Enable EnKF-only for atmosphere #4345
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| Original file line number | Diff line number | Diff line change |
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| #! /usr/bin/env bash | ||
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| ############################################################### | ||
| # Source UFSDA workflow modules | ||
| source "${HOMEgfs}/dev/ush/load_modules.sh" ufsda | ||
| status=$? | ||
| if [[ ${status} -ne 0 ]]; then | ||
| exit "${status}" | ||
| fi | ||
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| export job="prepatmanlbias" | ||
| export jobid="${job}.$$" | ||
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| ############################################################### | ||
| # Execute the JJOB | ||
| "${HOMEgfs}/dev/jobs/JGLOBAL_ATM_PREP_ANL_BIAS" | ||
| status=$? | ||
| exit "${status}" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,129 @@ | ||
| #! /usr/bin/env bash | ||
| export WIPE_DATA="NO" | ||
| export DATA=${DATA:-${DATAROOT}/${RUN}fetch_${cyc}} | ||
| source "${HOMEgfs}/ush/jjob_header.sh" -e "prepatmanlbias" -c "base prepatmanlbias" | ||
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| ############################################## | ||
| # Set variables used in the script | ||
| ############################################## | ||
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| ############################################## | ||
| # Begin JOB SPECIFIC work | ||
| ############################################## | ||
| # Ignore possible spelling error (nothing is misspelled) | ||
| # shellcheck disable=SC2153 | ||
| GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours") | ||
| export gPDY=${GDATE:0:8} | ||
| export gcyc=${GDATE:8:2} | ||
| export gyy=${GDATE:0:4} | ||
| export gmm=${GDATE:4:2} | ||
| export gdd=${GDATE:6:2} | ||
| export GDUMP="gdas" | ||
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| # Generate COM variables from templates | ||
| MEMDIR="ensstat" RUN="enkf${GDUMP}" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \ | ||
| COMOUT_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL | ||
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| # Process bias corrections files grabbed from HPSS in task gdas_fetchatmanlbias | ||
| BIASDIR=${DATA}/${GDUMP}.${gPDY}/${gcyc}/atmos | ||
| BIASFILES="${GDUMP}.t${gcyc}z.abias ${GDUMP}.t${gcyc}z.abias_air ${GDUMP}.t${gcyc}z.abias_int ${GDUMP}.t${gcyc}z.abias_pc ${GDUMP}.t${gcyc}z.radstat" | ||
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| ABIAS_SAT=${BIASDIR}/${GDUMP}.t${gcyc}z.abias | ||
| ABIASPC_SAT=${BIASDIR}/${GDUMP}.t${gcyc}z.abias_pc | ||
| ABIAS_SAT_JEDI_TAR=${COMOUT_ATMOS_ANALYSIS_PREV}/${GDUMP}.t${gcyc}z.rad_varbc_params.tar | ||
| ABIAS_AIR_JEDI_TAR=${COMOUT_ATMOS_ANALYSIS_PREV}/${GDUMP}.t${gcyc}z.air_varbc_params.tar | ||
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| SATBIAS2IODAX=${SATBIAS2IODAX:-${EXECgfs}/satbias2ioda.x} | ||
| SATBIAS2IODAY=${HOMEgfs}/sorc/gdas.cd/ush/satbias_converter.yaml.tmpl | ||
| OUTPUT=${DATA}/output | ||
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| if [[ ! -d "${COMOUT_ATMOS_ANALYSIS_PREV}" ]]; then mkdir -p "${COMOUT_ATMOS_ANALYSIS_PREV}"; fi | ||
| if [[ ! -d "${OUTPUT}" ]]; then mkdir -p "${OUTPUT}"; fi | ||
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| if [[ ${DO_JEDIATMENS} == "YES" ]]; then | ||
| # JEDI run | ||
| cd "${DATA}" || exit | ||
| if [[ ! -d "testrun/varbc" ]]; then mkdir -p "testrun/varbc"; fi | ||
| /bin/ln -sf "${ABIAS_SAT}" "./satbias_in" | ||
| /bin/ln -sf "${ABIASPC_SAT}" "./satbias_pc" | ||
| grep -i "NaN" satbias_in && echo "Stop. There are NaN in ${ABIAS}." && exit 1 | ||
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| # Get instruments from satbias_in | ||
| obsclass=$(grep "_" satbias_in | awk '{print $2}' | uniq) | ||
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| # Loop over instruments. Covert GSI abias to JEDI format | ||
| for instrument in ${obsclass}; do | ||
| echo "${instrument}" | ||
| /bin/cp -f "${SATBIAS2IODAY}" satbias_converter.yaml | ||
| sed -i -e "s/INSTRUMENT/${instrument}/g" satbias_converter.yaml | ||
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| ${SATBIAS2IODAX} satbias_converter.yaml | ||
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| export err=$? | ||
| if [[ ${err} -ne 0 ]]; then | ||
| err_exit "satbias2iodas.x failed for ${instrument}, ABORT!" | ||
| fi | ||
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| /bin/rm -f testrun/varbc/*nc | ||
| /bin/rm -f testrun/varbc/*txt | ||
