We created for GRASS a similar data processing scheme we used from the previous exercise ( HPC gdal data processing). Now the submitter script stay the same while the template GRASS script has a set of variable and GRASS environment settings and variable exports needed for accessing GRASS functions from each CPU.

This is needed for splitting data processing in multiple CPU.

| Grass_submitter.sh

#!/bin/bash
SCRIPTDIR=~/ost4sem/experiment/scripts
for file in  ~/usbstore1/input/20*.tif ; do
qsub -v file=$file $SCRIPTDIR/Grass_template.sh
done

This is the chore script which is used for defining the actual data processing tasks.

| Grass_template.sh

#$ -S /bin/bash
#$ -o /home/pi/ost4sem/experiment/stdout
#$ -e /home/pi/ost4sem/experiment/stderr
 
export INPUTDIR=/home/pi/usbstore1/input
export OUTPUTDIR=/home/pi/usbstore2/output
export FILENAME=$(basename $file .tif)
export GRASSDB=/home/pi/ost4sem/grassdb
export LOCATION=location3035
export MAPSET=mapset_$FILENAME
 
################################  Setting GRASS variables for GRASS bash job
echo "LOCATION_NAME: $LOCATION"           >  $HOME/.grassrc6_$$
echo "MAPSET: PERMANENT"                  >> $HOME/.grassrc6_$$
echo "DIGITIZER: none"                    >> $HOME/.grassrc6_$$
echo "GRASS_GUI: text"                    >> $HOME/.grassrc6_$$
echo "GISDBASE: $GRASSDB"                 >> $HOME/.grassrc6_$$
###############################  path to GRASS binaries and libraries:
export GISBASE=/usr/lib/grass64
export PATH=$PATH:$GISBASE/bin:$GISBASE/scripts
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$GISBASE/lib"
export GISRC=~/.grassrc6_$$
export GIS_LOCK=$$  #   use process ID (PID) as lock file number
##############################   Start processing using grass
 
# gdalinfo $file > $OUTPUTDIR/$(basename $file .tif).txt
# gdalwarp -cutline $INPUTDIR/poly_fr.shp -crop_to_cutline $file $OUTPUTDIR/$CROPFILE
# gdalinfo $OUTPUTDIR/$CROPFILE > $OUTPUTDIR/$(basename $CROPFILE .tif).txt
 
g.mapset -c mapset=$MAPSET
r.external input=$file output=virtual_grass_map --overwrite
gdalinfo $file > $OUTPUTDIR/$FILENAME"before.txt"
g.region res=10000
r.mapcalc resampled=virtual_grass_map
r.out.gdal    input=resampled  format=GTiff output=$OUTPUTDIR/"test_GRASS_"$FILENAME.tif
gdalinfo  $OUTPUTDIR/"test_GRASS_"$FILENAME.tif > $OUTPUTDIR/$FILENAME"after.txt"
g.mapset mapset=PERMANENT
rm -r $GRASSDB/$LOCATION/$MAPSET