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Concatenate CICE daily output #31

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Concatenate CICE daily output #31

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Add script to concatenate daily cice output into one file per month (…
anton-seaice Mar 22, 2024
bd7f4ea
Use nco from system modules and clean up concat ice script
anton-seaice Mar 27, 2024
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8 changes: 7 additions & 1 deletion config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,13 @@ env:
platform:
nodesize: 48

# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771
userscripts:
# sweep and resubmit on specific errors - see https://github.com/payu-org/payu/issues/241#issuecomment-610739771
error: tools/resub.sh
run: rm -f resubmit.count
# combine cice daily history files into one file per month
archive: tools/concat_ice_daily.sh

modules:
load:
- nco/5.0.5
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- nco/5.0.5

18 changes: 18 additions & 0 deletions tools/concat_ice_daily.sh
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@@ -0,0 +1,18 @@
#!/usr/bin/bash
#concatenate sea-ice daily output
#script inspired from https://github.com/COSIMA/1deg_jra55_ryf/blob/master/sync_data.sh#L87-L108

out_dir=$(ls -td archive/output??? | head -1)/ice/OUTPUT #latest output dir only
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out_dir=$(ls -td archive/output??? | head -1)/ice/OUTPUT #latest output dir only
out_dir=$(ls -dr archive/output??? | head -1)/ice/OUTPUT #latest output dir only


for f in $out_dir/iceh.????-??-01.nc; do
#concat daily files for this month
echo "doing ncrcat -O -L 5 -4 ${f/-01.nc/-??.nc} ${f/-01.nc/-daily.nc}"
ncrcat -O -L 5 -4 ${f/-01.nc/-??.nc} ${f/-01.nc/-daily.nc}
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ncrcat -O -L 5 -4 ${f/-01.nc/-??.nc} ${f/-01.nc/-daily.nc}
{PAYU_PATH}/ncrcat -O -L 5 -4 ${f/-01.nc/-??.nc} ${f/-01.nc/-daily.nc}


if [[ $? == 0 ]]; # ncrcat succeeded
then
#set permissions and delete indidual dailys
chmod g+r ${f/-01.nc/-daily.nc}
rm ${f/-01.nc/-??.nc}
fi
done
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