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Merged
WalterKolczynski-NOAA merged 1 commit into from
Nov 2, 2022
Merged

Correct syntax in remaining sorc scripts #1105

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21 changes: 11 additions & 10 deletions sorc/checkout.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Clones and checks out external components necessary for
cloning and just check out the requested version (unless
-c option is used).

Usage: $BASH_SOURCE [-c][-h][-m ufs_hash][-o]
Usage: ${BASH_SOURCE[0]} [-c][-h][-m ufs_hash][-o]
-c:
Create a fresh clone (delete existing directories)
-h:
Expand Down Expand Up @@ -51,7 +51,7 @@ function checkout() {
remote="$2"
version="$3"

name=$(echo ${dir} | cut -d '.' -f 1)
name=$(echo "${dir}" | cut -d '.' -f 1)
echo "Performing checkout of ${name}"

logfile="${logdir:-$(pwd)}/checkout_${name}.log"
Expand All @@ -60,8 +60,8 @@ function checkout() {
rm "${logfile}"
fi

cd "${topdir}"
if [[ -d "${dir}" && $CLEAN == "YES" ]]; then
cd "${topdir}" || exit 1
if [[ -d "${dir}" && ${CLEAN} == "YES" ]]; then
echo "|-- Removing existing clone in ${dir}"
rm -Rf "${dir}"
fi
Expand All @@ -74,10 +74,10 @@ function checkout() {
echo
return "${status}"
fi
cd "${dir}"
cd "${dir}" || exit 1
else
# Fetch any updates from server
cd "${dir}"
cd "${dir}" || exit 1
echo "|-- Fetching updates from ${remote}"
git fetch
fi
Expand Down Expand Up @@ -131,7 +131,7 @@ while getopts ":chgum:o" option; do
;;
m)
echo "Received -m flag with argument, will check out ufs-weather-model hash ${OPTARG} instead of default"
ufs_model_hash=$OPTARG
ufs_model_hash=${OPTARG}
;;
:)
echo "option -${OPTARG} needs an argument"
Expand All @@ -145,7 +145,8 @@ while getopts ":chgum:o" option; do
done
shift $((OPTIND-1))

export topdir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
topdir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
export topdir
export logdir="${topdir}/logs"
mkdir -p "${logdir}"

Expand Down Expand Up @@ -183,7 +184,7 @@ if [[ ${checkout_gtg} == "YES" ]]; then
################################################################################

echo "Checking out GTG extension for UPP"
cd "${topdir}/ufs_model.fd/FV3/upp"
cd "${topdir}/ufs_model.fd/FV3/upp" || exit 1
logfile="${logdir}/checkout_gtg.log"
git -c submodule."post_gtg.fd".update=checkout submodule update --init --recursive >> "${logfile}" 2>&1
status=$?
Expand All @@ -197,4 +198,4 @@ if (( errs > 0 )); then
echo "WARNING: One or more errors encountered during checkout process, please check logs before building"
fi
echo
exit $errs
exit "${errs}"
52 changes: 26 additions & 26 deletions sorc/link_workflow.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &> /dev/null && pwd)
top_dir=$(cd "$(dirname "${script_dir}")" &> /dev/null && pwd)
cd "${script_dir}"

COMPILER="intel"
export COMPILER="intel"
# shellcheck disable=SC1091
source gfs_utils.fd/ush/detect_machine.sh # (sets MACHINE_ID)
# shellcheck disable=
Expand Down Expand Up @@ -80,8 +80,8 @@ fi
[[ -d upp.fd ]] && rm -rf upp.fd
${LINK} ufs_model.fd/FV3/upp upp.fd

if [ ! -z "${FIX_DIR}" ]; then
if [ ! -d "${top_dir}/fix" ]; then mkdir "${top_dir}/fix" || exit 1; fi
if [[ -n "${FIX_DIR}" ]]; then
if [[ ! -d "${top_dir}/fix" ]]; then mkdir "${top_dir}/fix" || exit 1; fi
fi
cd "${top_dir}/fix" || exit 1
for dir in aer \
Expand All @@ -100,15 +100,15 @@ for dir in aer \
verif \
wave
do
if [ -d "${dir}" ]; then
if [[ -d "${dir}" ]]; then
[[ "${RUN_ENVIR}" == "nco" ]] && chmod -R 755 "${dir}"
rm -rf "${dir}"
fi
fix_ver="${dir}_ver"
${LINK} "${FIX_DIR}/${dir}/${!fix_ver}" "${dir}"
done

if [ -d "${script_dir}/ufs_utils.fd" ]; then
if [[ -d "${script_dir}/ufs_utils.fd" ]]; then
cd "${script_dir}/ufs_utils.fd/fix" || exit 1
./link_fixdirs.sh "${RUN_ENVIR}" "${machine}" 2> /dev/null
fi
Expand All @@ -118,7 +118,7 @@ fi
#--add files from external repositories
#---------------------------------------
cd "${top_dir}/parm" || exit 1
if [ -d "${script_dir}/gldas.fd" ]; then
if [[ -d "${script_dir}/gldas.fd" ]]; then
[[ -d gldas ]] && rm -rf gldas
${LINK} "${script_dir}/gldas.fd/parm" gldas
fi
Expand Down Expand Up @@ -146,7 +146,7 @@ cd "${top_dir}/ush" || exit 8

