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Merge branch 'NOAA-EMC:develop' into feature/orog_reorg
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@KateFriedman-NOAA
KateFriedman-NOAA authored Nov 14, 2023
2 parents 4601ec8 + 0a0d698 commit d671e69
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Showing 10 changed files with 119 additions and 67 deletions.
2 changes: 1 addition & 1 deletion ci/cases/pr/C48_S2SA_gefs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@ arguments:
resens: 48
nens: 2
gfs_cyc: 1
start: cold
comrot: {{ 'RUNTESTS' | getenv }}/COMROT
expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
icsdir: {{ 'ICSDIR_ROOT' | getenv }}/C48C48mx500
idate: 2021032312
edate: 2021032312
yaml: {{ HOMEgfs }}/ci/platforms/gefs_ci_defaults.yaml
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_FORECAST
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Expand Up @@ -46,7 +46,7 @@ declare -rx gcyc="${GDATE:8:2}"

# Construct COM variables from templates (see config.com)
YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \
COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_TOP
COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_TOP COM_CONF

RUN=${rCDUMP} YMD="${gPDY}" HH="${gcyc}" generate_com -rx \
COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
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7 changes: 6 additions & 1 deletion parm/config/gefs/config.base.emc.dyn
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Original file line number Diff line number Diff line change
Expand Up @@ -282,11 +282,16 @@ export NMEM_ENS=@NMEM_ENS@
export ENSMEM="000"
export MEMDIR="mem${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 cold starting
if [[ "${EXP_WARM_START}" = ".false." ]]; then
export IAU_FHROT=0
export IAU_FHROT=0
else
if [[ "${DOIAU}" = "YES" ]]; then
export IAU_FHROT=3
else
export IAU_FHROT=0
fi
fi

# turned on nsst in anal and/or fcst steps, and turn off rtgsst
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2 changes: 1 addition & 1 deletion scripts/exgdas_enkf_fcst.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ for imem in $(seq "${ENSBEG}" "${ENSEND}"); do
# Construct COM variables from templates (see config.com)
# Can't make these read-only because we are looping over members
MEMDIR="${memchar}" YMD=${PDY} HH=${cyc} generate_com -x COM_ATMOS_RESTART COM_ATMOS_INPUT COM_ATMOS_ANALYSIS \
COM_ATMOS_HISTORY COM_ATMOS_MASTER
COM_ATMOS_HISTORY COM_ATMOS_MASTER COM_CONF

MEMDIR="${memchar}" YMD="${gPDY}" HH="${gcyc}" generate_com -x COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL

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102 changes: 73 additions & 29 deletions scripts/exglobal_stage_ic.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@ gPDY="${GDATE:0:8}"
gcyc="${GDATE:8:2}"

MEMDIR_ARRAY=()
if [[ "${RUN}" == "gefs" ]]; then
if [[ "${RUN:-}" = "gefs" ]]; then
# Populate the member_dirs array based on the value of NMEM_ENS
for ((ii = 0; ii <= "${NMEM_ENS}"; ii++)); do
for ((ii = 0; ii <= "${NMEM_ENS:-0}"; ii++)); do
MEMDIR_ARRAY+=("mem$(printf "%03d" "${ii}")")
done
else
Expand All @@ -27,35 +27,58 @@ error_message() {

###############################################################
for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
# Stage the FV3 initial conditions to ROTDIR (cold start)
YMD=${PDY} HH=${cyc} generate_com COM_ATMOS_INPUT
[[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"
src="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${MEMDIR}/atmos/gfs_ctrl.nc"
tgt="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
for ftype in gfs_data sfc_data; do
for ((tt = 1; tt <= 6; tt++)); do
src="${BASE_CPLIC}/${CPL_ATMIC}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
${NCP} "${src}" "${tgt}"
rc=$?
tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"

