Merge branch 'develop' into feature/gocart_variable_fh

.gitignore

@@ -69,6 +69,7 @@ parm/post/params_grib2_tbl_new
 parm/post/post_tag_gfs128
 parm/post/gfs
 parm/post/gefs
+parm/post/sfs
 parm/post/ocean.csv
 parm/post/ice.csv
 parm/post/ocnicepost.nml.jinja2

ci/cases/pr/C96C48_ufs_hybatmDA.yaml

@@ -21,4 +21,4 @@ skip_ci_on_hosts:
   - gaea
   - orion
   - hercules
-
+  - wcoss2

ci/cases/sfs/C96mx100_S2S.yaml

@@ -0,0 +1,19 @@
+experiment:
+  system: gefs
+  mode: forecast-only
+
+arguments:
+  idate: 1994050100 
+  edate: 1994050100
+  pslot: {{ 'pslot' | getenv }}
+  app: S2S
+  resdetatmos: 96
+  resensatmos: 96
+  resdetocean: 1
+  start: 'cold'
+  nens: 10
+  comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
+  expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
+  icsdir: {{ 'TOPICDIR' | getenv }}/HR4/C96mx100
+  yaml: {{ HOMEgfs }}/ci/cases/yamls/sfs_defaults.yaml
+

ci/cases/yamls/gefs_defaults_ci.yaml

@@ -2,3 +2,11 @@ defaults:
   !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
 base:
   ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+  SFS_POST: "NO"
+  FHOUT_GFS: 6
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "NO"
+  USE_ATM_ENS_PERTURB_FILES: "NO"
+ocn:
+  MOM6_INTERP_ICS: "NO"
+

ci/cases/yamls/gefs_replay_ci.yaml

@@ -11,4 +11,8 @@ base:
   FHOUT_OCN_GFS: 24
   FHOUT_ICE_GFS: 24
   HOMEDIR: {{ 'RUNTESTS' | getenv }}/GLOBAL
+  SFS_POST: "NO"
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "YES"
+  USE_ATM_ENS_PERTURB_FILES: "YES"
 

ci/cases/yamls/sfs_defaults.yaml

@@ -0,0 +1,33 @@
+base:
+  DO_JEDIATMVAR: "NO"
+  DO_JEDIATMENS: "NO"
+  DO_JEDIOCNVAR: "NO"
+  DO_JEDISNOWDA: "NO"
+  DO_MERGENSST: "NO"
+  DO_BUFRSND: "NO"
+  DO_GEMPAK: "NO"
+  DO_AWIPS: "NO"
+  KEEPDATA: "YES"
+  DO_EXTRACTVARS: "NO"
+  FHMAX_GFS: 2976
+  FHMAX_HF_GFS: 0
+  FHOUT_HF_GFS: 1
+  FHOUT_GFS: 24
+  FHOUT_OCN_GFS: 24
+  FHOUT_ICE_GFS: 24
+  FCST_BREAKPOINTS: ""
+  REPLAY_ICS: "NO"
+  HPSSARCH: "NO"
+  LOCALARCH: "NO"
+  SFS_POST: "YES"
+  ACCOUNT: {{ 'HPC_ACCOUNT' | getenv }}
+fcst:
+  TYPE: "hydro"
+  MONO: "mono"
+  reforecast: "YES"
+  FHZER: 24
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "YES"
+  USE_ATM_ENS_PERTURB_FILES: "YES"
+ocn:
+  MOM6_INTERP_ICS: "YES"

ci/cases/yamls/ufs_hybatmDA_defaults.ci.yaml

@@ -17,4 +17,3 @@ nsst:
   NST_MODEL: "1"
 sfcanl:
   DONST: "NO"
-

modulefiles/module_gwsetup.wcoss2.lua

@@ -4,5 +4,8 @@ Load environment to run GFS workflow ci scripts on WCOSS2
 
 prepend_path("MODULEPATH", "/apps/ops/test/nco/modulefiles/core")
 load(pathJoin("rocoto","1.3.5"))
+load(pathJoin("PrgEnv-intel"))
+load(pathJoin("intel","19.1.3.304"))
+load(pathJoin("python", "3.8.6"))
 
 whatis("Description: GFS run setup environment")

