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Fix sorc/upp.fd link ordering to prevent broken symlinks #4480

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Fix sorc/upp.fd link ordering to prevent broken symlinks #4480

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84771f1
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Copilot Jan 28, 2026
2bba70f
Fix link_workflow.sh ordering - create upp.fd link before usage
Copilot Jan 28, 2026
6d481f5
Merge branch 'develop' into copilot/fix-link-workflow-issues
aerorahul Jan 28, 2026
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43 changes: 31 additions & 12 deletions sorc/link_workflow.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,17 @@ if [[ "${LINK_NEST:-OFF}" == "ON" ]]; then
done
fi

#------------------------------
#--link source code directories needed by subsequent steps
#------------------------------
cd "${HOMEgfs}/sorc" || exit 8
if [[ -d ufs_model.fd ]]; then
if [[ -d upp.fd ]]; then
rm -rf upp.fd
fi
${LINK} ufs_model.fd/UFSATM/upp upp.fd
fi

#---------------------------------------
#--link sorc/upp.fd before referencing files within it
#---------------------------------------
Expand All @@ -158,18 +169,24 @@ cd "${HOMEgfs}/parm/ufs" || exit 1
${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .

cd "${HOMEgfs}/parm/post" || exit 1
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" .

for dir in gfs gcafs gefs sfs; do
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
done
if [[ -d "${HOMEgfs}/sorc/upp.fd" ]]; then
[[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] && \
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[shfmt] reported by reviewdog 🐶

Suggested change
[[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] && \
[[ -f "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" ]] &&

${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" ]] && \
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[shfmt] reported by reviewdog 🐶

Suggested change
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" ]] && \
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" ]] &&

${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" .

for dir in gfs gcafs gefs sfs; do
[[ -d "${HOMEgfs}/sorc/upp.fd/parm/${dir}" ]] && \
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[shfmt] reported by reviewdog 🐶

Suggested change
[[ -d "${HOMEgfs}/sorc/upp.fd/parm/${dir}" ]] && \
[[ -d "${HOMEgfs}/sorc/upp.fd/parm/${dir}" ]] &&

${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
done

for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat; do
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
done
for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat; do
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" ]] && \
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[shfmt] reported by reviewdog 🐶

Suggested change
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" ]] && \
[[ -f "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" ]] &&

${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
done
fi

for file in ice_gfs.csv ice_gefs.csv ocean_gfs.csv ocean_gefs.csv ocnicepost.nml.jinja2; do
${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/parm/ocnicepost/${file}" .
Expand Down Expand Up @@ -404,7 +421,9 @@ done
if [[ -s "upp.x" ]]; then
rm -f upp.x
fi
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/exec/upp.x" .
if [[ -f "${HOMEgfs}/sorc/upp.fd/exec/upp.x" ]]; then
${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/exec/upp.x" .
fi

for ufs_utilsexe in emcsfc_ice_blend emcsfc_snow2mdl global_cycle fregrid regridStates.x; do
if [[ -s "${ufs_utilsexe}" ]]; then
Expand Down
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