Push more local changes to remote: hsd_case subdirs fv3_conf, parm, t…

…ests.

tests-dev/hsd_cases.yaml

@@ -3,8 +3,4 @@ atm_dyn32_intel:
     compiler: 'intel'
     option: '-DAPP=ATM -DCCPP_SUITES=FV3_GFS_v16,FV3_GFS_v16_flake,FV3_GFS_v17_p8,FV3_GFS_v17_p8_rrtmgp,FV3_GFS_v15_thompson_mynn_lam3km,FV3_WoFS_v0,FV3_GFS_v17_p8_mynn,FV3_GFS_v17_p8_ugwpv1 -D32BIT=ON'
   tests:
-    - control_c48: {'project':['daily'],'turnoff':['noaacloud']}
-    - control_c48.v2.sfc: {'project':['daily'],'turnoff':['noaacloud']}
     - 2020_CAPE: {'project':['daily'],'turnoff':['noaacloud']}
-    - baroclinic_wave: {'project':['daily'],'turnoff':['noaacloud']}
-    - tropical_cyclone: {'project':['daily'],'turnoff':['noaacloud']}

tests-dev/hsd_cases/fv3_conf/compile_slurm.IN_hera

@@ -0,0 +1,22 @@
+#!/bin/bash
+#SBATCH -e err
+#SBATCH -o out
+#SBATCH --account=@[ACCNR]
+#SBATCH --qos=@[QUEUE]
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=8
+#SBATCH --time=30
+#SBATCH --job-name="@[JBNME]"
+
+set -eux
+date_s_start=$(date +%s)
+date_start=$(date)
+echo -n "${date_s_start}," > job_timestamp.txt
+echo "Compile started: ${date_start}"
+
+"@[PATHRT]/compile.sh" "@[MACHINE_ID]" "@[MAKE_OPT]" "@[COMPILE_ID]" "@[RT_COMPILER]"
+
+date_end=$(date)
+echo "Compile ended: ${date_end}"
+date_s_end=$(date +%s)
+echo -n "${date_s_end}," >> job_timestamp.txt