parm/archive/gfs_downstream.yaml.j2

@@ -6,7 +6,7 @@ gfs_downstream:
         - "{{ COMIN_ATMOS_GEMPAK | relpath(ROTDIR) }}/gfs_{{ cycle_YMDH }}.sfc"
         - "{{ COMIN_ATMOS_GEMPAK | relpath(ROTDIR) }}/gfs_{{ cycle_YMDH }}.snd"
         {% for i in range(1, NUM_SND_COLLECTIVES) %}
-        - "{{ COMIN_ATMOS_WMO | relpath(ROTDIR) }}/gfs_collective{{ i }}.postsnd_{{ cycle_HH }}"
+        - "{{ COMIN_ATMOS_BUFR | relpath(ROTDIR) }}/gfs_collective{{ i }}.fil"
         {% endfor %}
-        - "{{ COMIN_ATMOS_BUFR | relpath(ROTDIR) }}/bufr.t{{ cycle_HH }}z"
+        - "{{ COMIN_ATMOS_BUFR | relpath(ROTDIR) }}/bufr.??????.{{ cycle_YMDH }}"
         - "{{ COMIN_ATMOS_BUFR | relpath(ROTDIR) }}/gfs.t{{ cycle_HH }}z.bufrsnd.tar.gz"

parm/config/gefs/config.atmos_products

@@ -25,9 +25,14 @@ fi
 export FLXGF="NO"  # Create interpolated sflux.1p00 file
 
 # paramlist files for the different forecast hours and downsets
-export paramlista="${PARMgfs}/product/gefs.0p25.fFFF.paramlist.a.txt"
-export paramlista_anl="${PARMgfs}/product/gefs.0p25.anl.paramlist.a.txt"
-export paramlista_f000="${PARMgfs}/product/gefs.0p25.f000.paramlist.a.txt"
-export paramlistb="${PARMgfs}/product/gefs.0p25.fFFF.paramlist.b.txt"
+if [[ ${SFS_POST} == "YES" ]]; then
+    export post_prefix='sfs'
+else
+    export post_prefix='gefs'
+fi
+export paramlista="${PARMgfs}/product/${post_prefix}.0p25.fFFF.paramlist.a.txt"
+export paramlista_anl="${PARMgfs}/product/${post_prefix}.0p25.anl.paramlist.a.txt"
+export paramlista_f000="${PARMgfs}/product/${post_prefix}.0p25.f000.paramlist.a.txt"
+export paramlistb="${PARMgfs}/product/${post_prefix}.0p25.fFFF.paramlist.b.txt"
 
 echo "END: config.atmos_products"

parm/config/gefs/config.base

@@ -64,6 +64,7 @@ export REALTIME="YES"
 
 # Experiment mode (cycled or forecast-only)
 export MODE="@MODE@" # cycled/forecast-only
+export SFS_POST="@SFS_POST@" # TODO, place holder until RUN=SFS is developed
 
 ####################################################
 # DO NOT ADD MACHINE DEPENDENT STUFF BELOW THIS LINE
@@ -206,12 +207,13 @@ case "${APP}" in
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
+        export WAVE_RUN="both"
         export cplwav2atm=".true."
     fi
     ;;
   *)
-    echo "Unrecognized APP: ${1}"
-    exit 1
+    echo "FATAL ERROR: Unrecognized APP: '${APP}'"
+    exit 2
     ;;
 esac
 
@@ -235,15 +237,14 @@ else
     export OFFSET_START_HOUR=0
 fi
 
-
 # GFS output and frequency
 export FHMIN_GFS=0
 export FHMAX_GFS="@FHMAX_GFS@"
 # Intermediate times to stop forecast when running in segments
 breakpnts="@FCST_BREAKPOINTS@"
 export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
 
-export FHOUT_GFS=6
+export FHOUT_GFS=@FHOUT_GFS@
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
 export FHOUT_HF_GFS=@FHOUT_HF_GFS@
 export FHOUT_OCN_GFS=@FHOUT_OCN_GFS@
@@ -293,6 +294,7 @@ export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
+
 # Check if cycle is warm starting with IAU
 if [[ "${EXP_WARM_START}" = ".true." ]]; then
   if [[ "${DOIAU}" = "YES" ]]; then
@@ -324,7 +326,7 @@ export HPSSARCH="@HPSSARCH@"        # save data to HPSS archive
 export LOCALARCH="@LOCALARCH@"        # save data to local archive
 if [[ ${HPSSARCH} = "YES" ]] && [[ ${LOCALARCH} = "YES" ]]; then
    echo "Both HPSS and local archiving selected.  Please choose one or the other."
-   exit 2
+   exit 3
 fi
 export ARCH_CYC=00           # Archive data at this cycle for warm_start capability
 export ARCH_WARMICFREQ=4     # Archive frequency in days for warm_start capability
@@ -335,10 +337,4 @@ export DELETE_COM_IN_ARCHIVE_JOB="YES"   # NO=retain ROTDIR.  YES default in arc
 # Number of regional collectives to create soundings for
 export NUM_SND_COLLECTIVES=${NUM_SND_COLLECTIVES:-9}
 
