Updated Exec files to consider the new env variables in the configuration when executing

Exec/BashScripts/createInitialNodelist.sh

 #!/bin/bash
 
-# Runs in a given current directory all .ini files
+# Gets the first nodelist that will be used during the emulation
 # Parameter 1(Optional) - Amount of executions per file. Must be a positive number
 #====== Do not modify these values =======
 
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
-
 numP=$1
 cores=$2
 nodelist=$3

Exec/BashScripts/getMaxNodesNeeded.sh

@@ -2,31 +2,27 @@
 
 # Obtains for a given configuration file how many nodes will be needed
 # Parameter 1 - Configuration file name for the emulation.
-# Parameter 2 - Base directory of the malleability benchmark
-# Parameter 3 - Number of cores in the machines. The machines must be homogenous. Must be a positive number.
+# Parameter 2 - Number of cores in the machines. The machines must be homogenous. Must be a positive number.
 #====== Do not modify these values =======
 
-codeDir="/Codes/build"
 execDir="/Exec"
-ResultsDir="/Results"
 
-if [ "$#" -lt "3" ]
+if [ "$#" -lt "2" ]
 then
   echo "Not enough arguments"
-  echo "Usage -> bash getMaxNodesNeeded.sh Configuration.ini BaseDirectory NumCores"
+  echo "Usage -> bash getMaxNodesNeeded.sh Configuration.ini NumCores"
   exit -1
 fi
 
 config_file=$1
-dir=$2
-cores=$3
+cores=$2
 
 max_numP=-1
 total_resizes=$(grep Total_Resizes $config_file | cut -d '=' -f2)
 total_groups=$(($total_resizes + 1))
 for ((j=0; j<total_groups; j++));
 do
-  numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $config_file $j)
+  numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $config_file $j)
   if [ "$numP" -gt "$max_numP" ];
   then
     max_numP=$numP

Exec/BashScripts/getNumPNeeded.sh

@@ -3,11 +3,6 @@
 # Runs in a given current directory all .ini files
 # Parameter 1(Optional) - Amount of executions per file. Must be a positive number
 #====== Do not modify these values =======
-
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
-
 config_file=$1
 group_index=$2
 

Exec/CheckRun.sh

@@ -19,10 +19,7 @@ partition="P1"
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/../Codes/build/config.txt
-codeDir="/Codes/"
-execDir="/Exec/"
-ResultsDir="/Results/"
-cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
+cores=$(bash $PROTEO_HOME$execDir/BashScripts/getCores.sh $partition)
 
 if [ "$#" -lt "6" ]
 then
@@ -195,10 +192,10 @@ do
 
     #2 - Obtain number of nodes needed
     config_file="$common_name$run.ini"
-    node_qty=$(bash $dir$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $dir $cores)
+    node_qty=$(bash $PROTEO_HOME$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $cores)
 
     #3 - Launch execution
-    sbatch -p $partition -N $node_qty -t $limit_time $dir$execDir./generalRun.sh $dir $cores $config_file $use_extrae $run $diff
+    sbatch -p $partition -N $node_qty -t $limit_time $PROTEO_HOME$execDir./generalRun.sh $cores $config_file $use_extrae $run $diff
   fi
 done
 

Exec/Extrae/worker_extrae.sh

 #!/bin/bash
 scriptDir="$(dirname "$0")"
 source $scriptDir/../../Codes/build/config.txt
-codeDir="/Codes/build"
 
 export EXTRAE_CONFIG_FILE=extrae.xml
 export LD_PRELOAD=$EXTRAE_HOME/lib/libmpitrace.so
 
-$dir$codeDir/./a.out
+$PROTEO_BIN

Exec/Valgrind/worker_valgrind.sh

 #!/bin/bash
 scriptDir="$(dirname "$0")"
 source $scriptDir/../../Codes/build/config.txt
-codeDir="/Codes/build"
 
-valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --log-file=vg.tp.%p $dir$codeDir/./a.out
+valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --log-file=vg.tp.%p $PROTEO_BIN

Exec/generalRun.sh

@@ -5,44 +5,39 @@
 
 # !!!!This script should only be called by others scripts, do not call it directly!!!
 # Runs a given configuration file with the indicated parameters with the aid of the RMS Slurm.
-# Parameter 1 - Base directory of the malleability benchmark
-# Parameter 2 - Number of cores in a single machine
-# Parameter 3 - Configuration file name for the emulation.
-# Parameter 4 - Use Valgrind(1), Extrae(2) or nothing(0).
-# Parameter 5 - Index to use for the output files. Must be a positive integer.
-# Parameter 6 - Amount of executions per file. Must be a positive number.
+# Parameter 1 - Number of cores in a single machine
+# Parameter 2 - Configuration file name for the emulation.
+# Parameter 3 - Use Valgrind(1), Extrae(2) or nothing(0).
+# Parameter 4 - Index to use for the output files. Must be a positive integer.
+# Parameter 5 - Amount of executions per file. Must be a positive number.
 #====== Do not modify these values =======
 
-codeDir="/Codes/build"
 execDir="/Exec"
-ResultsDir="/Results"
 
 echo "START TEST"
 
-#$1 == baseDir
-#$2 == cores
-#$3 == configFile
-#$4 == use_external
-#$5 == outFileIndex
-#$6 == qty
+#$1 == cores
+#$2 == configFile
+#$3 == use_external
+#$4 == outFileIndex
+#$5 == qty
 
 echo $@
-if [ $# -lt 4 ]
+if [ $# -lt 3 ]
 then
   echo "Internal ERROR generalRun.sh - Not enough arguments were given"
   exit -1
 fi
 
 #READ PARAMETERS AND ENSURE CORRECTNESS
-dir=$1
-cores=$2
-configFile=$3
-use_external=$4
-outFileIndex=$5
+cores=$1
+configFile=$2
+use_external=$3
+outFileIndex=$4
 qty=1
-if [ $# -ge 5 ]
+if [ $# -ge 4 ]
 then
-  qty=$6
+  qty=$5
 fi
 
 nodelist=$SLURM_JOB_NODELIST
@@ -52,8 +47,8 @@ then
   exit -1
 fi
 
-numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
-initial_nodelist=$(bash $dir$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
+numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+initial_nodelist=$(bash $PROTEO_HOME$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
 
 #EXECUTE RUN
 echo "Nodes=$nodelist"
@@ -62,26 +57,26 @@ then
   for ((i=0; i<qty; i++))
   do
     echo "Run $i starts"
-    mpirun -hosts $initial_nodelist -np $numP $dir$codeDir/a.out $configFile $outFileIndex
+    mpirun -hosts $initial_nodelist -np $numP $PROTEO_BIN $configFile $outFileIndex
     echo "Run $i ends"
   done
 elif [ $use_external -eq 1 ] #VALGRIND
 then
-  cp $dir$execDir/Valgrind/worker_valgrind.sh .
+  cp $PROTEO_HOME$execDir/Valgrind/worker_valgrind.sh .
   for ((i=0; i<qty; i++))
   do
     echo "Run $i starts"
-    mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID.$i $dir$codeDir/a.out $configFile $outIndex 
+    mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID.$i $PROTEO_BIN $configFile $outIndex 
     echo "Run $i ends"
   done
 else #EXTRAE
-  cp $dir$execDir/Extrae/extrae.xml .
-  cp $dir$execDir/Extrae/trace.sh .
-  cp $dir$execDir/Extrae/worker_extrae.sh .
+  cp $PROTEO_HOME$execDir/Extrae/extrae.xml .
+  cp $PROTEO_HOME$execDir/Extrae/trace.sh .
+  cp $PROTEO_HOME$execDir/Extrae/worker_extrae.sh .
   for ((i=0; i<qty; i++))
   do
     #FIXME Extrae not tested keeping in mind the initial nodelist - Could have some errors
-    srun -n$numP --mpi=pmi2 ./trace.sh $dir$codeDir/a.out $configFile $outFileIndex
+    srun -n$numP --mpi=pmi2 ./trace.sh $PROTEO_BIN $configFile $outFileIndex
   done
 fi
 

