Reenable Orion Cycling Support

.gitignore

@@ -53,11 +53,8 @@ parm/gdas/soca
 parm/gdas/jcb-gdas
 parm/gdas/jcb-algorithms
 parm/monitor
-parm/post/AEROSOL_LUTS.dat
 parm/post/nam_micro_lookup.dat
 parm/post/optics_luts_DUST.dat
-parm/post/gtg.config.gfs
-parm/post/gtg_imprintings.txt
 parm/post/optics_luts_DUST_nasa.dat
 parm/post/optics_luts_NITR_nasa.dat
 parm/post/optics_luts_SALT.dat
@@ -71,46 +68,14 @@ parm/post/optics_luts_WASO_nasa.dat
 parm/post/params_grib2_tbl_new
 parm/post/post_tag_gfs128
 parm/post/post_tag_gfs65
-parm/post/postcntrl_gefs.xml
-parm/post/postcntrl_gefs_aerosol.xml
-parm/post/postcntrl_gefs_anl.xml
-parm/post/postcntrl_gefs_chem.xml
-parm/post/postcntrl_gefs_f00.xml
-parm/post/postcntrl_gfs.xml
-parm/post/postcntrl_gfs_anl.xml
-parm/post/postcntrl_gfs_f00.xml
-parm/post/postcntrl_gfs_f00_two.xml
-parm/post/postcntrl_gfs_flux.xml
-parm/post/postcntrl_gfs_flux_f00.xml
-parm/post/postcntrl_gfs_goes.xml
-parm/post/postcntrl_gfs_goes.xml-new
-parm/post/postcntrl_gfs_two.xml
-parm/post/postcntrl_gfs_wafs.xml
-parm/post/postcntrl_gfs_wafs_anl.xml
-parm/post/postxconfig-NT-GEFS-ANL.txt
-parm/post/postxconfig-NT-GEFS-F00.txt
-parm/post/postxconfig-NT-GEFS-F00-aerosol.txt
-parm/post/postxconfig-NT-GEFS-WAFS.txt
-parm/post/postxconfig-NT-GEFS-aerosol.txt
-parm/post/postxconfig-NT-GEFS.txt
-parm/post/postxconfig-NT-GFS-ANL.txt
-parm/post/postxconfig-NT-GFS-F00-TWO.txt
-parm/post/postxconfig-NT-GFS-F00.txt
-parm/post/postxconfig-NT-GFS-FLUX-F00.txt
-parm/post/postxconfig-NT-GFS-FLUX.txt
-parm/post/postxconfig-NT-GFS-GOES.txt
-parm/post/postxconfig-NT-GFS-TWO.txt
-parm/post/postxconfig-NT-GFS-WAFS-ANL.txt
-parm/post/postxconfig-NT-GFS-WAFS.txt
-parm/post/postxconfig-NT-GFS.txt
-parm/post/postxconfig-NT-gefs-aerosol.txt
-parm/post/postxconfig-NT-gefs-chem.txt
+parm/post/gfs
+parm/post/gefs
 parm/post/ocean.csv
 parm/post/ice.csv
 parm/post/ocnicepost.nml.jinja2
 parm/ufs/noahmptable.tbl
 parm/ufs/model_configure.IN
-parm/ufs/model_configure_nest.IN
+parm/ufs/input_global_nest.nml.IN
 parm/ufs/MOM_input_*.IN
 parm/ufs/MOM6_data_table.IN
 parm/ufs/ice_in.IN

jobs/rocoto/upp.sh

@@ -36,7 +36,30 @@ if [[ "${MACHINE_ID}" = "wcoss2" ]]; then
   export PYTHONPATH
 
 else
-  . "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+  # For spack-stack 1.6.0, the UPP has its own environment (upp-addon-dev)
+  source "${HOMEgfs}/ush/module-setup.sh"
+  module use "${HOMEgfs}/sorc/ufs_model.fd/FV3/upp/modulefiles"
+  module load "${MACHINE_ID}"
+  source "${HOMEgfs}/versions/run.spack.ver"
+  module load "prod_util/${prod_util_ver}"
+  module load "grib-util/${grib_util_ver}"
+  # The numpy version in the UPP environment differs from the gsi-addon
+  module load "py-numpy/1.22.3"
+  module load "py-pyyaml/${py_pyyaml_ver}"
+  module load "py-netcdf4/${py_netcdf4_ver}"
+  module load "py-f90nml/${py_f90nml_ver}"
+
+  # The jinja2 version in the UPP environment differs from the gsi-addon
+  module load "py-jinja2/3.0.3"
+
+  # xarray is not in this environment...
+  # module load "py-xarray/${py_xarray_ver}"
+
+  wxflowPATH="${HOMEgfs}/ush/python"
+  PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush:${wxflowPATH}"
+  export PYTHONPATH
+  #. "${HOMEgfs}/ush/load_fv3gfs_modules.sh"
+
   status=$?
   if (( status != 0 )); then exit "${status}"; fi
 fi

parm/config/gefs/config.base

@@ -269,8 +269,8 @@ 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"
+export FLTFILEGFS="${PARMgfs}/post/gefs/postxconfig-NT-gefs.txt"
+export FLTFILEGFSF00="${PARMgfs}/post/gefs/postxconfig-NT-gefs-f00.txt"
 