-# The tracker, genesis, and METplus jobs are not supported on CSPs yet
-# TODO: we should place these in workflow/hosts/[aws|azure|google]pw.yaml as part of CSP's setup, not for general.
-if [[ "${machine}" =~ "PW" ]]; then
-   export DO_WAVE="NO"
-fi
-
 echo "END: config.base"

parm/config/gefs/config.efcs

@@ -27,7 +27,11 @@ source "${EXPDIR}/config.ufs" ${string}
 source "${EXPDIR}/config.resources" efcs
 
 # Stochastic physics parameters (only for ensemble forecasts)
-export DO_SKEB="YES"
+if [[ "${CASE}" == "C96" ]] ; then
+    export DO_SKEB="NO" # SKEB turned off for C96
+else
+    export DO_SKEB="YES" # SKEB turned on for all other resolutions
+fi
 export SKEB="0.8,-999,-999,-999,-999"
 export SKEB_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
 export SKEB_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"

parm/config/gefs/config.fcst

@@ -44,6 +44,7 @@ export FHOUT=${FHOUT_GFS}
 export FHOUT_HF=${FHOUT_HF_GFS}
 export FHOUT_OCN=${FHOUT_OCN_GFS}
 export FHOUT_ICE=${FHOUT_ICE_GFS}
+export FHZER=@FHZER@
 
 # Get task specific resources
 source "${EXPDIR}/config.resources" fcst
@@ -66,8 +67,8 @@ export FCSTEXEC="ufs_model.x"
 
 #######################################################################
 # Model configuration
-export TYPE="nh"
-export MONO="non-mono"
+export TYPE=@TYPE@
+export MONO=@MONO@
 
 # Use stratosphere h2o physics
 export h2o_phys=".true."
@@ -201,6 +202,11 @@ case ${imp_physics} in
         export hord_xx_nh_nonmono=5
         export vtdm4_nh_nonmono=0.02
         export nord=2
+        if [[ "${TYPE}" == "nh"* ]]; then
+            export dddmp=0.1
+        else
+            export dddmp=0.
+	    fi
         export dddmp=0.1
         export d4_bg=0.12
         ;;
@@ -221,7 +227,11 @@ case ${imp_physics} in
         export vtdm4_nh_nonmono=0.02
         export nord=2
         export d4_bg=0.12
-        export dddmp=0.1
+        if [[ "${TYPE}" == "nh"* ]]; then
+            export dddmp=0.1
+        else
+            export dddmp=0.
+	    fi
         ;;
     *) echo "Unknown microphysics option, ABORT!" ;;
 esac
@@ -268,9 +278,7 @@ else
   export io_layout="1,1"
 fi
 
-if (( OFFSET_START_HOUR != 0 )); then
-    export reforecast="YES"
-fi
+export reforecast=@reforecast@
 # Remember config.efcs will over-ride these values for ensemble forecasts
 # if these variables are re-defined there.
 # Otherwise, the ensemble forecast will inherit from config.fcst

parm/config/gefs/config.stage_ic

@@ -30,4 +30,8 @@ if [[ -z "${ICSDIR}" ]] ; then
 
 fi
 
+#use of perturbations files for ensembles
+export USE_OCN_ENS_PERTURB_FILES=@USE_OCN_ENS_PERTURB_FILES@
+export USE_ATM_ENS_PERTURB_FILES=@USE_ATM_ENS_PERTURB_FILES@
+
 echo "END: config.stage_ic"