# Stage atmosphere initial conditions to ROTDIR
if [[ ${EXP_WARM_START:-".false."} = ".true." ]]; then
# Stage the FV3 restarts to ROTDIR (warm start)
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
[[ ! -d "${COM_ATMOS_RESTART_PREV}" ]] && mkdir -p "${COM_ATMOS_RESTART_PREV}"
for ftype in coupler.res fv_core.res.nc; do
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${PDY}.${cyc}0000.${ftype}"
tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
done
done
for ftype in ca_data fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data; do
for ((tt = 1; tt <= 6; tt++)); do
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
tgt="${COM_ATMOS_RESTART_PREV}/${PDY}.${cyc}0000.${ftype}.tile${tt}.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
done
done
else
# Stage the FV3 cold-start initial conditions to ROTDIR
YMD=${PDY} HH=${cyc} generate_com COM_ATMOS_INPUT
[[ ! -d "${COM_ATMOS_INPUT}" ]] && mkdir -p "${COM_ATMOS_INPUT}"
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/gfs_ctrl.nc"
tgt="${COM_ATMOS_INPUT}/gfs_ctrl.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
for ftype in gfs_data sfc_data; do
for ((tt = 1; tt <= 6; tt++)); do
src="${BASE_CPLIC}/${CPL_ATMIC:-}/${PDY}${cyc}/${MEMDIR}/atmos/${ftype}.tile${tt}.nc"
tgt="${COM_ATMOS_INPUT}/${ftype}.tile${tt}.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
done
done
fi

# Stage ocean initial conditions to ROTDIR (warm start)
if [[ "${DO_OCN:-}" = "YES" ]]; then
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_OCEAN_RESTART
[[ ! -d "${COM_OCEAN_RESTART}" ]] && mkdir -p "${COM_OCEAN_RESTART}"
src="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res.nc"
tgt="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res.nc"
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL
[[ ! -d "${COM_OCEAN_RESTART_PREV}" ]] && mkdir -p "${COM_OCEAN_RESTART_PREV}"
src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res.nc"
tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.MOM.res.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
Expand All @@ -66,7 +89,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
;;
"025" )
for nn in $(seq 1 3); do
src="${BASE_CPLIC}/${CPL_OCNIC}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
tgt="${COM_OCEAN_RESTART}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
${NCP} "${src}" "${tgt}"
rc=$?
Expand All @@ -80,13 +103,33 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
err=$((err + rc))
;;
esac

# TODO: Do mediator restarts exists in a ATMW configuration?
# TODO: No mediator is presumably involved in an ATMA configuration
if [[ ${EXP_WARM_START:-".false."} = ".true." ]]; then
# Stage the mediator restarts to ROTDIR (warm start/restart the coupled model)
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_MED_RESTART_PREV:COM_MED_RESTART_TMPL
[[ ! -d "${COM_MED_RESTART_PREV}" ]] && mkdir -p "${COM_MED_RESTART_PREV}"
src="${BASE_CPLIC}/${CPL_MEDIC:-}/${PDY}${cyc}/${MEMDIR}/med/${PDY}.${cyc}0000.ufs.cpld.cpl.r.nc"
tgt="${COM_MED_RESTART_PREV}/${PDY}.${cyc}0000.ufs.cpld.cpl.r.nc"
if [[ -f "${src}" ]]; then
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
err=$((err + rc))
else
echo "WARNING: No mediator restarts available with warm_start=${EXP_WARM_START}"
fi
fi

fi

# Stage ice initial conditions to ROTDIR (warm start)
if [[ "${DO_ICE:-}" = "YES" ]]; then
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_ICE_RESTART
[[ ! -d "${COM_ICE_RESTART}" ]] && mkdir -p "${COM_ICE_RESTART}"
src="${BASE_CPLIC}/${CPL_ICEIC}/${PDY}${cyc}/${MEMDIR}/ice/${PDY}.${cyc}0000.cice_model.res.nc"
tgt="${COM_ICE_RESTART}/${PDY}.${cyc}0000.cice_model.res.nc"
RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
[[ ! -d "${COM_ICE_RESTART_PREV}" ]] && mkdir -p "${COM_ICE_RESTART_PREV}"
src="${BASE_CPLIC}/${CPL_ICEIC:-}/${PDY}${cyc}/${MEMDIR}/ice/${PDY}.${cyc}0000.cice_model.res.nc"
tgt="${COM_ICE_RESTART_PREV}/${PDY}.${cyc}0000.cice_model.res.nc"
${NCP} "${src}" "${tgt}"
rc=$?
((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
Expand All @@ -98,7 +141,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
YMD=${PDY} HH=${cyc} generate_com COM_WAVE_RESTART
[[ ! -d "${COM_WAVE_RESTART}" ]] && mkdir -p "${COM_WAVE_RESTART}"
for grdID in ${waveGRD}; do # TODO: check if this is a bash array; if so adjust
src="${BASE_CPLIC}/${CPL_WAVIC}/${PDY}${cyc}/${MEMDIR}/wave/${PDY}.${cyc}0000.restart.${grdID}"
src="${BASE_CPLIC}/${CPL_WAVIC:-}/${PDY}${cyc}/${MEMDIR}/wave/${PDY}.${cyc}0000.restart.${grdID}"
tgt="${COM_WAVE_RESTART}/${PDY}.${cyc}0000.restart.${grdID}"
${NCP} "${src}" "${tgt}"
rc=$?
Expand All @@ -108,6 +151,7 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
fi

