Merge branch 'develop' into feature/atmos_products

.github/workflows/docs.yaml

@@ -9,11 +9,16 @@ on:
       - release/*
     paths:
       - docs/**
-  pull_request:
-    types: [opened, reopened, synchronize]
+  pull_request_target:
+    types: [issues, opened, reopened, synchronize]
 
 jobs:
+
   documentation:
+
+    permissions:
+      pull-requests: 'write'
+
     runs-on: ubuntu-latest
     name: Build and deploy documentation
 
@@ -49,3 +54,17 @@ jobs:
         path: artifact/doc_warnings.log
         if-no-files-found: ignore
 
+    - name: Comment ReadDocs
+      uses: actions/github-script@v6
+      with:
+        script: |
+          const message = `
+          Link to ReadTheDocs sample build for this PR can be found at:
+          https://global-workflow--${{ github.event.pull_request.number }}.org.readthedocs.build/en/${{ github.event.pull_request.number }}
+          `
+          github.rest.issues.createComment({
+           issue_number: context.issue.number,
+           owner: context.repo.owner,
+           repo: context.repo.repo,
+           body: message 
+          })     

.pycodestyle

@@ -3,4 +3,4 @@ count = False
 ignore = E402,W504
 max-line-length = 160
 statistics = True
-exclude = Experimental,.git,.vscode,*.fd,*.cd
+exclude = .git,.github,.vscode,venv,*.fd,*.cd,docs/source/conf.py

.readthedocs.yaml

@@ -15,7 +15,9 @@ build:
 sphinx:
   configuration: docs/source/conf.py
 
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
     - requirements: docs/requirements.txt
-  system_packages: true

Externals.cfg

@@ -57,7 +57,7 @@ protocol = git
 required = False
 
 [GDASApp]
-hash = 7966501
+hash = 2774a10
 local_path = sorc/gdas.cd
 repo_url = https://github.com/NOAA-EMC/GDASApp.git
 protocol = git

ci/cases/C48_S2SA_gefs.yaml

@@ -0,0 +1,17 @@
+experiment:
+  type: gefs
+  mode: forecast-only
+
+arguments:
+  pslot: ${pslot}
+  app: S2SA
+  resdet: 48
+  resens: 48
+  nens: 2
+  gfs_cyc: 1
+  comrot: ${RUNTESTS}/COMROT
+  expdir: ${RUNTESTS}/EXPDIR
+  icsdir: ${ICSDIR_ROOT}/C48C48mx500
+  idate: 2021032312
+  edate: 2021032312
+  yaml: ${HOMEgfs_PR}/ci/platforms/gefs_ci_defaults.yaml

ci/platforms/gefs_ci_defaults.yaml

@@ -0,0 +1,4 @@
+defaults:
+  !INC {{ HOMEgfs }}/parm/config/gefs/yaml/defaults.yaml
+base:
+  ACCOUNT: ${SLURM_ACCOUNT}

docs/requirements.txt

@@ -1,2 +1,5 @@
-sphinxcontrib-bibtex
+sphinx
 sphinx_rtd_theme
+sphinxcontrib-bibtex
+sphinx-autobuild
+sphinx-copybutton

docs/source/conf.py

@@ -80,7 +80,17 @@
 # documentation.
 #
 # html_theme_options = {}
-html_theme_options = {"body_max_width": "none"}
+html_theme_options = {"body_max_width": "none",
+                      "footer_icons": [
+    {"name": "GitHub",
+     "url": "https://github.com/NOAA-EMC/global-workflow",
+     "html": """
+            <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
+                <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
+            </svg>
+             """,
+     "class": ""}]
+                      }
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

jobs/JGDAS_ENKF_FCST

@@ -8,7 +8,6 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "efcs" -c "base fcst efcs"
 # Set variables used in the script
 ##############################################
 export CDUMP=${RUN/enkf}
-export rCDUMP="enkfgdas"
 