Exec/generalRunCostum.sh

@@ -2,26 +2,22 @@
 
 # !!!!This script should only be called by others scripts, do not call it directly!!!
 # Runs a given configuration file with the indicated parameters.
-# Parameter 1 - Base directory of the malleability benchmark
-# Parameter 2 - Number of cores in a single machine
-# Parameter 3 - Configuration file name for the emulation.
-# Parameter 4 - Use Extrae(1) or not(0).
-# Parameter 5 - Index to use for the output files. Must be a positive integer.
-# Parameter 6 - Amount of executions per file. Must be a positive number.
+# Parameter 1 - Number of cores in a single machine
+# Parameter 2 - Configuration file name for the emulation.
+# Parameter 3 - Use Extrae(1) or not(0).
+# Parameter 4 - Index to use for the output files. Must be a positive integer.
+# Parameter 5 - Amount of executions per file. Must be a positive number.
 #====== Do not modify these values =======
 
-codeDir="/Codes/build"
 execDir="/Exec"
-ResultsDir="/Results"
 
 echo "START TEST"
 
-#$1 == baseDir
-#$2 == cores
-#$3 == configFile
-#$4 == use_external
-#$5 == outFileIndex
-#$6 == qty
+#$1 == cores
+#$2 == configFile
+#$3 == use_external
+#$4 == outFileIndex
+#$5 == qty
 
 echo $@
 if [ $# -lt 3 ]
@@ -31,36 +27,35 @@ then
 fi
 
 #READ PARAMETERS AND ENSURE CORRECTNESS
-dir=$1
-cores=$2
-configFile=$3
+cores=$1
+configFile=$2
 use_external=0
 outFileIndex=0
 qty=1
 
-if [ $# -ge 4 ]
+if [ $# -ge 3 ]
 then
-  use_external=$4
+  use_external=$3
 fi
 
-if [ $# -ge 5 ]
+if [ $# -ge 4 ]
 then
-  outFileIndex=$5
+  outFileIndex=$4
 fi
 
-if [ $# -ge 6 ]
+if [ $# -ge 5 ]
 then
-  qty=$6
+  qty=$5
 fi
 
-numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
 nodelist=$SLURM_JOB_NODELIST
 if [ -z "$nodelist" ];
 then
   nodelist="localhost"
   initial_nodelist="localhost"
 else
-  initial_nodelist=$(bash $dir$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
+  initial_nodelist=$(bash $PROTEO_HOME$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
 fi
 
 #EXECUTE RUN
@@ -70,25 +65,25 @@ then
   for ((i=0; i<qty; i++))
   do
     echo "Run $i starts"
-    mpirun -hosts $initial_nodelist -np $numP $dir$codeDir/a.out $configFile $outFileIndex
+    mpirun -hosts $initial_nodelist -np $numP $PROTEO_BIN $configFile $outFileIndex
     echo "Run $i ends"
   done
 elif [ $use_external -eq 1 ] #VALGRIND
 then
-  cp $dir$execDir/Valgrind/worker_valgrind.sh .
+  cp $PROTEO_HOME$execDir/Valgrind/worker_valgrind.sh .
   for ((i=0; i<qty; i++))
   do
     echo "Run $i starts"
-    mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID.$i $dir$codeDir/a.out $configFile $outIndex 
+    mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID.$i $PROTEO_BIN $configFile $outIndex 
     echo "Run $i ends"
   done
 else
-  cp $dir$execDir/Extrae/extrae.xml .
-  cp $dir$execDir/Extrae/trace.sh .
-  cp $dir$execDir/Extrae/worker_extrae.sh .
+  cp $PROTEO_HOME$execDir/Extrae/extrae.xml .
+  cp $PROTEO_HOME$execDir/Extrae/trace.sh .
+  cp $PROTEO_HOME$execDir/Extrae/worker_extrae.sh .
   for ((i=0; i<qty; i++))
   do
-    mpirun -hosts $initial_nodelist -np $numP ./trace.sh $dir$codeDir/a.out $configFile $outFileIndex 
+    mpirun -hosts $initial_nodelist -np $numP ./trace.sh $PROTEO_BIN $configFile $outFileIndex 
   done
 fi
 