done # for MEMDIR in "${MEMDIR_ARRAY[@]}"; do

###############################################################
# Check for errors and exit if any of the above failed
if [[ "${err}" -ne 0 ]]; then
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9 changes: 6 additions & 3 deletions ush/forecast_postdet.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -515,7 +515,10 @@ FV3_out() {
done
else
# No need to copy FV3 restart files when RUN=gfs or gefs
${NCP} "${DATA}/input.nml" "${COM_ATMOS_HISTORY}/input.nml"
${NCP} "${DATA}/input.nml" "${COM_CONF}/ufs.input.nml"
${NCP} "${DATA}/model_configure" "${COM_CONF}/ufs.model_configure"
${NCP} "${DATA}/nems.configure" "${COM_CONF}/ufs.nems.configure"
${NCP} "${DATA}/diag_table" "${COM_CONF}/ufs.diag_table"
fi
echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
}
Expand Down Expand Up @@ -854,7 +857,7 @@ MOM6_out() {

# Copy MOM_input from DATA to COM_OCEAN_INPUT after the forecast is run (and successfull)
if [[ ! -d ${COM_OCEAN_INPUT} ]]; then mkdir -p "${COM_OCEAN_INPUT}"; fi
${NCP} "${DATA}/INPUT/MOM_input" "${COM_OCEAN_INPUT}/"
${NCP} "${DATA}/INPUT/MOM_input" "${COM_CONF}/ufs.MOM_input"

# TODO: mediator should have its own CMEPS_out() function
# Copy mediator restarts from DATA to COM
Expand Down Expand Up @@ -992,7 +995,7 @@ CICE_out() {

# Copy ice_in namelist from DATA to COMOUTice after the forecast is run (and successfull)
if [[ ! -d "${COM_ICE_INPUT}" ]]; then mkdir -p "${COM_ICE_INPUT}"; fi
${NCP} "${DATA}/ice_in" "${COM_ICE_INPUT}/ice_in"
${NCP} "${DATA}/ice_in" "${COM_CONF}/ufs.ice_in"
}

GOCART_rc() {
Expand Down
2 changes: 1 addition & 1 deletion ush/forecast_predet.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ common_predet(){
tcyc=${scyc}
fi


mkdir -p "${COM_CONF}"
cd "${DATA}" || ( echo "FATAL ERROR: Unable to 'cd ${DATA}', ABORT!"; exit 8 )
}

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5 changes: 4 additions & 1 deletion workflow/applications/gfs_cycled.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ def _get_app_configs(self):
if self.do_ocean:
configs += ['ocnpost']

configs += ['sfcanl', 'analcalc', 'fcst', 'post', 'vrfy', 'fit2obs', 'arch', 'cleanup']
configs += ['sfcanl', 'analcalc', 'fcst', 'post', 'vrfy', 'arch', 'cleanup']

if self.do_hybvar:
if self.do_jediatmens:
Expand All @@ -56,6 +56,9 @@ def _get_app_configs(self):
configs += ['eobs', 'eomg', 'ediag', 'eupd']
configs += ['ecen', 'esfc', 'efcs', 'echgres', 'epos', 'earc']

if self.do_fit2obs:
configs += ['fit2obs']

if self.do_verfozn:
configs += ['verfozn']