 ##############################################
 # Begin JOB SPECIFIC work

jobs/JGFS_ATMOS_CYCLONE_GENESIS

@@ -4,9 +4,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
 
-# TODO (#1220) Determine if this is still needed
-export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-
 ##############################################
 # Set variables used in the exglobal script
 ##############################################

jobs/JGFS_ATMOS_CYCLONE_TRACKER

@@ -4,9 +4,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
 
-# TODO (#1220) Determine if this is still needed
-export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-
 export COMPONENT="atmos"
 
 

jobs/JGFS_ATMOS_FSU_GENESIS

@@ -3,8 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
-export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-
 export COMPONENT="atmos"
 
 

jobs/JGLOBAL_ATMOS_EMCSFC_SFC_PREP

@@ -3,8 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "sfc_prep" -c "base"
 
-export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-
 export SENDDBN=${SENDDBN:-NO}
 export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
 

jobs/JGLOBAL_ATMOS_SFCANL

@@ -8,9 +8,6 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "sfcanl" -c "base sfcanl"
 # Set variables used in the script
 ##############################################
 export CDUMP="${RUN/enkf}"
-if [[ ${RUN_ENVIR} = "nco" ]]; then
-    export ROTDIR=${COMROOT:?}/${NET}/${envir}
-fi
 
 
 ##############################################

jobs/JGLOBAL_ATMOS_TROPCY_QC_RELOC

@@ -3,9 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "prep" -c "base prep"
 
-# TODO (#1220) Evaluate if this is still needed
-export RUN_ENVIR=${RUN_ENVIR:-"nco"}
-
 
 ##############################################
 # Set variables used in the exglobal script

jobs/JGLOBAL_LAND_ANALYSIS

@@ -17,12 +17,12 @@ GDUMP="gdas"
 # Begin JOB SPECIFIC work
 ##############################################
 # Generate COM variables from templates
-YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS COM_LAND_ANALYSIS
+YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS COM_LAND_ANALYSIS COM_CONF
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
     COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
 
-mkdir -m 775 -p "${COM_LAND_ANALYSIS}"
+mkdir -m 775 -p "${COM_LAND_ANALYSIS}" "${COM_CONF}"
 
 ###############################################################
 # Run relevant script

jobs/rocoto/awips.sh

@@ -5,7 +5,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 ###############################################################
 ## Abstract:
 ## Inline awips driver script
-## RUN_ENVIR : runtime environment (emc | nco)
 ## HOMEgfs   : /full/path/to/workflow
 ## EXPDIR : /full/path/to/config/files
 ## CDATE  : current analysis date (YYYYMMDDHH)
@@ -49,17 +48,17 @@ for fhr in ${fhrlst}; do
             export fcsthrs=${fhr3}
             ${AWIPS20SH}
         fi
-    
+
         if ((fhr % 6 == 0)); then
             ${AWIPSG2SH}
         fi
     fi
 
     fhmin=90
     fhmax=240
-    if (( fhr >= fhmin && fhr <= fhmax )); then    
+    if (( fhr >= fhmin && fhr <= fhmax )); then
         if ((fhr % 6 == 0)); then
-            fhr3=$(printf %03i $((10#${fhr})))            
+            fhr3=$(printf %03i $((10#${fhr})))
             export fcsthrs=${fhr3}
             ${AWIPS20SH}
             ${AWIPSG2SH}

jobs/rocoto/metp.sh

@@ -5,7 +5,6 @@ source "${HOMEgfs}/ush/preamble.sh"
 ###############################################################
 ## Abstract:
 ## Inline METplus verification and diagnostics driver script
-## RUN_ENVIR : runtime environment (emc | nco)
 ## HOMEgfs   : /full/path/to/workflow
 ## EXPDIR : /full/path/to/config/files
 ## CDATE  : current analysis date (YYYYMMDDHH)

jobs/rocoto/ocnpost.sh

@@ -21,9 +21,6 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnpost" -c "base ocnpost"
 # Set variables used in the exglobal script
 ##############################################
 export CDUMP=${RUN/enkf}
-if [[ ${RUN_ENVIR} = "nco" ]]; then
-    export ROTDIR=${COMROOT:?}/${NET}/${envir}
-fi
 
