Merge branch 'NOAA-EMC:develop' into develop

kayeekayee · Dec 26, 2023 · 5adc47b · 5adc47b
2 parents a3ce9db + a3c5099
commit 5adc47b
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diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -10,7 +10,7 @@ Status
 ======
 
 * State of develop (HEAD) branch: GFSv17+ development
-* State of operations (dev/gfs.v16 branch): GFS v16.3.11 `tag: [gfs.v16.3.11] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.11>`_
+* State of operations (dev/gfs.v16 branch): GFS v16.3.12 `tag: [gfs.v16.3.12] <https://github.com/NOAA-EMC/global-workflow/releases/tag/gfs.v16.3.12>`_
 
 =============
 Code managers

diff --git a/jobs/JGLOBAL_PREP_OCEAN_OBS b/jobs/JGLOBAL_PREP_OCEAN_OBS
@@ -8,6 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prepoceanobs" -c "base prepoceanobs"
 ##############################################
 
 export COMIN_OBS="${DATA}"
+YMD=${PDY} HH=${cyc} generate_com -rx COMOUT_OBS:COM_OBS_TMPL
 
 ##############################################
 # Begin JOB SPECIFIC work

diff --git a/jobs/rocoto/atmos_products.sh b/jobs/rocoto/atmos_products.sh
@@ -22,7 +22,11 @@ IFS='_' read -ra fhrs <<< "${FHRLST//f}" # strip off the 'f's and convert to arr
 #---------------------------------------------------------------
 # Execute the JJOB
 for fhr in "${fhrs[@]}"; do
-    export FORECAST_HOUR=$(( 10#${fhr} ))
+    # The analysis fhr is -001.  Performing math on negative, leading 0 integers is tricky.
+    # The negative needs to be in front of "10#", so do some regex magic to make it happen.
+    fhr="10#${fhr}"
+    fhr=${fhr//10\#-/-10\#}
+    export FORECAST_HOUR=$(( fhr ))
     "${HOMEgfs}/jobs/JGLOBAL_ATMOS_PRODUCTS"
     status=$?
     if (( status != 0 )); then exit "${status}"; fi

diff --git a/parm/ufs/ufs.configure.atm.IN b/parm/ufs/ufs.configure.atm.IN
@@ -3,10 +3,20 @@ logKindFlag:            @[esmf_logkind]
 globalResourceControl:  true
 
 EARTH_component_list: ATM
+EARTH_attributes::
+  Verbosity = 0
+::
+
+# ATM #
 ATM_model:                      @[atm_model]
 ATM_petlist_bounds:             @[atm_petlist_bounds]
 ATM_omp_num_threads:            @[atm_omp_num_threads]
+ATM_attributes::
+  Verbosity = 0
+  Diagnostic = 0
+::
 
+# Run Sequence #
 runSeq::
   ATM
 ::
diff --git a/parm/ufs/ufs.configure.atm_aero.IN b/parm/ufs/ufs.configure.atm_aero.IN
@@ -9,23 +9,23 @@ globalResourceControl:  true
 # EARTH #
 EARTH_component_list: ATM CHM
 EARTH_attributes::
-  Verbosity = max
+  Verbosity = 0
 ::
 
 # ATM #
 ATM_model:                      @[atm_model]
 ATM_petlist_bounds:             @[atm_petlist_bounds]
 ATM_omp_num_threads:            @[atm_omp_num_threads]
 ATM_attributes::
-  Verbosity = max
+  Verbosity = 0
 ::
 
 # CHM #
 CHM_model:                      @[chm_model]
 CHM_petlist_bounds:             @[chm_petlist_bounds]
 CHM_omp_num_threads:            @[chm_omp_num_threads]
 CHM_attributes::
-  Verbosity = max
+  Verbosity = 0
 ::
 
 # Run Sequence #
@@ -38,13 +38,3 @@ runSeq::
     ATM phase2
   @
 ::
-
-# CMEPS variables
-
-DRIVER_attributes::
-  mediator_read_restart = .false.
-::
-
-ALLCOMP_attributes::
-  start_type = startup
-::
diff --git a/parm/ufs/ufs.configure.cpld.IN b/parm/ufs/ufs.configure.cpld.IN
@@ -39,6 +39,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -51,6 +53,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -107,9 +110,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/parm/ufs/ufs.configure.cpld_aero.IN b/parm/ufs/ufs.configure.cpld_aero.IN
@@ -47,6 +47,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -59,6 +61,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -119,9 +122,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/parm/ufs/ufs.configure.cpld_aero_outerwave.IN b/parm/ufs/ufs.configure.cpld_aero_outerwave.IN
@@ -47,6 +47,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -59,6 +61,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -71,10 +74,7 @@ WAV_omp_num_threads:            @[wav_omp_num_threads]
 WAV_attributes::
   Verbosity = 0
   OverwriteSlice = false
-  diro = "."
-  logfile = wav.log
   mesh_wav = @[MESH_WAV]
-  multigrid = @[MULTIGRID]
 ::
 