#-----------------------------------
#--add gfs_wafs link if checked out
if [ -d "${script_dir}/gfs_wafs.fd" ]; then
if [[ -d "${script_dir}/gfs_wafs.fd" ]]; then
#-----------------------------------
cd "${top_dir}/jobs" || exit 1
${LINK} "${script_dir}/gfs_wafs.fd/jobs"/* .
Expand All @@ -166,7 +166,7 @@ fi
#------------------------------
#--add GSI fix directory
#------------------------------
if [ -d "${script_dir}/gsi_enkf.fd" ]; then
if [[ -d "${script_dir}/gsi_enkf.fd" ]]; then
cd "${top_dir}/fix" || exit 1
[[ -d gsi ]] && rm -rf gsi
${LINK} "${script_dir}/gsi_enkf.fd/fix" gsi
Expand All @@ -175,12 +175,12 @@ fi
#------------------------------
#--add GDASApp fix directory
#------------------------------
if [ -d "${script_dir}/gdas.cd" ]; then
if [[ -d "${script_dir}/gdas.cd" ]]; then
cd "${top_dir}/fix" || exit 1
[[ ! -d gdas ]] && mkdir -p gdas
cd gdas || exit 1
for gdas_sub in bump crtm fv3jedi gsibec; do
if [ -d "${gdas_sub}" ]; then
if [[ -d "${gdas_sub}" ]]; then
rm -rf "${gdas_sub}"
fi
fix_ver="gdas_${gdas_sub}_ver"
Expand All @@ -191,16 +191,16 @@ fi
#------------------------------
#--add GDASApp files
#------------------------------
if [ -d "${script_dir}/gdas.cd" ]; then
cd "${top_dir}/ush"
if [[ -d "${script_dir}/gdas.cd" ]]; then
cd "${top_dir}/ush" || exit 1
${LINK} "${script_dir}/gdas.cd/ush/ufsda" .
fi


#------------------------------
#--add DA Monitor file (NOTE: ensure to use correct version)
#------------------------------
if [ -d "${script_dir}/gsi_monitor.fd" ]; then
if [[ -d "${script_dir}/gsi_monitor.fd" ]]; then

cd "${top_dir}/fix" || exit 1
[[ ! -d gdas ]] && ( mkdir -p gdas || exit 1 )
Expand All @@ -227,7 +227,7 @@ fi
#--link executables
#------------------------------

if [ ! -d "${top_dir}/exec" ]; then mkdir "${top_dir}/exec" || exit 1 ; fi
if [[ ! -d "${top_dir}/exec" ]]; then mkdir "${top_dir}/exec" || exit 1 ; fi
cd "${top_dir}/exec" || exit 1

for utilexe in fbwndgfs.x gaussian_sfcanl.x gfs_bufr.x regrid_nemsio.x supvit.x syndat_getjtbul.x \
Expand All @@ -243,7 +243,7 @@ ${LINK} "${script_dir}/ufs_model.fd/tests/ufs_model.x" .
[[ -s "upp.x" ]] && rm -f upp.x
${LINK} "${script_dir}/upp.fd/exec/upp.x" .

if [ -d "${script_dir}/gfs_wafs.fd" ]; then
if [[ -d "${script_dir}/gfs_wafs.fd" ]]; then
for wafsexe in \
wafs_awc_wafavn.x wafs_blending.x wafs_blending_0p25.x \
wafs_cnvgrib2.x wafs_gcip.x wafs_grib2_0p25.x \
Expand All @@ -260,15 +260,15 @@ for ufs_utilsexe in \
done

# GSI
if [ -d "${script_dir}/gsi_enkf.fd" ]; then
if [[ -d "${script_dir}/gsi_enkf.fd" ]]; then
for gsiexe in enkf.x gsi.x; do
[[ -s "${gsiexe}" ]] && rm -f "${gsiexe}"
${LINK} "${script_dir}/gsi_enkf.fd/install/bin/${gsiexe}" .
done
fi

# GSI Utils
if [ -d "${script_dir}/gsi_utils.fd" ]; then
if [[ -d "${script_dir}/gsi_utils.fd" ]]; then
for exe in calc_analysis.x calc_increment_ens_ncio.x calc_increment_ens.x \
getsfcensmeanp.x getsigensmeanp_smooth.x getsigensstatp.x \
interp_inc.x recentersigp.x;do
Expand All @@ -278,23 +278,23 @@ if [ -d "${script_dir}/gsi_utils.fd" ]; then
fi