Exec/multipleRuns.sh

@@ -8,14 +8,10 @@
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/../Codes/build/config.txt
-codeDir="/Codes"
-execDir="/Exec"
-ResultsDir="/Results"
 
 complex_file=$1
 output_name=$2
 
-python3 $dir$execDir/PythonCodes/read_multiple.py $complex_file $output_name
-
-echo "END TEST"
+python3 $PROTEO_HOME$execDir/PythonCodes/read_multiple.py $complex_file $output_name
 
+echo "END GENERATION"

Exec/runAll.sh

@@ -10,10 +10,7 @@ exclude="c00,c01,c02"
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/../Codes/build/config.txt
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
-cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
+cores=$(bash $PROTEO_HOME$execDir/BashScripts/getCores.sh $partition)
 use_extrae=0
 
 qty=1
@@ -33,7 +30,7 @@ internalIndex=$(echo $files | tr -cd ' ' | wc -c)
 index=$((0))
 for config_file in $files
 do
-  node_qty=$(bash $dir$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $dir $cores)
+  node_qty=$(bash $PROTEO_HOME$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $cores)
 
   outFileIndex=$(echo $config_file | sed s/[^0-9]//g)
   if [[ $outFileIndex ]]; then 
@@ -45,6 +42,6 @@ do
 
   #Execute test
   echo "Execute job $index with Nodes=$node_qty and config_file=$config_file"
-  sbatch -p $partition --exclude=$exclude -N $node_qty -t $limit_time $dir$execDir/generalRun.sh $dir $cores $config_file $use_extrae $index $qty
+  sbatch -p $partition --exclude=$exclude -N $node_qty -t $limit_time $PROTEO_HOME$execDir/generalRun.sh $cores $config_file $use_extrae $index $qty
 done
 echo "End"

Exec/singleRun.sh

@@ -15,10 +15,7 @@ exclude="c00,c01,c02"
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/../Codes/build/config.txt
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
-cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
+cores=$(bash $PROTEO_HOME$execDir/BashScripts/getCores.sh $partition)
 
 if [ $# -lt 1 ]
 then
@@ -62,9 +59,9 @@ then
 fi
 
 #Obtain amount of nodes neeeded
-node_qty=$(bash $dir$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $dir $cores)
+node_qty=$(bash $PROTEO_HOME$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $cores)
 #Run with the expected amount of nodes
-sbatch -p $partition --exclude=$exclude -N $node_qty -t $limit_time $dir$execDir/generalRun.sh $dir $cores $config_file $use_external $outFileIndex $qty
+sbatch -p $partition --exclude=$exclude -N $node_qty -t $limit_time $PROTEO_HOME$execDir/generalRun.sh $cores $config_file $use_external $outFileIndex $qty
 
 if ! [ -z "$output" ]
 then

Exec/singleRunCostum.sh

@@ -13,9 +13,6 @@ cores=20
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/../Codes/build/config.txt
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
 
 if [ $# -lt 1 ]
 then
@@ -52,7 +49,7 @@ then
   output=$5
 fi
 
-bash $dir$execDir/generalRunCostum.sh $dir $cores $config_file $use_external $outFileIndex $qty
+bash $PROTEO_HOME$execDir/generalRunCostum.sh $cores $config_file $use_external $outFileIndex $qty
 
 if ! [ -z "$output" ]
 then