tests-dev/hsd_cases/fv3_conf/control_run.IN

@@ -0,0 +1,173 @@
+rm -fr INPUT RESTART
+if [ $NPX = 97 ]; then
+  inputdir=FV3_input_data
+elif [ $NPX = 49 ]; then
+  inputdir=FV3_input_data48
+elif [ $NPX = 193 ]; then
+  inputdir=FV3_input_data192
+elif [ $NPX = 385 ]; then
+  inputdir=FV3_input_data384
+elif [ $NPX = 769 ]; then
+  inputdir=FV3_input_data768
+fi
+
+echo "inputdir=$inputdir,NPX=$NPX,NESTED=$NESTED"
+
+OPNREQ_TEST=${OPNREQ_TEST:-false}
+V2_SFC_FILE=${V2_SFC_FILE:-false}
+SUFFIX=${RT_SUFFIX}
+if [ $WARM_START = .false. ]; then
+  mkdir INPUT RESTART
+  if [ "$NESTED" = .true. ]; then
+    cp -r @[INPUTDATA_ROOT]/${inputdir}/INPUT_L127_nested/* ./INPUT/.
+  elif [ "$V2_SFC_FILE" = "true" ]; then
+    cp -r @[INPUTDATA_ROOT]/${inputdir}/INPUT_L127_v2_sfc/* ./INPUT/.
+  else
+    cp -r @[INPUTDATA_ROOT]/${inputdir}/INPUT_L127_gfsv17/* ./INPUT/.
+  fi
+else
+  mkdir INPUT RESTART
+
+  if [[ ${OPNREQ_TEST} == true ]]; then
+    SUFFIX=${BL_SUFFIX}
+  fi
+
+  # WAVE restart file for ATMW ORT tests
+  if [[ $CPLWAV == .true. ]]; then
+    if [[ $med_model == cmeps ]] && [[ $RUNTYPE == continue ]]; then
+      # CMEPS restart and pointer files
+      RFILE=ufs.atmw.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
+      cp  ../${DEP_RUN}${SUFFIX}/RESTART/${RFILE} .
+      ls -1 ${RFILE}>rpointer.cpl
+    fi
+    RFILE=ufs.atmw.ww3.r.${RESTART_FILE_SUFFIX_SECS}
+    cp ../${DEP_RUN}${SUFFIX}/${RFILE} .
+  fi
+
+  if [ $MODEL_INITIALIZATION = false ]; then
+    #read_inc and iau tests restart from fh=24
+    CURRDIR=`pwd`
+    FILEDIR=${CURRDIR}/../${DEP_RUN}${SUFFIX}/RESTART
+  else
+    #for warm start from initialiation time
+    FILEDIR=@[INPUTDATA_ROOT]/${inputdir}/INPUT_L127_GDAS
+  fi
+
+  if [[ ${IAU_OFFSET} != 0 ]] || [[ $READ_INCREMENT = .true. ]]; then
+
+    if [ $MODEL_INITIALIZATION = false ]; then
+      cp ${FILEDIR}/../INPUT/fv3_increment.nc INPUT/.
+      cp ${FILEDIR}/../INPUT/grid_spec.nc INPUT/.
+      cp ${FILEDIR}/../INPUT/*_grid.tile*.nc INPUT/.
+      cp ${FILEDIR}/../INPUT/oro_data.tile*.nc INPUT/.
+    else
+      cp ${FILEDIR}/fv_increment*.nc INPUT/.
+      cp ${FILEDIR}/grid_spec.nc INPUT/.
+      cp ${FILEDIR}/*_grid.tile*.nc INPUT/.
+      cp ${FILEDIR}/oro_data.tile*.nc INPUT/.
+    fi
+    cp ${FILEDIR}/coupler.res INPUT/.
+    cp ${FILEDIR}/fv_core.res.* INPUT/.
+    cp ${FILEDIR}/fv_srf_wnd.res.* INPUT/.
+    cp ${FILEDIR}/fv_tracer.* INPUT/.
+    cp ${FILEDIR}/phy_data.* INPUT/.
+    cp ${FILEDIR}/sfc_data.* INPUT/.
+  else
+    #restart test start from fh FHROT
+    cp -r ../${DEP_RUN}${SUFFIX}/RESTART/${RESTART_FILE_PREFIX}.* ./INPUT
+    rm -f INPUT/fv_core.res.*
+    rm -f INPUT/fv_srf_wnd.res.*
+    rm -f INPUT/fv_tracer.res.*
+    rm -f INPUT/phy_data.*
+    rm -f INPUT/sfc_data.*
+    cp ${FILEDIR}/../INPUT/grid_spec.nc INPUT/.
+    cp ${FILEDIR}/../INPUT/*_grid.tile*.nc INPUT/.
