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#! /usr/bin/env bash |
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# |
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# $Header: /u/gcmpack/MITgcm/utils/scripts/gluemnc,v 1.14 2011/10/25 15:40:19 mlosch Exp $ |
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# $Name: $ |
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|
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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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# A lot of hard drive activity is needed. If you have a fast drive |
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# export TMPDIR=<path of hard drive>. On some high-performance |
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# systems, this is already done for you. |
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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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# The nco operator ncks is adept at shortening files to fewer snapshots. |
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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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LOGFILE="/dev/null" |
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|
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DIRORIG=`pwd` |
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|
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if [ ! ${#TMPDIR} -gt 0 ]; then |
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TMPDIR=$DIRORIG |
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fi |
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|
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export DIRNAME="$TMPDIR/gluedir.$RANDOM" |
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mkdir $DIRNAME |
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|
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echo Using temporary directory $DIRNAME |
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|
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if [ -f xplodemnc ]; then |
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cp xplodemnc $DIRNAME |
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else |
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cp `which xplodemnc` $DIRNAME |
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fi |
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|
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# find an unambiguous name for a new record dimension |
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myrecname=record`echo $DIRNAME | awk -F. '{print $NF}'` |
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|
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cd $DIRNAME |
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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 $DIRORIG/$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=$sprels |
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|
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# ML: determine the coordinate variable (this is hack for the unlikely |
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# case that we do not have X or Y as coordinate variables; this can |
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# happen, when only U-point or V-point variables are written to a |
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# diagnostics stream; I do not know if this always works, but it works for me) |
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echo Determine a usable coordinate variable |
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somefile=${prels}.t001.nc |
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# first try X and Y |
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Xcoord=X |
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Ycoord=Y |
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Xtest=$(ncdump -vX -l 10000 $somefile | grep "X = ") |
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Ytest=$(ncdump -vY -l 10000 $somefile | grep "Y = ") |
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if [ ${#Xtest} = 0 ]; then |
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echo "X not found, trying Xp1" |
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Xtest=$(ncdump -vXp1 -l 10000 $somefile | grep "Xp1 = ") |
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Xcoord=Xp1 |
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fi |
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if [ ${#Xtest} = 0 ]; then |
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echo "no X-coordinate found" |
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Xcoord= |
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fi |
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if [ ${#Ytest} = 0 ]; then |
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echo "Y not found, trying Yp1" |
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Ytest=$(ncdump -vYp1 -l 10000 $somefile | grep "Yp1 = ") |
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Ycoord=Yp1 |
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fi |
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if [ ${#Ytest} = 0 ]; then |
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echo "no Y-coordinate found" |
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Ycoord= |
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fi |
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if [ ${#Xcoord} = 0 ]; then |
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echo cannot continue |
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exit |
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fi |
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if [ ${#Ycoord} = 0 ]; then |
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echo cannot continue |
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exit |
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fi |
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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 -v${Xcoord} -l 10000 $somefile | grep "${Xcoord} = ") |
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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 -v${Ycoord} -l 10000 $somefile | grep "${Ycoord} = ") |
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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 -v${Xcoord} -l 10000 $somefile | grep "${Xcoord} = ") |
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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 $somefile |
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if [ -f iter.$somefile ]; then |
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mv iter.$somefile iter.${somefile%t???.nc}glob.nc |
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fi |
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for somesplit in $(ls *.$somefile) |
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do |
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# Added to account for grid files with no T dimension defined: |
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# Search for the unlimited dimension and get its name, assuming |
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# that its first character is a letter from the alphabet, the "tr" |
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# removes the blank characters |
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recname=$(ncdump -h $somesplit \ |
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| sed -n 's/\([a-z,A-Z]*\) = \(UNLIMITED\) .*/\1/p' \ |
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| tr -d ' \t' ) |
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if [[ -z "$recname" ]]; then |
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echo "No record dimension found, adding one now: "$myrecname |