 ##############################################
 # Begin JOB SPECIFIC work
@@ -49,7 +46,7 @@ export ENSMEM=${ENSMEM:-000}
 export IDATE=${PDY}${cyc}
 
 for fhr in ${fhrlst}; do
-  export fhr=${fhr}  
+  export fhr=${fhr}
   # Ignore possible spelling error (nothing is misspelled)
   # shellcheck disable=SC2153
   VDATE=$(${NDATE} "${fhr}" "${IDATE}")
@@ -110,7 +107,7 @@ for fhr in ${fhrlst}; do
       status=$?
       [[ ${status} -ne 0 ]] && exit "${status}"
     fi
-  fi 
+  fi
 done
 
 # clean up working folder

jobs/rocoto/prep.sh

@@ -65,14 +65,12 @@ fi
 if [[ ${PROCESS_TROPCY} = "YES" ]]; then
 
     export COMINsyn=${COMINsyn:-$(compath.py gfs/prod/syndat)}
-    if [[ ${RUN_ENVIR} != "nco" ]]; then
-        export ARCHSYND=${ROTDIR}/syndat
-        if [[ ! -d ${ARCHSYND} ]]; then mkdir -p ${ARCHSYND}; fi
-        if [[ ! -s ${ARCHSYND}/syndat_akavit ]]; then
-            for file in syndat_akavit syndat_dateck syndat_stmcat.scr syndat_stmcat syndat_sthisto syndat_sthista ; do
-                cp ${COMINsyn}/${file} ${ARCHSYND}/.
-            done
-        fi
+    export ARCHSYND=${ROTDIR}/syndat
+    if [[ ! -d ${ARCHSYND} ]]; then mkdir -p ${ARCHSYND}; fi
+    if [[ ! -s ${ARCHSYND}/syndat_akavit ]]; then
+        for file in syndat_akavit syndat_dateck syndat_stmcat.scr syndat_stmcat syndat_sthisto syndat_sthista ; do
+            cp ${COMINsyn}/${file} ${ARCHSYND}/.
+        done
     fi
 
     if [[ ${ROTDIR_DUMP} = "YES" ]]; then rm "${COM_OBS}/${CDUMP}.t${cyc}z.syndata.tcvitals.tm00"; fi

parm/config/gefs/config.base.emc.dyn

@@ -262,6 +262,10 @@ export OUTPUT_GRID="gaussian_grid"
 export WRITE_DOPOST=".true." # WRITE_DOPOST=true, use inline POST
 export WRITE_NSFLIP=".true."
 
+# Override normal post flat files for GEFS
+export FLTFILEGFS="${PARMgfs}/post/postxconfig-NT-GEFS.txt"
+export FLTFILEGFSF00="${PARMgfs}/post/postxconfig-NT-GEFS-F00.txt"
+
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
 export imp_physics=@IMP_PHYSICS@
 

parm/config/gefs/yaml/defaults.yaml

@@ -1 +1,6 @@
-# This file intentionally left blank
+base:
+  DO_JEDIATMVAR: "NO"
+  DO_JEDIATMENS: "NO"
+  DO_JEDIOCNVAR: "NO"
+  DO_JEDILANDDA: "NO"
+  DO_MERGENSST: "NO"

parm/config/gfs/config.aeroanl

@@ -19,6 +19,5 @@ export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
 export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
-export crtm_VERSION="2.3.0"
 
 echo "END: config.aeroanl"

parm/config/gfs/config.atmanl

@@ -20,6 +20,5 @@ export io_layout_x=1
 export io_layout_y=1
 
 export JEDIEXE=${HOMEgfs}/exec/fv3jedi_var.x
-export crtm_VERSION="2.3.0"
 
 echo "END: config.atmanl"

parm/config/gfs/config.atmensanl

@@ -17,6 +17,5 @@ export io_layout_x=1
 export io_layout_y=1
 
 export JEDIEXE=${HOMEgfs}/exec/fv3jedi_letkf.x
-export crtm_VERSION="2.3.0"
 
 echo "END: config.atmensanl"

parm/config/gfs/config.com

@@ -48,6 +48,7 @@ COM_BASE='${ROTDIR}/${RUN}.${YMD}/${HH}/${MEMDIR}'
 
 declare -rx COM_TOP_TMPL='${ROTDIR}/${RUN}.${YMD}/${HH}'
 
