Pass 'prune' flag from scheduleScenarios.sh to runPlum.sh

data/shockProbabilities.csv

 ssp,protectionism,automation,diet,climate,cyber,financial
-SSP1,0.1,0.5,0.9,0.01,0.05,0.01
-SSP2,0.7,0.5,0.3,0.07,0.05,0.03
-SSP3,0.9,0.1,0.1,0.07,0.01,0.09
-SSP4,0.3,0.7,0.3,0.09,0.07,0.05
-SSP5,0.1,0.9,0.1,0.09,0.09,0.03
+SSP1,0,1,0,0,0,0
+SSP2,0,1,0,0,0,0
+SSP3,0,1,0,0,0,0
+SSP4,0,1,0,0,0,0
+SSP5,0,1,0,0,0,0

scripts/scheduleScenarios.sh

 #!/bin/sh
 
-while getopts ":t:b:" opt; do
+while getopts ":t:p:b:" opt; do
   case ${opt} in
     b )
       build=${OPTARG}
       ;;
+    p )
+      prune=${OPTARG}
+      ;;
     t )
       filename=${OPTARG}
       ;;
@@ -28,6 +31,11 @@ then
    exit -1
 fi
 
+if [ -z ${prune+x} ];
+then
+   prune="y"
+fi
+
 output_dir=/exports/csce/eddie/geos/groups/LURG/models/PLUM/output
 echo "Starting scenarios in $output_dir"
 
@@ -50,8 +58,8 @@ do
 
      jobName="$(echo $ensemble | sed 's,\.\/,,' | sed 's,\/,_,g')_$scenario"
 
-     echo "qsub -hold_jid calib -N $jobName /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh -s $ensemble/$scenario -b $build -r y -p y"
-     qsub -hold_jid calib -N $jobName /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh -s $ensemble/$scenario -b $build -r y -p y
+     echo "qsub -hold_jid calib -N $jobName /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh -s $ensemble/$scenario -b $build -r y -p $prune"
+     qsub -hold_jid calib -N $jobName /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/runPlum.sh -s $ensemble/$scenario -b $build -r y -p $prune
   fi
 done < $filename