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ncecat $DEBUG -O -u $myrecname $somesplit $somesplit > $LOGFILE |
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recname=$myrecname |
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fi |
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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 $DEBUG -O -a Y,$recname $somesplit $somesplit > $LOGFILE |
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mv $somesplit i$countxx.$somesplit |
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fi |
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|
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if [ -f $somesplit ]; then |
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withYp1=$(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 $DEBUG -O -a Yp1,$recname -F -d Yp1,1,$Yp1len $somesplit $somesplit > $LOGFILE |
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mv $somesplit i$countxx.$somesplit |
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fi |
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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 i$countxx.*) |
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oldvar= |
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for somefile in $cxfilels |
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do |
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varname=`echo $somefile | sed 's/^i[0-9][0-9][0-9][0-9]\.//; s/\..*nc//'` |
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if [ "$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 $somevar files in Y |
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echo YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY |
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|
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filelist=(`ls i$countxx.$somevar.$somepre.*.nc`) |
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withY=$(ncdump -h ${filelist[0]} | grep "Y =") |
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withYp1=$(ncdump -h ${filelist[0]} | grep "Yp1 =") |
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|
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ncrcat $DEBUG i$countxx.$somevar.$somepre.*.nc $somevar.$somepre.gloy.$countxx.nc > $LOGFILE |
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echo Just combined $countxx.$somevar |
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rm i$countxx.$somevar.$somepre.t???.nc |
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|
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# Recover the name of the record variable, there are two possibilities: |
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# T (MITgcm convention) and $myrecname. |
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# I must admit that this could be more elegant. |
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recname=$(ncdump -h $somevar.$somepre.gloy.$countxx.nc | grep $myrecname) |
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if [[ -z $recname ]]; then |
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recname=T |
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else |
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recname=$myrecname |
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fi |
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if [ ${#withY} -gt 1 ]; then |
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echo Changing $recname to record variable in $somevar.$somepre.gloy.$countxx.nc |
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ncpdq $DEBUG -O -a $recname,Y $somevar.$somepre.gloy.$countxx.nc $somevar.$somepre.gloy.$countxx.nc > $LOGFILE |
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fi |
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|
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if [ ${#withYp1} -gt 1 ]; then |
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echo Changing $recname to record variable in $somevar.$somepre.gloy.$countxx.nc |
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ncpdq $DEBUG -O -a $recname,Yp1 $somevar.$somepre.gloy.$countxx.nc $somevar.$somepre.gloy.$countxx.nc > $LOGFILE |
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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 $somegloy | grep "Xp1 =") |
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recname=$(ncdump -h $somegloy \ |
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| sed -n 's/\([a-z,A-Z]*\) = \(UNLIMITED\) .*/\1/p' \ |
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| tr -d ' \t' ) |
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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 $DEBUG -O -a X,$recname $somegloy $somegloy > $LOGFILE |
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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 $DEBUG -O -a Xp1,$recname -F -d Xp1,1,$Xp1len $somegloy $somegloy > $LOGFILE |
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ncpdq $DEBUG -O -a Xp1,$recname -F -d Xp1,1,$Xp1len $somegloy $somegloy > $LOGFILE |
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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 > $LOGFILE |
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# rm $somevar.$somepre.gloy.*.nc |
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|
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# recname is still valid, so change back to it without testing for it again |
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if [ ${#withX} -gt 1 ]; then |
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echo Changing $recname to record variable in $somevar.$somepre.glob.nc |
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ncpdq $DEBUG -O -a $recname,X $somevar.$somepre.glob.nc $somevar.$somepre.glob.nc > $LOGFILE |
| 357 |
fi |
| 358 |
|
| 359 |
if [ ${#withXp1} -gt 1 ]; then |
| 360 |
echo Changing $recname to record variable in $somevar.$somepre.glob.nc |
| 361 |
ncpdq $DEBUG -O -a $recname,Xp1 $somevar.$somepre.glob.nc $somevar.$somepre.glob.nc > $LOGFILE |
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fi |
| 363 |
if [ "$recname" = "$myrecname" ]; then |
| 364 |
# only for variables that did not have a record dimension to begin with |
| 365 |
echo "removing record dimension $recname from $somevar.$somepre.glob.nc" |
| 366 |
ncwa $DEBUG -O -a $recname $somevar.$somepre.glob.nc $somevar.$somepre.glob.nc |
| 367 |
fi |
| 368 |
ncks $DEBUG -A $somevar.$somepre.glob.nc $somepre.glob.nc > $LOGFILE |
| 369 |
# rm $somevar.$somepre.glob.nc |
| 370 |
done |
| 371 |
if [ -f iter.$somepre.glob.nc ]; then |
| 372 |
ncks $DEBUG -A iter.$somepre.glob.nc $somepre.glob.nc > $LOGFILE |
| 373 |
fi |
| 374 |
# rm iter.$somepre.glob.nc |
| 375 |
|
| 376 |
# another hack by rpa to accomodate grid.nc files |
| 377 |
# (there are several variables with just Z dimension that we want to keep) |
| 378 |
# varsz=$( ncdump -h $somepre.t001.nc | sed -n 's/^\s*\(double\|float\).* \(\w*\)(Z\w*).*/\2/p' ) |
| 379 |
# The OR ("\|") and "\s", "\w" only work for GNU-sed, but not for |
| 380 |
# BSD-sed or SunOS-sed, therefore we need to use some work-arounds: |
| 381 |
varsz=$( ncdump -h $somepre.t001.nc | egrep "double|float" \ |
| 382 |
| grep -v , | sed -n 's/.* \(.*\)(Z.*).*/\1/p' ) |
| 383 |
fixed= |
| 384 |
for varz in $varsz |
| 385 |
do |
| 386 |
# check to make sure the variable does not already exist in the glob file |
| 387 |
if [[ -z $( ncdump -h $somepre.glob.nc | grep " $varz(" ) ]] |
| 388 |
then |
| 389 |
echo "Adding variable $varz to $somepre.glob.nc" |
| 390 |
ncks $DEBUG -A -v $varz $somepre.t001.nc $somepre.glob.nc > $LOGFILE |
| 391 |
fixed='yes' |
| 392 |
fi |
| 393 |
done |
| 394 |
|
| 395 |
cp $somepre.glob.nc $DIRORIG |
| 396 |
done |
| 397 |
|
| 398 |
|
| 399 |
cd $DIRORIG |
| 400 |
rm -rf $DIRNAME |
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