+declare -rx COM_CONF_TMPL=${COM_BASE}'/conf'
 declare -rx COM_ATMOS_INPUT_TMPL=${COM_BASE}'/model_data/atmos/input'
 declare -rx COM_ATMOS_RESTART_TMPL=${COM_BASE}'/model_data/atmos/restart'
 declare -rx COM_ATMOS_ANALYSIS_TMPL=${COM_BASE}'/analysis/atmos'

parm/config/gfs/config.prep

@@ -13,8 +13,6 @@ export cdate10=${PDY}${cyc}
 
 # Relocation and syndata QC
 export PROCESS_TROPCY=${PROCESS_TROPCY:-NO}
-[[ $RUN_ENVIR == "nco" && $envir == "prod" ]] && export PROCESS_TROPCY="YES"
-export DO_RELOCATE="NO"
 export TROPCYQCRELOSH="$HOMEgfs/scripts/exglobal_atmos_tropcy_qc_reloc.sh"
 export SENDCOM=YES
 

parm/config/gfs/config.ufs

@@ -171,7 +171,7 @@ case "${fv3_res}" in
         export WRITE_GROUP=2
         export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE=10
         export WRITE_GROUP_GFS=4
-        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=10
+        export WRTTASK_PER_GROUP_PER_THREAD_PER_TILE_GFS=20
         ;;
     "C1152")
         export DELTIM=120

parm/config/gfs/config.wave

@@ -135,7 +135,9 @@ if [[ "${CDUMP}" != gfs ]]; then    # Setting is valid for GDAS and GEFS
 else                              # This is a GFS run
   rst_dt_gfs=$(( restart_interval_gfs * 3600 ))  # TODO: This calculation needs to move to parsing_namelists_WW3.sh
   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_1_RST_WAV=0 #${rst_dt_gfs:-0}   # time between restart files, set to DTRST=1 for a single restart file
+                                          #temporarily set to zero to avoid a clash in requested restart times 
+                                          #which makes the wave model crash a fix for the model issue will be coming
     export DT_2_RST_WAV=${rst_dt_gfs:-0}   # restart stride for checkpointing restart
   else
     rst_dt_fhmax=$(( FHMAX_WAV * 3600 ))

parm/gdas/aero_crtm_coeff.yaml

@@ -1,13 +1,13 @@
 mkdir:
-- $(DATA)/crtm/
+- {{ DATA }}/crtm/
 copy:
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/AerosolCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/CloudCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/v.viirs-m_npp.SpcCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/v.viirs-m_npp.TauCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/v.viirs-m_j1.SpcCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/v.viirs-m_j1.TauCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/NPOESS.VISice.EmisCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/NPOESS.VISland.EmisCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/NPOESS.VISsnow.EmisCoeff.bin, $(DATA)/crtm/]
-- [$(FV3JEDI_FIX)/crtm/$(crtm_VERSION)/NPOESS.VISwater.EmisCoeff.bin, $(DATA)/crtm/]
+- [{{ CRTM_FIX }}/AerosolCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/CloudCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/v.viirs-m_npp.SpcCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/v.viirs-m_npp.TauCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/v.viirs-m_j1.SpcCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/v.viirs-m_j1.TauCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/NPOESS.VISice.EmisCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/NPOESS.VISland.EmisCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/NPOESS.VISsnow.EmisCoeff.bin, {{ DATA }}/crtm/]
+- [{{ CRTM_FIX }}/NPOESS.VISwater.EmisCoeff.bin, {{ DATA }}/crtm/]