From 2fbe399a1c91739fd726e1f0ff3da6aa2291e973 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Wed, 28 Jun 2023 02:05:57 -0500 Subject: [PATCH 1/8] Update fit2obs for COM refactor Updated the fit2obs j-job for COM refactor. Logs show some failed copies due to non-existant files, but not sure if those are related. Fixes #1486 --- jobs/JGDAS_FIT2OBS | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index d673845404..c14d263909 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -17,11 +17,14 @@ export CDATE vday=${CDATE:0:8} vcyc=${CDATE:8:2} -export COM_INA=${ROTDIR}/gdas.${vday}/${vcyc}/atmos +YMD=${vday} HH=${vcyc} generate_com -rx COM_ATMOS_ANALYSIS_VERIF:COM_ATMOS_ANALYSIS_TMPL +RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_OBS_VERIF:COM_OBS_TMPL + +export COM_INA=${COM_ATMOS_ANALYSIS_VERIF} # We want to defer variable expansion, so ignore warning about single quotes # shellcheck disable=SC2016 export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz' -export COM_PRP=${ROTDIR}/gdas.${vday}/${vcyc}/obs +export COM_PRP=${COM_OBS_VERIF} export PRPI=${COM_PRP}/${RUN}.t${vcyc}z.prepbufr export sig1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc From 415455fe96c2a533766132136a9a0d572f754d80 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Wed, 28 Jun 2023 21:57:42 -0500 Subject: [PATCH 2/8] Shellcheck updates for fit2obs j-job --- jobs/JGDAS_FIT2OBS | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index c14d263909..c85c14aa87 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -40,8 +40,8 @@ export HORZ_DIR=${ARCDIR}/horiz export COMLOX=${DATA}/fitx [[ ! -d "${COMLOX}" ]] && mkdir -p "${COMLOX}" -echo "echo err_chk">"${DATA}"/err_chk; chmod 755 "${DATA}"/err_chk -echo "echo postmsg">"${DATA}"/postmsg; chmod 755 "${DATA}"/postmsg +echo "echo err_chk">"${DATA}/err_chk"; chmod 755 "${DATA}/err_chk" +echo "echo postmsg">"${DATA}/postmsg"; chmod 755 "${DATA}/postmsg" ############################################## # Check spinup and available inputs From fd0aef63cdd4f93397cf67f5745495e889c91d44 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Sat, 8 Jul 2023 02:33:23 -0500 Subject: [PATCH 3/8] Fix path of history files for fit2obs archive The archive job was using the incorrect source path for the history files when copying to the local archive for fit2obs. Refs: #1486 --- scripts/exglobal_archive.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/exglobal_archive.sh b/scripts/exglobal_archive.sh index 294f3941c8..2695799613 100755 --- a/scripts/exglobal_archive.sh +++ b/scripts/exglobal_archive.sh @@ -103,8 +103,8 @@ if [[ "${RUN}" == "gfs" ]] && [[ "${FITSARC}" = "YES" ]]; then fhr=0 while [[ ${fhr} -le ${fhmax} ]]; do fhr3=$(printf %03i "${fhr}") - sfcfile="${COM_ATMOS_MASTER}/${prefix}.sfcf${fhr3}.nc" - sigfile="${COM_ATMOS_MASTER}/${prefix}.atmf${fhr3}.nc" + sfcfile="${COM_ATMOS_HISTORY}/${prefix}.sfcf${fhr3}.nc" + sigfile="${COM_ATMOS_HISTORY}/${prefix}.atmf${fhr3}.nc" nb_copy "${sfcfile}" "${VFYARC}/${RUN}.${PDY}/${cyc}/" nb_copy "${sigfile}" "${VFYARC}/${RUN}.${PDY}/${cyc}/" (( fhr = 10#${fhr} + 6 )) From 404fd0d80370973156703ddfded29c621db37f89 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Sat, 8 Jul 2023 02:36:28 -0500 Subject: [PATCH 4/8] Turn fit2obs back on by default Fit2obs had been turned off during the COM refactor because it had not yet been updated for the new paths. Now that the job has been updated, it can be turned back on. Refs: #1486 --- parm/config/gfs/config.base.emc.dyn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/parm/config/gfs/config.base.emc.dyn b/parm/config/gfs/config.base.emc.dyn index 282e5a53d3..29aff2980e 100644 --- a/parm/config/gfs/config.base.emc.dyn +++ b/parm/config/gfs/config.base.emc.dyn @@ -384,7 +384,7 @@ export binary_diag=".false." # Verification