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#!/bin/bash |
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# This is a shell script to combine multiple MITgcm mnc output files from |
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# different tiles into one global file. |
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# All of the variables should be in one directory, where this script is run. |
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# |
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# To combine all state.0000000000.t*.nc files, |
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# gluemnc state.0000000000.*.nc |
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# This will result in an output file state.0000000000.glob.nc |
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# Where glob is for global. |
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# |
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# You can even combine all mnc files, use |
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# gluemnc *.nc |
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# This will result in a series of global files, |
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# state.0000000000.glob.nc state.0000000100.glob.nc, ... |
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# grid.0000000000.glob.nc grid.0000000100.glob.nc, ... |
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# diag.0000000000.glob.nc diag.0000000100.glob.nc, ... |
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# |
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# **********WARNINGS********** |
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# This will probably not work at all with exch2/cubed sphere. |
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# In that case, you probably can assemble all of the tiles on a face, |
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# but combining faces is currently not implemented. |
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# |
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# Be sure you have enough disk space for the copies! In this version |
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# nothing is done to assure all of the data is copied. |
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# |
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# Be careful! It will be easy to exceed the 2 GB limit for the old 32-bit |
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# version of netcdf. If you do not have large-file support or 64-bit netcdf |
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# you will have to be clever in dividing up your tiled files, |
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# e.g., along the time dimension before combining to global files. |
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# ***************************** |
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# |
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# Good luck and happy gluing, |
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# Baylor Fox-Kemper |
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|
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DEBUG=--dbg_lvl=0 |
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|
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mkdir gluedir |
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ln -s `which xplodemnc` gluedir |
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cd gluedir |
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|
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inone=$1 |
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inone=${1:?"You must input mnc filenames to be glued"} |
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|
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for somefile in $@ |
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do |
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ln -s ../$somefile . |
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if [ ! -s $somefile ]; then |
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echo "Error: $somefile is missing or empty" |
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exit 1 |
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fi |
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done |
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|
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prels=${@%.t???.nc} |
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|
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for somepre in $prels |
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do |
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inls=0 |
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for somepres in $sprels |
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do |
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if [ "$somepre" = "$somepres" ]; then |
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inls=1 |
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fi |
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done |
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if [ "$inls" = "0" ]; then |
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sprels=$sprels" "$somepre |
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fi |
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done |
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|
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prels=$sprels |
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|
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for somepre in $prels |
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do |
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echo Making $somepre.glob.nc... |
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Xsls= |
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Ysls= |
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|
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for somefile in $@ |
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do |
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if [ "${somefile%.t???.nc}" = "$somepre" ]; then |
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echo Scanning $somefile... |
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Xs=$(ncdump -vX -l 10000 $somefile | grep "X = ") |
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Xs=${Xs#*;} |
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Xs=${Xs%;*} |
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Xs=$(echo $Xs | sed s/' '//g) |
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Xsls=$Xsls$Xs" " |
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|
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Ys=$(ncdump -vY -l 10000 $somefile | grep "Y = ") |
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Ys=${Ys#*;} |
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Ys=${Ys%;*} |
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Ys=$(echo $Ys | sed s/' '//g) |
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Ysls=$Ysls$Ys" " |
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fi |
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done |
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|
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sYsls= |
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sXsls= |
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|
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# Determine all the X locations |
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countx=0 |
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for someXs in $Xsls |
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do |
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inls=0 |
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for somesXs in $sXsls |
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do |
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if [ "$someXs" = "$somesXs" ]; then |
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inls=1 |
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fi |
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done |
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if [ "$inls" = "0" ]; then |
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sXsls=$sXsls$someXs" " |
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countx=$((countx))+1 |
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fi |
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done |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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echo $((countx)) tiles found in x-direction. |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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|
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# Determine all the Y locations |
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county=0 |
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for someYs in $Ysls |
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do |
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inls=0 |
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for somesYs in $sYsls |
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do |
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if [ "$someYs" = "$somesYs" ]; then |
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inls=1 |
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fi |
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done |
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if [ "$inls" = "0" ]; then |
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sYsls=$sYsls$someYs" " |
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county=$((county))+1 |
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fi |
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done |
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echo YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY |
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echo $((county)) tiles found in y-direction. |
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echo YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY |
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|
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countyy=1000 |
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countxx=1000 |
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|
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cntls= |
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for someX in $sXsls |
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do |
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countxx=$((countxx+1)) |