 # Microphysics Options: 99-ZhaoCarr, 8-Thompson; 6-WSM6, 10-MG, 11-GFDL
 export imp_physics=8

parm/config/gfs/config.resources.ORION

@@ -9,8 +9,13 @@ case ${step} in
     # Remove this block once GSI issue is resolved
     # https://github.com/NOAA-EMC/GSI/pull/764
     # https://github.com/JCSDA/spack-stack/issues/1166
-    export wtime_anal_gdas="02:40:00"
-    export wtime_anal_gfs="02:00:00"
+    export walltime_gdas="02:40:00"
+    export walltime_gfs="02:00:00"
+  ;;
+  "eobs")
+    # TODO:
+    # Remove this block once the GSI issue is resolved.
+    export walltime="00:45:00"
   ;;
   *)
   ;;

parm/post/upp.yaml

@@ -18,7 +18,7 @@ analysis:
     rdaod: True
   data_in:
     copy:
-      - ["{{ PARMgfs }}/post/postxconfig-NT-GFS-ANL.txt", "{{ DATA }}/postxconfig-NT.txt"]
+      - ["{{ PARMgfs }}/post/postxconfig-NT-gfs-anl.txt", "{{ DATA }}/postxconfig-NT.txt"]
       - ["{{ COM_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmanl.nc", "{{ DATA }}/{{ atmos_filename }}"]
       - ["{{ COM_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcanl.nc", "{{ DATA }}/{{ flux_filename }}"]
   data_out:
@@ -32,9 +32,9 @@ forecast:
   data_in:
     copy:
       {% if forecast_hour == 0 %}
-      - ["{{ PARMgfs }}/post/postxconfig-NT-GFS-F00-TWO.txt", "{{ DATA }}/postxconfig-NT.txt"]
+      - ["{{ PARMgfs }}/post/postxconfig-NT-gfs-f00-two.txt", "{{ DATA }}/postxconfig-NT.txt"]
       {% else %}
-      - ["{{ PARMgfs }}/post/postxconfig-NT-GFS-TWO.txt", "{{ DATA }}/postxconfig-NT.txt"]
+      - ["{{ PARMgfs }}/post/postxconfig-NT-gfs-two.txt", "{{ DATA }}/postxconfig-NT.txt"]
       {% endif %}
       - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
       - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
@@ -81,7 +81,7 @@ goes:
       {% endfor %}
       - ["{{ 'CRTM_FIX' | getenv }}/AerosolCoeff.bin", "{{ DATA }}/"]
       - ["{{ 'CRTM_FIX' | getenv }}/CloudCoeff.bin", "{{ DATA }}/"]
-      - ["{{ PARMgfs }}/post/postxconfig-NT-GFS-GOES.txt", "{{ DATA }}/postxconfig-NT.txt"]
+      - ["{{ PARMgfs }}/post/postxconfig-NT-gfs-goes.txt", "{{ DATA }}/postxconfig-NT.txt"]
       - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.atmf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ atmos_filename }}"]
       - ["{{ COM_ATMOS_HISTORY }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.sfcf{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/{{ flux_filename }}"]
   data_out:

sorc/build_all.sh

@@ -131,16 +131,16 @@ build_jobs["ufs"]=8
 big_jobs=$((big_jobs+1))
 build_opts["ufs"]="${_wave_opt} ${_verbose_opt} ${_build_ufs_opt} ${_build_debug}"
 
-build_jobs["upp"]=2
+build_jobs["upp"]=1
 build_opts["upp"]="${_build_debug}"
 
-build_jobs["ufs_utils"]=2
+build_jobs["ufs_utils"]=1
 build_opts["ufs_utils"]="${_verbose_opt} ${_build_debug}"
 
 build_jobs["gfs_utils"]=1
 build_opts["gfs_utils"]="${_verbose_opt} ${_build_debug}"
 
-build_jobs["ww3prepost"]=2
+build_jobs["ww3prepost"]=1
 build_opts["ww3prepost"]="${_wave_opt} ${_verbose_opt} ${_build_ufs_opt} ${_build_debug}"
 
 # Optional DA builds
@@ -154,7 +154,7 @@ if [[ "${_build_ufsda}" == "YES" ]]; then
    fi
 fi
 if [[ "${_build_gsi}" == "YES" ]]; then
-   build_jobs["gsi_enkf"]=8
+   build_jobs["gsi_enkf"]=2
    build_opts["gsi_enkf"]="${_verbose_opt} ${_build_debug}"
 fi
 if [[ "${_build_gsi}" == "YES" || "${_build_ufsda}" == "YES" ]] ; then

sorc/link_workflow.sh

@@ -162,15 +162,14 @@ cd "${HOMEgfs}/parm/ufs" || exit 1
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .
 