 # CMEPS warm run sequence
@@ -139,9 +139,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/parm/ufs/ufs.configure.cpld_aero_wave.IN b/parm/ufs/ufs.configure.cpld_aero_wave.IN
@@ -47,6 +47,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -59,6 +61,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -71,10 +74,7 @@ WAV_omp_num_threads:            @[wav_omp_num_threads]
 WAV_attributes::
   Verbosity = 0
   OverwriteSlice = false
-  diro = "."
-  logfile = wav.log
   mesh_wav = @[MESH_WAV]
-  multigrid = @[MULTIGRID]
 ::
 
 # CMEPS warm run sequence
@@ -139,9 +139,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/parm/ufs/ufs.configure.cpld_outerwave.IN b/parm/ufs/ufs.configure.cpld_outerwave.IN
@@ -39,6 +39,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -51,6 +53,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -63,10 +66,7 @@ WAV_omp_num_threads:            @[wav_omp_num_threads]
 WAV_attributes::
   Verbosity = 0
   OverwriteSlice = false
-  diro = "."
-  logfile = wav.log
   mesh_wav = @[MESH_WAV]
-  multigrid = @[MULTIGRID]
 ::
 
 # CMEPS warm run sequence
@@ -127,9 +127,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/parm/ufs/ufs.configure.cpld_wave.IN b/parm/ufs/ufs.configure.cpld_wave.IN
@@ -39,6 +39,8 @@ OCN_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ocn = @[MESH_OCN_ICE]
+  use_coldstart = @[use_coldstart]
+  use_mommesh = @[use_mommesh]
 ::
 
 # ICE #
@@ -51,6 +53,7 @@ ICE_attributes::
   ProfileMemory = false
   OverwriteSlice = true
   mesh_ice = @[MESH_OCN_ICE]
+  eps_imesh = @[eps_imesh]
   stop_n = @[RESTART_N]
   stop_option = nhours
   stop_ymd = -999
@@ -63,10 +66,7 @@ WAV_omp_num_threads:            @[wav_omp_num_threads]
 WAV_attributes::
   Verbosity = 0
   OverwriteSlice = false
-  diro = "."
-  logfile = wav.log
   mesh_wav = @[MESH_WAV]
-  multigrid = @[MULTIGRID]
 ::
 
 # CMEPS warm run sequence
@@ -127,9 +127,6 @@ ALLCOMP_attributes::
       restart_option = nhours
       restart_ymd = -999
       dbug_flag = @[cap_dbug_flag]
-      use_coldstart = @[use_coldstart]
-      use_mommesh = @[use_mommesh]
-      eps_imesh = @[eps_imesh]
       stop_n = @[FHMAX]
       stop_option = nhours
       stop_ymd = -999

diff --git a/scripts/exgfs_aero_init_aerosol.py b/scripts/exgfs_aero_init_aerosol.py
@@ -41,14 +41,14 @@
 from functools import partial
 
 # Constants
-atm_base_pattern = "{rot_dir}/{cdump}.%Y%m%d/%H/atmos/INPUT"           		  # Location of atmosphere ICs
+atm_base_pattern = "{rot_dir}/{cdump}.%Y%m%d/%H/model_data/atmos/input"       # Location of atmosphere ICs
 atm_file_pattern = "{path}/gfs_data.{tile}.nc"                                # Atm IC file names
 atm_ctrl_pattern = "{path}/gfs_ctrl.nc"                                       # Atm IC control file name
-restart_base_pattern = "{rot_dir}/{cdump}.%Y%m%d/%H/atmos/RERUN_RESTART"      # Location of restart files (time of previous run)
+restart_base_pattern = "{rot_dir}/{cdump}.%Y%m%d/%H/model_data/atmos/restart"   # Location of restart files (time of previous run)
 restart_file_pattern = "{file_base}/{timestamp}fv_core.res.{tile}.nc"         # Name of restart data files (time when restart is valid)
 tracer_file_pattern = "{file_base}/{timestamp}fv_tracer.res.{tile}.nc"        # Name of restart tracer files (time when restart is valid)
 dycore_file_pattern = "{file_base}/{timestamp}fv_core.res.nc"                 # Name of restart dycore file (time when restart is valid)
-tracer_list_file_pattern = "{parm_gfs}/chem/gocart_tracer.list"               # Text list of tracer names to copy
+tracer_list_file_pattern = "{parm_gfs}/ufs/gocart/gocart_tracer.list"               # Text list of tracer names to copy
 merge_script_pattern = "{ush_gfs}/merge_fv3_aerosol_tile.py"
 n_tiles = 6
 max_lookback = 4                                                              # Maximum number of past cycles to look for for tracer data