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cntls=$cntls$countxx" " |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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echo Prepping X tile $((countxx-1000)) |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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|
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for somefile in $@ |
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do |
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if [ "${somefile%.t???.nc}" = "$somepre" ]; then |
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Xs=$(ncdump -vX -l 10000 $somefile | grep "X = ") |
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Xs=${Xs#*;} |
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Xs=${Xs%;*} |
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Xs=$(echo $Xs | sed s/' '//g) |
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|
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if [ "$someX" = $Xs ]; then |
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./xplodemnc $somefile |
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for somesplit in $(ls *.$somefile) |
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do |
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withY=$(ncdump -h $somesplit | grep "Y =") |
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if [ ${#withY} -gt 1 ]; then |
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echo Changing Y to record variable in $somesplit |
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ncpdq $DEBUG -O -a Y,T $somesplit $somesplit |
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mv $somesplit $countxx.$somesplit |
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fi |
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|
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withYp1=$(ncdump -h $somesplit | grep "Yp1 =") |
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if [ ${#withYp1} -gt 1 ]; then |
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Yp1len=${withYp1#*= } |
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Yp1len=$((${Yp1len% ;}-1)) |
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# Strip off the repeated value in Yp1 |
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echo Changing Yp1 to record variable in $somesplit |
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ncpdq $DEBUG -O -a Yp1,T -F -d Yp1,1,$Yp1len $somesplit $somesplit |
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mv $somesplit $countxx.$somesplit |
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fi |
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done |
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fi |
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fi |
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done |
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done |
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echo Tile names $cntls |
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for countxx in $cntls |
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do |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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echo Combining X tile $((countxx-1000)) |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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varls= |
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cxfilels=$(ls $countxx.*) |
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oldvar= |
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for somefile in $cxfilels |
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do |
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varname=${somefile%.*} |
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varname=${varname%.*} |
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varname=${varname%.*} |
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varname=${varname%.*} |
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varname=${varname#*.} |
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if [ "$varname" = "$oldvar" ]; then |
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echo $varname repeated |
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else |
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varls=$varls$varname" " |
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fi |
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oldvar=$varname |
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done |
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|
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echo Found these variables to combine: $varls |
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|
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for somevar in $varls |
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do |
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echo YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY |
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echo Combining $somevar files in Y |
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echo YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY |
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|
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withY=$(ncdump -h $countxx.$somevar.$somepre.*.nc | grep "Y =") |
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withYp1=$(ncdump -h $countxx.$somevar.$somepre.*.nc | grep "Yp1 =") |
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|
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ncrcat $DEBUG $countxx.$somevar.$somepre.*.nc $somevar.$somepre.gloy.$countxx.nc |
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echo Just combined $countxx.$somevar |
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rm $countxx.$somevar.$somepre.t???.nc |
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|
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if [ ${#withY} -gt 1 ]; then |
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echo Changing T to record variable in $somevar.$somepre.gloy.$countxx.nc |
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ncpdq $DEBUG -O -a T,Y $somevar.$somepre.gloy.$countxx.nc $somevar.$somepre.gloy.$countxx.nc |
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fi |
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|
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if [ ${#withYp1} -gt 1 ]; then |
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echo Changing T to record variable in $somevar.$somepre.gloy.$countxx.nc |
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ncpdq $DEBUG -O -a T,Yp1 $somevar.$somepre.gloy.$countxx.nc $somevar.$somepre.gloy.$countxx.nc |
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fi |
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done |
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done |
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for somevar in $varls |
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do |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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echo Combining $somevar files in X... |
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echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX |
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for somegloy in $(ls $somevar.$somepre.gloy.*.nc) |
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do |
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withX=$(ncdump -h $somegloy | grep "X =") |
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withXp1=$(ncdump -h $somegloy | grep "Xp1 =") |
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|
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if [ ${#withX} -gt 1 ]; then |
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echo Changing X to record variable in $somegloy |
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ncpdq $DEBUG -O -a X,T $somegloy $somegloy |
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fi |
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|
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if [ ${#withXp1} -gt 1 ]; then |
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Xp1len=${withXp1#*= } |
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Xp1len=$((${Xp1len% ;}-1)) |
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# Strip off the repeated value in Xp1 |
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echo Changing Xp1 to record variable in $somegloy |
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echo ncpdq $DEBUG -O -a Xp1,T -F -d Xp1,1,$Xp1len $somegloy $somegloy |
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ncpdq $DEBUG -O -a Xp1,T -F -d Xp1,1,$Xp1len $somegloy $somegloy |
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fi |
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done |
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echo Combining $somevar.gloy files... |
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ncrcat $DEBUG $somevar.$somepre.gloy.*.nc $somevar.$somepre.glob.nc |
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rm $somevar.$somepre.gloy.*.nc |
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|
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if [ ${#withX} -gt 1 ]; then |
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echo Changing T to record variable in $somevar.$somepre.glob.nc |
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ncpdq $DEBUG -O -a T,X $somevar.$somepre.glob.nc $somevar.$somepre.glob.nc |
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fi |
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|
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if [ ${#withXp1} -gt 1 ]; then |
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echo Changing T to record variable in $somevar.$somepre.glob.nc |
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ncpdq $DEBUG -O -a T,Xp1 $somevar.$somepre.glob.nc $somevar.$somepre.glob.nc |
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fi |
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ncrcat $DEBUG -A $somevar.$somepre.glob.nc $somepre.glob.nc |
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rm $somevar.$somepre.glob.nc |
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done |
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done |
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|
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cp *.glob.nc .. |
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cd .. |
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rm -rf gluedir |
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