Remove implicit symlink names

Lustre has a defect under Rocky 9 that results in symlink sometimes failing when the link name is not explicit. This updates all link creation to use explicit names. `config.base` is updated to turn off two monitor jobs on Hercules because the executables are not yet built there. This, combined with the previous change, should make workflow available for use on Hercules. Also removes the redundant utility names for NCP, NLN, etc. in the gdas scripts that are already defined in `config.base`. Resolves NOAA-EMC#2131 Resolves NOAA-EMC#2522
WalterKolczynski-NOAA · Apr 24, 2024 · d0051a7 · d0051a7
1 parent f11bf3d
commit d0051a7
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Showing 16 changed files with 27 additions and 56 deletions.
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
@@ -78,6 +78,12 @@ export DO_VERFRAD="YES"    # Radiance data assimilation monitoring
 export DO_VMINMON="YES"    # GSI minimization monitoring
 export DO_MOS="NO"         # GFS Model Output Statistics - Only supported on WCOSS2
 
+if [[ ${machine} == "HERCULES" ]]; then
+    # TODO - Monitor jobs are not yet able to build on Hercules
+    export DO_VERFOZN="NO"
+    export DO_VERFRAD="NO"
+fi
+
 # NO for retrospective parallel; YES for real-time parallel
 #  arch.sh uses REALTIME for MOS.  Need to set REALTIME=YES
 #  if want MOS written to HPSS.   Should update arch.sh to

diff --git a/scripts/exgdas_atmos_chgres_forenkf.sh b/scripts/exgdas_atmos_chgres_forenkf.sh
@@ -36,9 +36,6 @@ bPDY=$(echo $BDATE | cut -c1-8)
 bcyc=$(echo $BDATE | cut -c9-10)
 
 # Utilities
-export NCP=${NCP:-"/bin/cp"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 

diff --git a/scripts/exgdas_enkf_ecen.sh b/scripts/exgdas_enkf_ecen.sh
@@ -29,8 +29,6 @@ export CASE=${CASE:-384}
 ntiles=${ntiles:-6}
 
 # Utilities
-NCP=${NCP:-"/bin/cp -p"}
-NLN=${NLN:-"/bin/ln -sf"}
 NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 
 # Scripts

diff --git a/scripts/exgdas_enkf_post.sh b/scripts/exgdas_enkf_post.sh
@@ -22,10 +22,6 @@ source "${USHgfs}/preamble.sh"
 # Directories.
 pwd=$(pwd)
 
-# Utilities
-NCP=${NCP:-"/bin/cp"}
-NLN=${NLN:-"/bin/ln -sf"}
-
 APRUN_EPOS=${APRUN_EPOS:-${APRUN:-""}}
 NTHREADS_EPOS=${NTHREADS_EPOS:-1}
 

diff --git a/scripts/exgdas_enkf_select_obs.sh b/scripts/exgdas_enkf_select_obs.sh
@@ -22,9 +22,6 @@ source "${USHgfs}/preamble.sh"
 # Directories.
 pwd=$(pwd)
 
-# Utilities
-export NLN=${NLN:-"/bin/ln -sf"}
-
 # Scripts.
 ANALYSISSH=${ANALYSISSH:-${SCRgfs}/exglobal_atmos_analysis.sh}
 

diff --git a/scripts/exgdas_enkf_sfc.sh b/scripts/exgdas_enkf_sfc.sh
@@ -30,8 +30,6 @@ export CASE=${CASE:-384}
 ntiles=${ntiles:-6}
 
 # Utilities
-NCP=${NCP:-"/bin/cp -p"}
-NLN=${NLN:-"/bin/ln -sf"}
 NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 
 # Scripts

diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
@@ -23,8 +23,6 @@ source "${USHgfs}/preamble.sh"
 pwd=$(pwd)
 