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| cd ./testrun/varbc/ | ||
| grep "${instrument}" ../../satbias_in | awk '{print $2" "$3" "$4}' > \ | ||
| "${OUTPUT}"/gdas.t"${gcyc}"z."${instrument}".tlapse.txt | ||
| /bin/cp -p satbias_"${instrument}".nc4 "${OUTPUT}"/gdas.t"${gcyc}"z."${instrument}".satbias.nc | ||
| /bin/mv satbias_"${instrument}".nc4 "${OUTPUT}"/gdas.t"${gcyc}"z."${instrument}".satbias_cov.nc | ||
| cd "${DATA}" | ||
| /bin/rm -rf satbias_converter.yaml | ||
| done | ||
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| if [[ ${err} -eq 0 ]]; then | ||
| cd "${OUTPUT}" || exit | ||
| for file in ${BIASFILES}; do | ||
| cpreq "${BIASDIR}/${file}" "./enkf${file}.txt" | ||
| err=$? | ||
| if [[ ${err} -ne 0 ]]; then | ||
| err_exit "Error copying operational anl bias correction files" | ||
| fi | ||
| done | ||
| # TODO: Temporary solution and need to process abias_air for JEDI when ready | ||
| tar -cvf "${ABIAS_AIR_JEDI_TAR}" "./enkf${GDUMP}.t${gcyc}z.abias_air.txt" | ||
| rm -rf "./enkf${GDUMP}.t${gcyc}z.abias_air.txt" | ||
| tar -cvf "${ABIAS_SAT_JEDI_TAR}" ./*.nc ./*.txt | ||
| err=$? | ||
| fi | ||
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| else | ||
| # GSI run | ||
| for file in ${BIASFILES}; do | ||
| cpreq "${BIASDIR}/${file}" "${COMOUT_ATMOS_ANALYSIS_PREV}/enkf${file}.txt" | ||
| err=$? | ||
| if [[ ${err} -ne 0 ]]; then | ||
| err_exit "Error copying operational anl bias correction files" | ||
| fi | ||
| done | ||
| fi | ||
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| if [[ ${err} -ne 0 ]]; then | ||
| err_exit "Error executing ${EXSCRIPT}" | ||
| fi | ||
| set_trace | ||
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| ############################################## | ||
| # End JOB SPECIFIC work | ||
| ############################################## | ||
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| ############################################## | ||
| # Final processing | ||
| ############################################## | ||
| if [[ -e "${pgmout}" ]]; then | ||
| cat "${pgmout}" | ||
| fi | ||
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| ################################### | ||
| # Remove temp directories | ||
| ################################### | ||
| if [[ "${KEEPDATA}" != "YES" ]]; then | ||
| rm -rf "${DATA}" | ||
| fi | ||
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| exit 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| #! /usr/bin/env bash | ||
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| ########## config.prepatmiodaobs ########## | ||
| # Atm Operational Anl Bias Correction specific | ||
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| echo "BEGIN: config.prepatmanlbias" | ||
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| # Get task specific resources | ||
| . "${EXPDIR}/config.resources" prepatmanlbias | ||
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| echo "END: config.prepatmanlbias" |
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| Original file line number | Diff line number | Diff line change | ||||||||
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@@ -28,7 +28,8 @@ def main(): | |||||||||
| 'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU', 'DO_CA', | ||||||||||
| 'DO_CALC_INCREMENT', 'assim_freq', 'ARCH_CYC', 'DO_JEDISNOWDA', | ||||||||||
| 'ARCH_WARMICFREQ', 'ARCH_FCSTICFREQ', 'DOHYBVAR_OCN', | ||||||||||
| 'DOLETKF_OCN', 'IAUFHRS_ENKF', 'NET', 'NMEM_ENS_GFS', 'DO_GSISOILDA', 'DO_LAND_IAU', | ||||||||||
| 'DOENKFONLY_ATM'] | ||||||||||
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Comment on lines
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Contributor
There was a problem hiding this comment. Cleans up the format of this block better
Suggested change
Author
There was a problem hiding this comment. @TravisElless-NOAA Will modify as suggested in the updated PR. Thanks. |
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| archive_dict = AttrDict() | ||||||||||
| for key in keys: | ||||||||||
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Is this block actually needed? I haven't run with this enkf setting yet, but in default testing
PROCESS_TROPCY=NOgets set 3 lines earlier. Does this default change for enkf only?There was a problem hiding this comment.
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@TravisElless-NOAA I remember I added this block because
PROCESS_TROPCYwas set to "YES" somewhere and it failed the task whenDOENKFONLY_ATM= "YES". Looks like this block is not needed any more here. I will remove this block and test it in the updated PR.