parm/config/gefs/config.ufs

@@ -80,7 +80,7 @@ case "${fv3_res}" in
         export nthreads_fv3_gfs=1
         export nthreads_ufs=1
         export nthreads_ufs_gfs=1
-        export xr_cnvcld=.false. # Do not pass conv. clouds to Xu-Randall cloud fraction
+        export xr_cnvcld=".true."  # Pass conv. clouds to Xu-Randall cloud fraction
         export cdmbgwd="0.071,2.1,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="40.0,1.77,1.0,1.0"   # settings for GSL drag suite
         export k_split=1
@@ -98,13 +98,13 @@ case "${fv3_res}" in
         export DELTIM=600
         export layout_x=2
         export layout_y=2
-        export layout_x_gfs=2
-        export layout_y_gfs=2
+        export layout_x_gfs=4
+        export layout_y_gfs=4
         export nthreads_fv3=1
         export nthreads_fv3_gfs=1
         export nthreads_ufs=1
         export nthreads_ufs_gfs=1
-        export xr_cnvcld=".false."  # Do not pass conv. clouds to Xu-Randall cloud fraction
+        export xr_cnvcld=".true."  # Pass conv. clouds to Xu-Randall cloud fraction
         export cdmbgwd="0.14,1.8,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="20.0,2.5,1.0,1.0"   # settings for GSL drag suite
         export knob_ugwp_tauamp=3.0e-3      # setting for UGWPv1 non-stationary GWD
@@ -131,6 +131,7 @@ case "${fv3_res}" in
         export cdmbgwd="0.23,1.5,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="10.0,3.5,1.0,1.0"   # settings for GSL drag suite
         export knob_ugwp_tauamp=1.5e-3      # setting for UGWPv1 non-stationary GWD
+        export xr_cnvcld=".true."  # Pass conv. clouds to Xu-Randall cloud fraction
         export k_split=2
         export n_split=4
         export tau=6.0
@@ -337,7 +338,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       DT_THERM_MOM6='3600'
       FRUNOFF="runoff.daitren.clim.1deg.nc"
       CHLCLIM="seawifs_1998-2006_smoothed_2X.nc"
-      MOM6_RESTART_SETTING='r'
+      MOM6_RESTART_SETTING=${MOM6_RESTART_SETTING:-'r'}
       MOM6_RIVER_RUNOFF='False'
       eps_imesh="2.5e-1"
       TOPOEDITS="ufs.topo_edits_011818.nc"

parm/config/gefs/yaml/defaults.yaml

@@ -15,7 +15,20 @@ base:
   FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"
+  FHOUT_GFS: 6
   FHOUT_OCN_GFS: 6
   FHOUT_ICE_GFS: 6
   HPSSARCH: "NO"
   LOCALARCH: "NO"
+  SFS_POST: "NO"
+fcst:
+  reforecast: "NO"
+  FHZER: 6
+  TYPE: "nh"
+  MONO: "non-mono"
+stage_ic:
+  USE_OCN_ENS_PERTURB_FILES: "NO"
+  USE_ATM_ENS_PERTURB_FILES: "NO"
+ocn:
+  MOM6_INTERP_ICS: "NO"
+

parm/config/gfs/config.aero

@@ -2,36 +2,8 @@
 
 # UFS-Aerosols settings
 
-# Turn off warnings about unused variables
-# shellcheck disable=SC2034
-
-
 # Path to the input data tree
-case ${machine} in
-  "HERA")
-    AERO_INPUTS_DIR="/scratch1/NCEPDEV/global/glopara/data/gocart_emissions"
-    ;;
-  "ORION" | "HERCULES")
-    AERO_INPUTS_DIR="/work2/noaa/global/wkolczyn/noscrub/global-workflow/gocart_emissions"
-    ;;
-  "S4")
-    AERO_INPUTS_DIR="/data/prod/glopara/gocart_emissions"
-    ;;
-  "WCOSS2")
-    AERO_INPUTS_DIR="/lfs/h2/emc/global/noscrub/emc.global/data/gocart_emissions"
-    ;;
-  "GAEA")
-    AERO_INPUTS_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/gocart_emissions"
-    ;;
-  "JET")
-    AERO_INPUTS_DIR="/lfs5/HFIP/hfv3gfs/glopara/data/gocart_emissions"
-    ;;
-  *)
-    echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
-    exit 2
-    ;;
-esac
-export AERO_INPUTS_DIR
+export AERO_INPUTS_DIR=@AERO_INPUTS_DIR@
 
 export AERO_DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table.aero"
 export AERO_FIELD_TABLE="${PARMgfs}/ufs/fv3/field_table.aero"