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solarPOT/sbatch/create_grass_array.sh
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create_grass_array.sh
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#!/bin/bash
if [ "$1" == "-h" ] ; then
echo ""
echo "####################################################"
echo "This script replaces lines in a template file (template_grass_array.sh) and copies the file in /scratch/walch/grassgis/scripts/executables."
echo "You need to specify/have:"
echo "- a template file 'template_grass_array.sh' in the directory where you are executing the script"
echo "- a text file to evaluate the number of jobs and a grass executable (if necessary)"
echo "By invoking this script (bash create_grass_array.sh) you will create a workspace in your /scripts/executables that is a frame for the further editing."
echo "Go to the complete the executable in /scratch and submit your executable(s) with the command: sbatch <name>.sh"
echo "Parallel and fast submission of tasks testing different values of parameters in input is automatically done using the slurm job-array feature."
echo "Author: alina.walch@epfl.ch"
echo "Last update: 20/09/2018 "
echo "####################################################"
echo ""
exit 0
fi
## STATIC inputs #####################################
TEMPLATE_FILE="template_grass_array.sh"
TARGET_DIR="/scratch/walch/grassgis/scripts/executables"
GRASS_DBASE="/scratch/walch/grassgis"
######################################################
## CUSTOMIZABLE inputs ###############################
######################################################
## == Sbatch inputs
MAIL="alina.walch@epfl.ch"
TASKS="1"
CORES="1" ## number of CPUs per tasks
NODES="1" ## number of nodes
TIME="12:00:00" #set the maximum time in the format XX:YY:ZZ
MEM="32G" ## memory requirment for the node
JOB_NAME=proj_SIS
LOCATION=CH_LV03
GRASS_EXECUTABLE=/home/walch/code/energy-potential/grass_scripts/project_GHI.sh ## comment out (no value) if not needed
CONTROL_FILE= #/scratch/walch/grassgis/files/SOLPOS_rnd_regions.txt ## comment out (no value) if not needed
NUM_BATCHES= #16 # alternatively, give number of batches (if no control file is used) - omment out (no value) if not needed
####################################################
####################################################
WORKSPACE=$TARGET_DIR\/workspace_$JOB_NAME
echo "[MSG] Creating workspace for the dataset $DATA"
echo ""
if [ ! -d $WORKSPACE ]
then
mkdir $WORKSPACE
mkdir $WORKSPACE\/output
fi
## == Copying the executable in the folder
REPLACEMENT_FILE=$WORKSPACE\/exec_$JOB_NAME\.sh
cp $TEMPLATE_FILE $REPLACEMENT_FILE
echo "..."
## == Replacing the custom choice in a temporary file
sed -i "s/\_mem/$MEM/g" $REPLACEMENT_FILE
sed -i "s/\_time/$TIME/g" $REPLACEMENT_FILE
sed -i "s/\_tasks/$TASKS/g" $REPLACEMENT_FILE
sed -i "s/\_nodes/$NODES/g" $REPLACEMENT_FILE
sed -i "s/\_cores/$CORES/g" $REPLACEMENT_FILE
sed -i "s/\_mail/$MAIL/g" $REPLACEMENT_FILE
sed -i "s/\_job/$JOB_NAME/g" $REPLACEMENT_FILE
echo ".."
## == Replace grass executable (if given) and working directories
LOCATION_PATH=$GRASS_DBASE\/$LOCATION
sed -i "s+_grassPath+$LOCATION_PATH+g" $REPLACEMENT_FILE
sed -i "s+_workdir+$WORKSPACE+g" $REPLACEMENT_FILE
if [ "$GRASS_EXECUTABLE" != "" ]; then
cp $GRASS_EXECUTABLE $WORKSPACE\/.
GRASS_SCRIPT=`basename "$GRASS_EXECUTABLE"`
sed -i "s/\_grassScript/$GRASS_SCRIPT/g" $REPLACEMENT_FILE
chmod +x $WORKSPACE\/$GRASS_SCRIPT
else
STRING=" ## ADD NAME ##"
sed -i "s/\_grassScript/$STRING/g" $REPLACEMENT_FILE
fi
echo "."
## == Replace placeholders for control files and correct number of batches as appropriate
if [ "$CONTROL_FILE" != "" ]; then
# if a control file is given, use the control file
cp $CONTROL_FILE $WORKSPACE\/.
CONTROL_TXT=`basename "$CONTROL_FILE"`
sed -i "s/\_controlFile/$CONTROL_TXT/g" $REPLACEMENT_FILE
NUM_LINES=$(wc -l < $CONTROL_FILE ) ## replace with number if no control file is needed
sed -i "s/\_lines/$NUM_LINES/g" $REPLACEMENT_FILE
STRING="VARIABLE"
sed -i "s/\_var/$STRING/g" $REPLACEMENT_FILE
elif [ "$NUM_BATCHES" != "" ]; then
# if no control file is given, but the number of batches, set only the number of lines
sed -i "s/\_lines/$NUM_BATCHES/g" $REPLACEMENT_FILE
STRING="## "
sed -i "s/\_var/$STRING/g" $REPLACEMENT_FILE
else
# if no information is given, assume that there is only one task
STRING=1
sed -i "s/\_lines/$STRING/g" $REPLACEMENT_FILE
STRING="## "
sed -i "s/\_var/$STRING/g" $REPLACEMENT_FILE
fi
## == Terminating the script
echo "[DONE] The files and relative scripts for the submission on batch queues have been created inside "$WORKSPACE"/"
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