diff --git a/sorc/build_all.sh b/sorc/build_all.sh
@@ -98,9 +98,9 @@ fi
 #------------------------------------
 # Disable shellcheck warning about single quotes not being substituted.
 # shellcheck disable=SC2016
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
+ERRSCRIPT=${ERRSCRIPT:-'eval [[ $errs = 0 ]]'}
 # shellcheck disable=
-err=0
+errs=0
 
 declare -A build_jobs
 declare -A build_opts
@@ -219,7 +219,6 @@ while [[ ${builds_started} -lt ${#build_jobs[@]} ]]; do
 done
 
 # Wait for all jobs to complete and check return statuses
-errs=0
 while [[ ${#build_jobs[@]} -gt 0 ]]; do
    for build in "${!build_jobs[@]}"; do
       # Test if each job is complete and if so, notify and remove from the array
@@ -252,7 +251,7 @@ if (( errs != 0 )); then
 BUILD ERROR: One or more components failed to build
   Check the associated build log(s) for details.
 EOF
-  ${ERRSCRIPT} || exit "${err}"
+  ${ERRSCRIPT} || exit "${errs}"
 fi
 
 echo;echo " .... Build system finished .... "

diff --git a/sorc/link_workflow.sh b/sorc/link_workflow.sh
@@ -122,12 +122,6 @@ do
 done
 
 
-if [[ -d "${HOMEgfs}/sorc/ufs_utils.fd" ]]; then
-  cd "${HOMEgfs}/sorc/ufs_utils.fd/fix" || exit 1
-  ./link_fixdirs.sh "${RUN_ENVIR}" "${machine}" 2> /dev/null
-fi
-
-
 #---------------------------------------
 #--add files from external repositories
 #---------------------------------------

diff --git a/sorc/ufs_model.fd b/sorc/ufs_model.fd
diff --git a/ush/merge_fv3_aerosol_tile.py b/ush/merge_fv3_aerosol_tile.py
@@ -88,14 +88,6 @@ def merge_tile(base_file_name: str, ctrl_file_name: str, core_file_name: str, re
         print("FATAL ERROR: Inconsistent size of B(k) arrays: src=", bk.size, ", dst=", bi.size)
         sys.exit(108)
 
-    if not np.array_equal(ak, ai):
-        print("FATAL ERROR: A(k) coefficients must be identical")
-        sys.exit(109)
-
-    if not np.array_equal(bk, bi):
-        print("FATAL ERROR: B(k) coefficients must be identical")
-        sys.exit(110)
-
     dp = np.zeros(delp.shape)
     for k in range(0, dp.shape[0]):
         dp[k, :, :] = ak[k + 1] - ak[k] + psfc * (bk[k + 1] - bk[k])

diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
@@ -41,6 +41,7 @@ write_groups:            ${WRITE_GROUP:-1}
 write_tasks_per_group:   ${WRTTASK_PER_GROUP:-24}
 itasks:                  1
 output_history:          ${OUTPUT_HISTORY:-".true."}
+history_file_on_native_grid: .false.
 write_dopost:            ${WRITE_DOPOST:-".false."}
 write_nsflip:            ${WRITE_NSFLIP:-".false."}
 num_files:               ${NUM_FILES:-2}
@@ -54,7 +55,8 @@ ichunk3d:                ${ichunk3d:-0}
 jchunk3d:                ${jchunk3d:-0}
 kchunk3d:                ${kchunk3d:-0}
 ideflate:                ${ideflate:-1}
-nbits:                   ${nbits:-14}
+quantize_mode:           'quantize_bitround'
+quantize_nsd:            ${QUANTIZE_NSD:-0}
 imo:                     ${LONB_IMO}
 jmo:                     ${LATB_JMO}
 output_fh:               ${FV3_OUTPUT_FH}