Expand Down
52 changes: 24 additions & 28 deletions workflow/rocoto/gfs_tasks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -922,11 +922,8 @@ def fit2obs(self):
deps.append(rocoto.add_dependency(dep_dict))
dependencies = rocoto.create_dependency(dep=deps)

cycledef = 'gdas_half,gdas' if self.cdump in ['gdas'] else self.cdump

resources = self.get_resource('fit2obs')
task = create_wf_task('fit2obs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies,
cycledef=cycledef)
task = create_wf_task('fit2obs', resources, cdump=self.cdump, envar=self.envars, dependency=dependencies)

return task

Expand Down Expand Up @@ -957,33 +954,32 @@ def metp(self):
def arch(self):
deps = []
dependencies = []
if self.app_config.do_verfozn or self.app_config.do_verfrad or self.app_config.do_vminmon:
if self.app_config.mode in ['cycled']:
if self.cdump in ['gfs']:
if self.app_config.do_vminmon:
dep_dict = {'type': 'task', 'name': f'{self.cdump}vminmon'}
deps.append(rocoto.add_dependency(dep_dict))
elif self.cdump in ['gdas']:
deps2 = []
if self.app_config.do_verfozn:
dep_dict = {'type': 'task', 'name': f'{self.cdump}verfozn'}
deps2.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_verfrad:
dep_dict = {'type': 'task', 'name': f'{self.cdump}verfrad'}
deps2.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_vminmon:
dep_dict = {'type': 'task', 'name': f'{self.cdump}vminmon'}
deps2.append(rocoto.add_dependency(dep_dict))
dependencies = rocoto.create_dependency(dep_condition='and', dep=deps2)
dep_dict = {'type': 'cycleexist', 'condition': 'not', 'offset': '-06:00:00'}
dependencies.append(rocoto.add_dependency(dep_dict))
dependencies = rocoto.create_dependency(dep_condition='or', dep=dependencies)
if self.app_config.mode in ['cycled']:
if self.cdump in ['gfs']:
if self.app_config.do_vminmon:
dep_dict = {'type': 'task', 'name': f'{self.cdump}vminmon'}
deps.append(rocoto.add_dependency(dep_dict))
elif self.cdump in ['gdas']: # Block for handling half cycle dependencies
deps2 = []
if self.app_config.do_fit2obs:
dep_dict = {'type': 'task', 'name': f'{self.cdump}fit2obs'}
deps2.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_verfozn:
dep_dict = {'type': 'task', 'name': f'{self.cdump}verfozn'}
deps2.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_verfrad:
dep_dict = {'type': 'task', 'name': f'{self.cdump}verfrad'}
deps2.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_vminmon:
dep_dict = {'type': 'task', 'name': f'{self.cdump}vminmon'}
deps2.append(rocoto.add_dependency(dep_dict))
dependencies = rocoto.create_dependency(dep_condition='and', dep=deps2)
dep_dict = {'type': 'cycleexist', 'condition': 'not', 'offset': '-06:00:00'}
dependencies.append(rocoto.add_dependency(dep_dict))
dependencies = rocoto.create_dependency(dep_condition='or', dep=dependencies)
if self.app_config.do_vrfy:
dep_dict = {'type': 'task', 'name': f'{self.cdump}vrfy'}
deps.append(rocoto.add_dependency(dep_dict))
if self.cdump in ['gdas'] and self.app_config.do_fit2obs:
dep_dict = {'type': 'task', 'name': f'{self.cdump}fit2obs'}
deps.append(rocoto.add_dependency(dep_dict))
if self.app_config.do_wave:
dep_dict = {'type': 'task', 'name': f'{self.cdump}wavepostsbs'}
deps.append(rocoto.add_dependency(dep_dict))
Expand Down
3 changes: 2 additions & 1 deletion workflow/setup_expt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -432,7 +432,8 @@ def _gfs_or_gefs_forecast_args(parser):
return parser

def _gefs_args(parser):
parser.add_argument('--start', help=SUPPRESS, type=str, required=False, default='cold')
parser.add_argument('--start', help='restart mode: warm or cold', type=str,
choices=['warm', 'cold'], required=False, default='cold')
parser.add_argument('--configdir', help=SUPPRESS, type=str, required=False,
default=os.path.join(_top, 'parm/config/gefs'))
parser.add_argument('--yaml', help='Defaults to substitute from', type=str, required=False,
Expand Down

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