 # Utilities
-NCP=${NCP:-"/bin/cp -p"}
-NLN=${NLN:-"/bin/ln -sf"}
 NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 USE_CFP=${USE_CFP:-"NO"}
 CFP_MP=${CFP_MP:-"NO"}

diff --git a/scripts/exgfs_wave_init.sh b/scripts/exgfs_wave_init.sh
@@ -216,7 +216,7 @@ if (( NMEM_ENS > 0 )); then
     MEMDIR="mem${mem}" YMD=${PDY} HH=${cyc} declare_from_tmpl COM_WAVE_PREP_MEM:COM_WAVE_PREP_TMPL
     mkdir -p "${COM_WAVE_PREP_MEM}"
     for grdID in ${grdALL}; do
-      ${NLN} "${COM_WAVE_PREP}/${RUN}wave.mod_def.${grdID}" "${COM_WAVE_PREP_MEM}/"
+      ${NLN} "${COM_WAVE_PREP}/${RUN}wave.mod_def.${grdID}" "${COM_WAVE_PREP_MEM}/${RUN}wave.mod_def.${grdID}"
     done
   done
 fi

diff --git a/scripts/exglobal_atmos_analysis.sh b/scripts/exglobal_atmos_analysis.sh
@@ -38,9 +38,6 @@ bPDY=$(echo ${BDATE} | cut -c1-8)
 bcyc=$(echo ${BDATE} | cut -c9-10)
 
 # Utilities
-export NCP=${NCP:-"/bin/cp"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 COMPRESS=${COMPRESS:-gzip}
@@ -387,8 +384,13 @@ ${NLN} ${FIXgfs}/gsi/IASI_CLDDET.NL   IASI_CLDDET.NL
 #If using correlated error, link to the covariance files
 if [ ${USE_CORRELATED_OBERRS} == "YES" ];  then
   if grep -q "Rcov" ${ANAVINFO} ;  then
-     if ls ${FIXgfs}/gsi/Rcov* 1> /dev/null 2>&1; then
-       ${NLN} ${FIXgfs}/gsi/Rcov* ${DATA}
+     # shellcheck disable=SC2312
+     mapfile -t covfile_array < <(find "${FIXgfs}/gsi/" -name "Rcov*")
+     if (( ${#covfile_array[@]} > 0 )); then
+       for covfile in "${covfile_array[@]}"; do
+         covfile_base=$(basename "${covfile}")
+         ${NLN} "${covfile}" "${DATA}/${covfile_base}"
+       done
        echo "using correlated obs error"
      else
        echo "FATAL ERROR: Satellite error covariance files (Rcov) are missing."

diff --git a/scripts/exglobal_atmos_analysis_calc.sh b/scripts/exglobal_atmos_analysis_calc.sh
@@ -29,9 +29,6 @@ CDUMP=${CDUMP:-"gdas"}
 GDUMP=${GDUMP:-"gdas"}
 
 # Utilities
-export NCP=${NCP:-"/bin/cp"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 COMPRESS=${COMPRESS:-gzip}

diff --git a/scripts/exglobal_atmos_sfcanl.sh b/scripts/exglobal_atmos_sfcanl.sh
@@ -33,9 +33,6 @@ bPDY=${BDATE:0:8}
 bcyc=${BDATE:8:2}
 
 # Utilities
-export NCP=${NCP:-"/bin/cp"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 COMPRESS=${COMPRESS:-gzip}

diff --git a/scripts/exglobal_diag.sh b/scripts/exglobal_diag.sh
@@ -30,9 +30,6 @@ CDUMP=${CDUMP:-"gdas"}
 GDUMP=${GDUMP:-"gdas"}
 
 # Utilities
-export NCP=${NCP:-"/bin/cp"}
-export NMV=${NMV:-"/bin/mv"}
-export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-${USHgfs}/getncdimlen}
 export CATEXEC=${CATEXEC:-${ncdiag_ROOT:-${gsi_ncdiag_ROOT}}/bin/ncdiag_cat_serial.x}

diff --git a/ush/gaussian_sfcanl.sh b/ush/gaussian_sfcanl.sh
@@ -122,7 +122,6 @@ SIGLEVEL=${SIGLEVEL:-${FIXgfs}/am/global_hyblev.l${LEVSP1}.txt}
 CDATE=${CDATE:?}
 
