if [[ ${DO_ENSFCST} == "TRUE" ]] ; then
-  for i in {0..23..12}; do FCST_LEN_HRS_CYCLES[$i]=24; done 
-  POSTPROC_LEN_HRS="24"
+  for i in {0..23..12}; do FCST_LEN_HRS_CYCLES[$i]=36; done 
+  POSTPROC_LEN_HRS="36"
   BOUNDARY_PROC_GROUP_NUM="8"
 fi
 DA_CYCLE_INTERV="1"
 RESTART_INTERVAL="1"
-RESTART_INTERVAL_LONG="1 2"
+RESTART_INTERVAL_LONG="1"
 netcdf_diag=.true.
 binary_diag=.false.
 NFHOUT="3"
@@ -118,11 +123,11 @@ FV3GFS_FILE_FMT_ICS="grib2"
 FV3GFS_FILE_FMT_LBCS="grib2"
 
 envir="para"
+NET="rrfs_a"
+TAG="cenkf36"
+ARCHIVEDIR="/NCEPDEV/emc-meso/1year/emc.lam"
 NCL_REGION="conus"
 MODEL="rrfs_b"
-NET="rrfs_a"
-TAG="cenkf32"
-ARCHIVEDIR="/1year/BMC/wrfruc/rrfs_dev1"
 
 if [[ ${DO_ENSEMBLE}  == "TRUE" ]]; then
    NUM_ENS_MEMBERS=30
@@ -142,16 +147,18 @@ if [[ ${DO_ENSEMBLE}  == "TRUE" ]]; then
 #     SPPT_MAG=0.5
      WTIME_RUN_FCST="04:45:00"
      WTIME_MAKE_LBCS="01:30:00"
+     TAG="cefcst36"
    fi
    RADAR_REF_THINNING="2"
    ARCHIVEDIR="/5year/BMC/wrfruc/rrfs_ens"
    NNODES_RUN_RECENTER="3"
-   PPN_RUN_RECENTER="$(( ${NUM_ENS_MEMBERS} + 1 ))"
+   PPN_RUN_RECENTER="128"
    CLEAN_OLDFCST_HRS="48"
    CLEAN_OLDSTMPPOST_HRS="48"
    cld_bld_hgt=0.0
    l_precip_clear_only=.true.
    write_diag_2=.true.
+   START_TIME_SPINUP="00:30:00"
 fi
 
 RUN="rrfs_a"
@@ -162,13 +169,13 @@ COMINgfs=""
 
 . set_rrfs_config.sh
 
-STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/stmp"  # Path to directory STMP that mostly contains input files.
+STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains input files.
 if [[ ${DO_ENSFCST} == "TRUE" ]] ; then
   STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/enfcst"  # Path to directory STMP that mostly contains input files.
 fi
 PTMP="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains input files.
-NWGES="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/nwges"  # Path to directory NWGES that save boundary, cold initial, restart files
-ENSCTRL_STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/stmp"  # Path to directory STMP that mostly contains control input files for ensemble recentering.
+NWGES="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges"  # Path to directory NWGES that save boundary, cold initial, restart files
+ENSCTRL_STMP="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains control input files for ensemble recentering.
 ENSCTRL_PTMP="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}"  # Path to directory STMP that mostly contains control input files for ensemble recentering.
-ENSCTRL_NWGES="/lfs/h2/emc/stmp/emc.lam/rrfs/${version}/nwges"  # Path to directory STMP that mostly contains control input files for ensemble recentering.
+ENSCTRL_NWGES="/lfs/h2/emc/ptmp/emc.lam/rrfs/${version}/nwges"  # Path to directory STMP that mostly contains control input files for ensemble recentering.