# GSI Monitor
if [ -d "${script_dir}/gsi_monitor.fd" ]; then
if [[ -d "${script_dir}/gsi_monitor.fd" ]]; then
for exe in oznmon_horiz.x oznmon_time.x radmon_angle.x \
radmon_bcoef.x radmon_bcor.x radmon_time.x; do
[[ -s "${exe}" ]] && rm -f "${exe}"
${LINK} "${script_dir}/gsi_monitor.fd/install/bin/${exe}" .
done
fi

if [ -d "${script_dir}/gldas.fd" ]; then
if [[ -d "${script_dir}/gldas.fd" ]]; then
for gldasexe in gdas2gldas gldas2gdas gldas_forcing gldas_model gldas_post gldas_rst; do
[[ -s "${gldasexe}" ]] && rm -f "${gldasexe}"
${LINK} "${script_dir}/gldas.fd/exec/${gldasexe}" .
done
fi

# GDASApp
if [ -d "${script_dir}/gdas.cd" ]; then
if [[ -d "${script_dir}/gdas.cd" ]]; then
for gdasexe in fv3jedi_addincrement.x fv3jedi_diffstates.x fv3jedi_ensvariance.x fv3jedi_hofx.x \
fv3jedi_var.x fv3jedi_convertincrement.x fv3jedi_dirac.x fv3jedi_error_covariance_training.x \
fv3jedi_letkf.x fv3jedi_convertstate.x fv3jedi_eda.x fv3jedi_forecast.x fv3jedi_plot_field.x \
Expand All @@ -307,17 +307,17 @@ fi
#------------------------------
#--link source code directories
#------------------------------
cd "${script_dir}" || exit 8
cd "${script_dir}" || exit 8

if [ -d gsi_enkf.fd ]; then
if [[ -d gsi_enkf.fd ]]; then
[[ -d gsi.fd ]] && rm -rf gsi.fd
${SLINK} gsi_enkf.fd/src/gsi gsi.fd

[[ -d enkf.fd ]] && rm -rf enkf.fd
${SLINK} gsi_enkf.fd/src/enkf enkf.fd
fi

if [ -d gsi_utils.fd ]; then
if [[ -d gsi_utils.fd ]]; then
[[ -d calc_analysis.fd ]] && rm -rf calc_analysis.fd
${SLINK} gsi_utils.fd/src/netcdf_io/calc_analysis.fd calc_analysis.fd

Expand All @@ -343,7 +343,7 @@ cd "${script_dir}" || exit 8
${SLINK} gsi_utils.fd/src/netcdf_io/interp_inc.fd interp_inc.fd
fi

if [ -d gsi_monitor.fd ] ; then
if [[ -d gsi_monitor.fd ]] ; then
[[ -d oznmon_horiz.fd ]] && rm -rf oznmon_horiz.fd
${SLINK} gsi_monitor.fd/src/Ozone_Monitor/nwprod/oznmon_shared/sorc/oznmon_horiz.fd oznmon_horiz.fd

Expand Down Expand Up @@ -401,7 +401,7 @@ cd "${script_dir}" || exit 8
${LINK} "gfs_utils.fd/src/${prog}" .
done

if [ -d "${script_dir}/gfs_wafs.fd" ]; then
if [[ -d "${script_dir}/gfs_wafs.fd" ]]; then
${SLINK} gfs_wafs.fd/sorc/wafs_awc_wafavn.fd wafs_awc_wafavn.fd
${SLINK} gfs_wafs.fd/sorc/wafs_blending.fd wafs_blending.fd
${SLINK} gfs_wafs.fd/sorc/wafs_blending_0p25.fd wafs_blending_0p25.fd
Expand All @@ -412,7 +412,7 @@ cd "${script_dir}" || exit 8
${SLINK} gfs_wafs.fd/sorc/wafs_setmissing.fd wafs_setmissing.fd
fi

if [ -d gldas.fd ]; then
if [[ -d gldas.fd ]]; then
for prog in gdas2gldas.fd gldas2gdas.fd gldas_forcing.fd gldas_model.fd gldas_post.fd gldas_rst.fd ;do
[[ -d "${prog}" ]] && rm -rf "${prog}"
${SLINK} "gldas.fd/sorc/${prog}" "${prog}"
Expand Down
6 changes: 3 additions & 3 deletions sorc/ncl.setup
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
#!/bin/bash

set +x
case $target in
case ${target} in
'jet'|'hera')
module load ncl/6.5.0
export NCARG_LIB=$NCARG_ROOT/lib
export NCARG_LIB=${NCARG_ROOT}/lib
;;
*)
echo "[${BASH_SOURCE}]: unknown $target"
echo "[${BASH_SOURCE[0]}]: unknown ${target}"
;;
esac
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