 #  Other variables.
-export NLN=${NLN:-"/bin/ln -sf"}
 export PGMOUT=${PGMOUT:-${pgmout:-'&1'}}
 export PGMERR=${PGMERR:-${pgmerr:-'&2'}}
 export REDOUT=${REDOUT:-'1>'}
@@ -133,17 +132,9 @@ export REDERR=${REDERR:-'2>'}
 #  Preprocessing
 ${INISCRIPT:-}
 pwd=$(pwd)
-if [[ -d $DATA ]]
-then
-   mkdata=NO
-else
-   mkdir -p $DATA
-   mkdata=YES
-fi
-cd $DATA||exit 99
+cd "${DATA}" || exit 99
 [[ -d "${COM_ATMOS_ANALYSIS}" ]] || mkdir -p "${COM_ATMOS_ANALYSIS}"
 [[ -d "${COM_ATMOS_RESTART}" ]] || mkdir -p "${COM_ATMOS_RESTART}"
-cd $DATA
 
 ################################################################################
 #  Make surface analysis
@@ -207,6 +198,5 @@ $ERRSCRIPT||exit 2
 ################################################################################
 #  Postprocessing
 cd $pwd
-[[ $mkdata = YES ]]&&rmdir $DATA
 
 exit ${err}
diff --git a/ush/link_crtm_fix.sh b/ush/link_crtm_fix.sh
@@ -22,16 +22,16 @@ for what in "amsre_aqua" "imgr_g11" "imgr_g12" "imgr_g13" \
 	"ssmi_f13" "ssmi_f14" "ssmi_f15" "ssmis_f16" \
 	"ssmis_f17" "ssmis_f18" "ssmis_f19" "ssmis_f20" \
 	"tmi_trmm" "v.seviri_m10" "imgr_insat3d" "abi_gr" "ahi_himawari8" ; do
-	ln -s "${CRTM_FIX}/${what}.TauCoeff.bin" .
-	ln -s "${CRTM_FIX}/${what}.SpcCoeff.bin" .
+	ln -s "${CRTM_FIX}/${what}.TauCoeff.bin" "${what}.TauCoeff.bin"
+	ln -s "${CRTM_FIX}/${what}.SpcCoeff.bin" "${what}.SpcCoeff.bin"
 done
 
 for what in 'Aerosol' 'Cloud' ; do
-	ln -s "${CRTM_FIX}/${what}Coeff.bin" .
+	ln -s "${CRTM_FIX}/${what}Coeff.bin" "${what}Coeff.bin"
 done
 
-for what in  ${CRTM_FIX}/*Emis* ; do
-	ln -s ${what} .
+for what in "${CRTM_FIX}/"*Emis* ; do
+	ln -s "${what}" "$(basename "${what}")"
 done
 
 exit 0
diff --git a/ush/wave_grid_interp_sbs.sh b/ush/wave_grid_interp_sbs.sh
@@ -85,18 +85,16 @@ source "${USHgfs}/preamble.sh"
   rm -f ${DATA}/output_${ymdh}0000/out_grd.$grdID
 
   if [ ! -f ${DATA}/${grdID}_interp.inp.tmpl ]; then
-    cp ${PARMgfs}/wave/${grdID}_interp.inp.tmpl ${DATA}
+    cp "${PARMgfs}/wave/${grdID}_interp.inp.tmpl" "${DATA}/${grdID}_interp.inp.tmpl"
   fi
-  ln -sf ${DATA}/${grdID}_interp.inp.tmpl .
+  ln -sf "${DATA}/${grdID}_interp.inp.tmpl" "${grdID}_interp.inp.tmpl"
 
-  for ID in $waveGRD
-  do
-    ln -sf ${DATA}/output_${ymdh}0000/out_grd.$ID .
+  for ID in ${waveGRD}; do
+    ln -sf "${DATA}/output_${ymdh}0000/out_grd.${ID}" "out_grd.${ID}"
   done
 
-  for ID in $waveGRD $grdID
-  do
-    ln -sf ${DATA}/mod_def.$ID .
+  for ID in ${waveGRD} ${grdID}; do
+    ln -sf "${DATA}/mod_def.${ID}" "mod_def.${ID}"
   done
 
 # --------------------------------------------------------------------------- #

diff --git a/ush/wave_prnc_ice.sh b/ush/wave_prnc_ice.sh
@@ -36,7 +36,7 @@ source "${USHgfs}/preamble.sh"
   rm -rf ice
   mkdir ice
   cd ice
-  ln -s ${DATA}/postmsg .
+  ln -s "${DATA}/postmsg" postmsg
 
 # 0.b Define directories and the search path.
 #     The tested variables should be exported by the postprocessor script.