options export DO_METP="YES" # Run METPLUS jobs - set METPLUS settings in config.metp -export DO_FIT2OBS="NO" # Run fit to observations package +export DO_FIT2OBS="YES" # Run fit to observations package # Archiving options export HPSSARCH="@HPSSARCH@" # save data to HPSS archive From 50ab97b086f74078798124d9ce64eaf06a83d763 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Wed, 12 Jul 2023 17:51:28 -0500 Subject: [PATCH 5/8] Add comment about why fit2obs variable name not updated --- jobs/JGDAS_FIT2OBS | 1 + 1 file changed, 1 insertion(+) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index c85c14aa87..0a3528b974 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -20,6 +20,7 @@ vcyc=${CDATE:8:2} YMD=${vday} HH=${vcyc} generate_com -rx COM_ATMOS_ANALYSIS_VERIF:COM_ATMOS_ANALYSIS_TMPL RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_OBS_VERIF:COM_OBS_TMPL +# These are used by fit2obs, so we can't change them to the standard COM variable names export COM_INA=${COM_ATMOS_ANALYSIS_VERIF} # We want to defer variable expansion, so ignore warning about single quotes # shellcheck disable=SC2016 From 8147d5e37a6077de49d94065d8fe8458e82da40d Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Thu, 13 Jul 2023 15:24:23 -0500 Subject: [PATCH 6/8] Remove intermediary COM variables in fit2obs --- jobs/JGDAS_FIT2OBS | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index 0a3528b974..06989df0d4 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -17,15 +17,13 @@ export CDATE vday=${CDATE:0:8} vcyc=${CDATE:8:2} -YMD=${vday} HH=${vcyc} generate_com -rx COM_ATMOS_ANALYSIS_VERIF:COM_ATMOS_ANALYSIS_TMPL -RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_OBS_VERIF:COM_OBS_TMPL - # These are used by fit2obs, so we can't change them to the standard COM variable names -export COM_INA=${COM_ATMOS_ANALYSIS_VERIF} +YMD=${vday} HH=${vcyc} generate_com -rx COM_INA:COM_ATMOS_ANALYSIS_TMPL +RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_PRP:COM_OBS_TMPL + # We want to defer variable expansion, so ignore warning about single quotes # shellcheck disable=SC2016 export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz' -export COM_PRP=${COM_OBS_VERIF} export PRPI=${COM_PRP}/${RUN}.t${vcyc}z.prepbufr export sig1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc From 62c6533fc00188ff044e06289a0be278e0a72231 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Thu, 13 Jul 2023 15:27:56 -0500 Subject: [PATCH 7/8] Fix shellcheck complaint --- jobs/JGDAS_FIT2OBS | 1 + 1 file changed, 1 insertion(+) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index 06989df0d4..d9a4af83d8 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -18,6 +18,7 @@ vday=${CDATE:0:8} vcyc=${CDATE:8:2} # These are used by fit2obs, so we can't change them to the standard COM variable names +# shellcheck disable=SC2153 YMD=${vday} HH=${vcyc} generate_com -rx COM_INA:COM_ATMOS_ANALYSIS_TMPL RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_PRP:COM_OBS_TMPL From fee5e032496aaa418cb389ae17f15235ea879222 Mon Sep 17 00:00:00 2001 From: "Walter.Kolczynski" Date: Thu, 13 Jul 2023 15:49:42 -0500 Subject: [PATCH 8/8] Ignore shellcheck complaint --- jobs/JGDAS_FIT2OBS | 1 + 1 file changed, 1 insertion(+) diff --git a/jobs/JGDAS_FIT2OBS b/jobs/JGDAS_FIT2OBS index d9a4af83d8..7638e4f0c8 100755 --- a/jobs/JGDAS_FIT2OBS +++ b/jobs/JGDAS_FIT2OBS @@ -27,6 +27,7 @@ RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_PRP:COM_OBS_TMPL export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz' export PRPI=${COM_PRP}/${RUN}.t${vcyc}z.prepbufr +# shellcheck disable=SC2153 export sig1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc export sfc1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc export CNVS=${COM_INA}/${RUN}.t${vcyc}z.cnvstat