+    cp ${FILEDIR}/../INPUT/oro_data*.nc INPUT/.
+    for RFILE in ../${DEP_RUN}${SUFFIX}/RESTART/${RESTART_FILE_PREFIX}.*; do
+      [ -e $RFILE ] || exit 1
+      RFILE_OLD=$(basename $RFILE)
+      RFILE_NEW="${RFILE_OLD//${RESTART_FILE_PREFIX}./}"
+      cp $RFILE INPUT/${RFILE_NEW}
+    done
+  fi
+fi
+
+if [ $TILEDFIX = .true. ]; then
+    if [ $CPLLND == .true. ]; then
+        cp    @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]/@[ATMRES]*.nc INPUT/.
+    else
+        cp    @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]/@[ATMRES]*.nc .
+    fi
+    cp    @[INPUTDATA_ROOT]/FV3_fix/global_glacier.2x2.grb .
+    cp    @[INPUTDATA_ROOT]/FV3_fix/global_maxice.2x2.grb .
+    cp    @[INPUTDATA_ROOT]/FV3_fix/RTGSST.1982.2012.monthly.clim.grb .
+    cp    @[INPUTDATA_ROOT]/FV3_fix/global_snoclim.1.875.grb .
+    cp    @[INPUTDATA_ROOT]/FV3_fix/IMS-NIC.blended.ice.monthly.clim.grb .
+    cp    @[INPUTDATA_ROOT]/${inputdir}/@[FNSMCC] .
+    cp    @[INPUTDATA_ROOT]/${inputdir}/@[FNMSKH_control] .
+else
+    cp    @[INPUTDATA_ROOT]/${inputdir}/*grb .
+fi
+
+if [ $CPLWAV = .true. ]; then
+  if [ $WW3_MULTIGRID = 'true' ]; then
+    cp    @[INPUTDATA_ROOT_WW3]/mod_def.pointsatmw mod_def.points
+    cp    @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] .
+    cp    @[INPUTDATA_ROOT_WW3]/rmp_src* .
+  else
+    cp    @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] mod_def.ww3
+    cp    @[INPUTDATA_ROOT_WW3]/@[MESH_WAV] .
+  fi
+fi
+
+#inline post
+if [[ $POSTAPP = 'global' ]]; then
+  cp    ${PATHRT}/parm/@[POST_ITAG] itag
+  cp    ${PATHRT}/parm/@[POSTXCONFIG] postxconfig-NT.txt
+  cp    ${PATHRT}/parm/@[POSTXCONFIG_FH00] postxconfig-NT_FH00.txt
+  cp    ${PATHRT}/parm/params_grib2_tbl_new params_grib2_tbl_new
+fi
+
+#rrtmgp
+if [ $DO_RRTMGP = .true. ]; then
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_RRTMGP/* .
+fi
+
+#merra2
+if [ $USE_MERRA2 = .true. ]; then
+  for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
+    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
+  done
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat
+fi
+
+#rad_c_gocart
+if [ $IAER = 2011 ]; then
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
+  cp    @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat
+fi
+#ugwpv1
+if [ $DO_UGWP_V1 = .true. ]; then
+  cp    @[INPUTDATA_ROOT]/FV3_input_data/ugwp_c384_tau.nc ./ugwp_limb_tau.nc
+fi
+
+#Thompson
+if [ $IMP_PHYSICS = 8 ]; then
+  cp    @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qsV2.dat .
+  cp    @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qgV2.dat .
+  cp    @[INPUTDATA_ROOT]/FV3_fix/freezeH2O.dat .
+  cp    @[INPUTDATA_ROOT]/FV3_fix/CCN_ACTIVATE.BIN .
+fi
+
+#prognostic aerosols
+if [ $CPLCHM = .true. ]; then
+  cp      ${PATHRT}/parm/gocart/*.rc .
+  ln -sf  @[INPUTDATA_ROOT]/GOCART/p8/ExtData .
+fi