 cd "${HOMEgfs}/parm/post" || exit 1
-for file in postxconfig-NT-GEFS-F00.txt postxconfig-NT-GEFS.txt postxconfig-NT-GEFS-WAFS.txt \
-    postxconfig-NT-GEFS-F00-aerosol.txt postxconfig-NT-GEFS-aerosol.txt \
-    postxconfig-NT-GFS-ANL.txt postxconfig-NT-GFS-F00.txt postxconfig-NT-GFS-FLUX-F00.txt \
-    postxconfig-NT-GFS.txt postxconfig-NT-GFS-FLUX.txt postxconfig-NT-GFS-GOES.txt \
-    postxconfig-NT-GFS-F00-TWO.txt postxconfig-NT-GFS-TWO.txt \
-    params_grib2_tbl_new post_tag_gfs128 post_tag_gfs65 nam_micro_lookup.dat
+for file in params_grib2_tbl_new nam_micro_lookup.dat
 do
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${file}" .
 done
+for dir in gfs gefs
+do
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
+done
 for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
     optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
     optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat
@@ -202,7 +201,7 @@ done
 
 # Link these templates from ufs-weather-model
 cd "${HOMEgfs}/parm/ufs" || exit 1
-declare -a ufs_templates=("model_configure.IN" "model_configure_nest.IN"\
+declare -a ufs_templates=("model_configure.IN" "input_global_nest.nml.IN"\
                           "MOM_input_025.IN" "MOM_input_050.IN" "MOM_input_100.IN" "MOM_input_500.IN" \
                           "MOM6_data_table.IN" \
                           "ice_in.IN" \

ush/forecast_predet.sh

@@ -537,10 +537,10 @@ FV3_predet(){
 
   # Inline UPP fix files
   if [[ "${WRITE_DOPOST:-}" == ".true." ]]; then
-    ${NCP} "${PARMgfs}/post/post_tag_gfs${LEVS}"                              "${DATA}/itag"
-    ${NCP} "${FLTFILEGFS:-${PARMgfs}/post/postxconfig-NT-GFS-TWO.txt}"        "${DATA}/postxconfig-NT.txt"
-    ${NCP} "${FLTFILEGFSF00:-${PARMgfs}/post/postxconfig-NT-GFS-F00-TWO.txt}" "${DATA}/postxconfig-NT_FH00.txt"
-    ${NCP} "${POSTGRB2TBL:-${PARMgfs}/post/params_grib2_tbl_new}"             "${DATA}/params_grib2_tbl_new"
+    ${NCP} "${PARMgfs}/post/post_tag_gfs${LEVS}"                                  "${DATA}/itag"
+    ${NCP} "${FLTFILEGFS:-${PARMgfs}/post/gfs/postxconfig-NT-gfs-two.txt}"        "${DATA}/postxconfig-NT.txt"
+    ${NCP} "${FLTFILEGFSF00:-${PARMgfs}/post/gfs/postxconfig-NT-gfs-f00-two.txt}" "${DATA}/postxconfig-NT_FH00.txt"
+    ${NCP} "${POSTGRB2TBL:-${PARMgfs}/post/params_grib2_tbl_new}"                 "${DATA}/params_grib2_tbl_new"
   fi
 
 }

ush/parsing_model_configure_FV3.sh

@@ -55,7 +55,7 @@ local IAU_OFFSET=${IAU_OFFSET:-0}
 if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
   local NEST_IMO=${npx_nest}
   local NEST_JMO=${npy_nest}
-  template="${PARMgfs}/ufs/model_configure_nest.IN"
+  template="${PARMgfs}/ufs/input_global_nest.nml.IN"
 else
   template="${PARMgfs}/ufs/model_configure.IN"
 fi

ush/python/pygfs/__init__.py

@@ -6,13 +6,22 @@
 from .task.aero_analysis import AerosolAnalysis
 from .task.atm_analysis import AtmAnalysis
 from .task.atmens_analysis import AtmEnsAnalysis
-from .task.marine_bmat import MarineBMat
 from .task.snow_analysis import SnowAnalysis
 from .task.snowens_analysis import SnowEnsAnalysis
 from .task.upp import UPP
-from .task.oceanice_products import OceanIceProducts
 from .task.gfs_forecast import GFSForecast
-from .utils import marine_da_utils
+
+# TODO Move this out of a try block once moving to spack-stack 1.8.0
+try:
+    # For spack-stack 1.6.0, the UPP requires its own environment
+    # This environment does not include xarray, which is required
+    # by marine tasks
+    from .task.marine_bmat import MarineBMat
+    from .task.oceanice_products import OceanIceProducts
+    from .utils import marine_da_utils
+
+except ModuleNotFoundError:
+    print("WARNING: not all required python modules were found!")
 
 __docformat__ = "restructuredtext"
 __version__ = "0.1.0"

versions/run.spack.ver

@@ -23,6 +23,7 @@ export py_jinja2_ver=3.1.2
 export py_pandas_ver=1.5.3
 export py_python_dateutil_ver=2.8.2
 export py_f90nml_ver=1.4.3
+export py_numpy_ver=1.23.4
 
 export met_ver=9.1.3
 export metplus_ver=3.1.1