tests-dev/hsd_cases/fv3_conf/fv3_slurm.IN_hera

@@ -0,0 +1,54 @@
+#!/bin/bash
+#SBATCH -e err
+#SBATCH -o out
+#SBATCH --account=@[ACCNR]
+#SBATCH --qos=@[QUEUE]
+### #SBATCH --ntasks=@[TASKS]
+#SBATCH --nodes=@[NODES]
+#SBATCH --ntasks-per-node=@[TPN]
+#SBATCH --time=@[WLCLK]
+#SBATCH --job-name="@[JBNME]"
+### #SBATCH --exclusive
+
+set -eux
+date_s_start=$(date +%s)
+echo -n "${date_s_start}," > job_timestamp.txt
+
+set +x
+export MACHINE_ID=hera
+source ./module-setup.sh
+module use "${PWD}/modulefiles"
+module load modules.fv3
+module list
+set -x
+
+date_start=$(date)
+echo "Model started: ${date_start}"
+
+export MPI_TYPE_DEPTH=20
+export OMP_STACKSIZE=512M
+# shellcheck disable=SC2125
+export OMP_NUM_THREADS=@[THRD]
+export ESMF_RUNTIME_COMPLIANCECHECK=OFF:depth=4
+export ESMF_RUNTIME_PROFILE=ON
+export ESMF_RUNTIME_PROFILE_OUTPUT="SUMMARY"
+export PSM_RANKS_PER_CONTEXT=4
+export PSM_SHAREDCONTEXTS=1
+
+# Avoid job errors because of filesystem synchronization delays
+sync && sleep 1
+
+# This "if" block is part of the rt.sh self-tests in error-test.conf. It emulates the model failing to run.
+if [ "${JOB_SHOULD_FAIL:-NO}" = WHEN_RUNNING ] ; then
+    echo "The job should abort now, with exit status 1." 1>&2
+    echo "If error checking is working, the metascheduler should mark the job as failed." 1>&2
+    false
+fi
+
+# shellcheck disable=SC2102
+srun --label -n @[TASKS] ./fv3.exe
+
+date_end=$(date)
+echo "Model ended: ${date_end}"
+date_s_end=$(date +%s)
+echo -n "${date_s_end}," >> job_timestamp.txt

tests-dev/hsd_cases/parm/model_configure.IN

@@ -0,0 +1,38 @@
+start_year:              @[SYEAR]
+start_month:             @[SMONTH]
+start_day:               @[SDAY]
+start_hour:              @[SHOUR]
+start_minute:            0
+start_second:            0
+nhours_fcst:             @[FHMAX]
+fhrot:                   @[FHROT]
+
+dt_atmos:                @[DT_ATMOS]
+restart_interval:        @[RESTART_INTERVAL]
+
+quilting:                @[QUILTING]
+quilting_restart:        @[QUILTING_RESTART]
+write_groups:            @[WRITE_GROUP]
+write_tasks_per_group:   @[WRTTASK_PER_GROUP]
+itasks:                  @[ITASKS]
+output_history:          @[OUTPUT_HISTORY]
+history_file_on_native_grid: @[HISTORY_FILE_ON_NATIVE_GRID]
+write_dopost:            @[WRITE_DOPOST]
+write_nsflip:            @[WRITE_NSFLIP]
+num_files:               @[NUM_FILES]
+filename_base:           @[FILENAME_BASE]
+output_grid:             @[OUTPUT_GRID]
+output_file:             @[OUTPUT_FILE]
+zstandard_level:         @[ZSTANDARD_LEVEL]
+ideflate:                @[IDEFLATE]
+quantize_mode:           'quantize_bitround'
+quantize_nsd:            @[QUANTIZE_NSD]
+ichunk2d:                @[ICHUNK2D]
+jchunk2d:                @[JCHUNK2D]
+ichunk3d:                @[ICHUNK3D]
+jchunk3d:                @[JCHUNK3D]
+kchunk3d:                @[KCHUNK3D]
+imo:                     @[IMO]
+jmo:                     @[JMO]
+output_fh:               @[OUTPUT_FH]
+iau_offset:              @[IAU_OFFSET]

tests-dev/hsd_cases/parm/ufs.configure.atm_esmf.IN

@@ -0,0 +1,27 @@
+#############################################
+####  UFS Run-Time Configuration File  ######
+#############################################
+
+# ESMF #
+logKindFlag:            @[esmf_logkind]
+globalResourceControl:  true
+
+# EARTH #
+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
+::

tests-dev/hsd_cases/2020_CAPE → tests-dev/hsd_cases/tests/2020_CAPE

@@ -6,7 +6,7 @@
 
 export TEST_DESCR="Compare global control C48L127 v2.sfc results with previous trunk version"
 
-export CNTL_DIR=2020_cape
+export CNTL_DIR=2020_CAPE
 
 export LIST_FILES="sfcf000.nc \
                    sfcf024.nc \