Added scripts for Costum runs where Slurm is not needed. Refactor of some Exec scripts.

Exec/CheckRun.sh

@@ -180,7 +180,8 @@ do
 
       #3 - Launch execution
       echo "Run$run lacks $diff repetitions"
-      echo "sbatch -N $node_qty $dir$execDir./singleRun.sh config$run.ini $run $diff"
+      use_extrae=0
+      sbatch -N $node_qty $dir$execDir./generalRun.sh $dir $config_file $use_extrae $run $diff
     fi
   else
     echo "File R${run}_Global.out does not exist -- Could it be it must still be executed?"

Exec/generalRun.sh

@@ -4,6 +4,8 @@
 #SBATCH --exclude=c02,c01,c00
 #SBATCH -p P1
 codeDir="/Codes/build"
+execDir="/Exec"
+ResultsDir="/Results"
 
 echo "START TEST"
 
@@ -20,36 +22,52 @@ then
   exit -1
 fi
 
+#READ PARAMETERS AND ENSURE CORRECTNESS
 dir=$1
 configFile=$2
 use_extrae=$3
 outFileIndex=$4
 qty=1
-if [ $# -ge 5 ]
+if [ $# -ge 6 ]
 then
   qty=$5
 fi
 
+nodelist=$SLURM_JOB_NODELIST
+nodes=$SLURM_JOB_NUM_NODES
+if [ -z "$nodelist" ];
+then
+  echo "Internal ERROR in generalRun.sh - Nodelist not provided"
+  exit -1
+fi
+if [ -z "$nodes" ];
+then
+  nodes=1
+fi
+
 aux=$(grep "\[resize0\]" -n $configFile | cut -d ":" -f1)
 read -r ini fin <<<$(echo $aux)
 diff=$(( fin - ini ))
 numP=$(head -$fin $configFile | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
 
-echo "Nodes=$SLURM_JOB_NODELIST"
+#EXECUTE RUN
+echo "Nodes=$nodelist"
 if [ $use_extrae -ne 1 ]
 then
   for ((i=0; i<qty; i++))
   do
-    mpirun -np $numP $dir$codeDir/a.out $configFile $outFileIndex $SLURM_JOB_NODELIST $SLURM_JOB_NUM_NODES 
+    mpirun -np $numP $dir$codeDir/a.out $configFile $outFileIndex $nodelist $nodes 
   done
 else
+  cp $dir$execDir/Extrae/extrae.xml .
+  cp $dir$execDir/Extrae/trace.sh .
+  cp $dir$execDir/Extrae/trace_worker.sh .
   for ((i=0; i<qty; i++))
   do
-    srun -n$numP --mpi=pmi2 ./trace.sh $dir$codeDir/a.out $configFile $outFileIndex $SLURM_JOB_NODELIST $SLURM_JOB_NUM_NODES
+    srun -n$numP --mpi=pmi2 ./trace.sh $dir$codeDir/a.out $configFile $outFileIndex $nodelist $nodes
   done
 fi
 
-
 echo "END TEST"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
 sed -i 's/Abort(-100)/shrink cleaning/g' slurm-$SLURM_JOB_ID.out

Exec/generalRunCostum.sh

+#!/bin/bash
+#This script should only be called by others scripts, do not call it directly
+codeDir="/Codes/build"
+
+echo "START TEST"
+
+#$1 == baseDir
+#$2 == configFile
+#$3 == use_extrae
+#$4 == outFileIndex
+#$5 == qty
+
+echo $@
+if [ $# -lt 3 ]
+then
+  echo "Internal ERROR generalRun.sh - Not enough arguments were given"
+  exit -1
+fi
+
+#READ PARAMETERS AND ENSURE CORRECTNESS
+dir=$1
+configFile=$2
+use_extrae=0
+outFileIndex=0
+qty=1
+
+if [ $# -ge 4 ]
+then
+  use_extrae=$3
+fi
+
+if [ $# -ge 5 ]
+then
+  outFileIndex=$4
+fi
+
+if [ $# -ge 6 ]
+then
+  qty=$5
+fi
+
+nodelist=$SLURM_JOB_NODELIST
+nodes=$SLURM_JOB_NUM_NODES
+if [ -z "$nodelist" ];
+then
+  nodelist="localhost"
+fi
+if [ -z "$nodes" ];
+then
+  nodes=1
+fi
+
+aux=$(grep "\[resize0\]" -n $configFile | cut -d ":" -f1)
+read -r ini fin <<<$(echo $aux)
+diff=$(( fin - ini ))
+numP=$(head -$fin $configFile | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
+
+#EXECUTE RUN
+echo "Nodes=$nodelist"
+if [ $use_extrae -ne 1 ]
+then
+  for ((i=0; i<qty; i++))
+  do
+    mpirun -np $numP $dir$codeDir/a.out $configFile $outFileIndex $nodelist $nodes 
+  done
+else
+  cp $dir$execDir/Extrae/extrae.xml .
+  cp $dir$execDir/Extrae/trace.sh .
+  cp $dir$execDir/Extrae/trace_worker.sh .
+  for ((i=0; i<qty; i++))
+  do
+    mpirun -np $numP ./trace.sh $dir$codeDir/a.out $configFile $outFileIndex $nodelist $nodes 
+  done
+fi
+
+echo "END TEST"

Exec/runTrace.sh

-dir="/home/martini/malleability_benchmark"
-partition="P1"
-exclude="c00,c01,c02"
-procs=(2 10 20 40 80 120 160)
-cores=20
-
-
-#====== Do not modify these values =======
-
-codeDir="/Codes/build"
-execDir="/Exec"
-ResultsDir="/Results"
-use_extrae=1
-
-#Extrae config
-qty=1
-outFileIndex=$2
-
-if [ $# -ge 1 ]
-then
-  qty=$1
-fi
-
-for proc in "${procs[@]}"
-do
-  echo "------------------------------------------run np=$proc"
-
-  node_qty=$(($proc / $cores))
-  if [ $node_qty -eq 0 ]
-  then
-    node_qty=1
-  fi
-
-  config_file="test$proc"".ini"
-  upper_dir="Proc$proc"
-  mkdir $upper_dir
-  cd $upper_dir
-  for ((i=0; i<qty; i++))
-  do
-    # Move data to new directory
-    lower_dir="Run$i"
-    mkdir $lower_dir
-    cd $lower_dir
-    cp $dir$execDir/Extrae/extrae.xml .
-    cp $dir$execDir/Extrae/trace.sh .
-    cp ../../$config_file .
-
-    #Execute test
-    sbatch -p $partition --exclude=$exclude -N $node_qty $dir$execDir/generalRun.sh $dir $config_file $use_extrae $outFileIndex
-    cd ..
-  done
-  cd ..
-
-done
-echo "End"

Exec/singleRun.sh

 #!/bin/bash
 
-#SBATCH --exclude=c02,c01,c00
-#SBATCH -p P1
-
 dir="/home/martini/malleability_benchmark"
-codeDir="/Codes/build"
+partition="P1"
+exclude="c00,c01,c02"
+cores=20
+
+# Executes a given configuration file with the aid of
+# the RMS Slurm.
+# Parameter 1: Configuration file name for the emulation.
+# Parameter 2(Optional): Index to use for the output files. Must be a positive integer.
+# Parameter 3(Optional): Number of repetitions to perform. Must be a positive integer.
+# Parameter 4(Optional): Use Extrae(1) or not(0).
+# Parameter 5(Optional): Path where the output files should be saved. 
+#====== Do not modify these values =======
 
-nodelist=$SLURM_JOB_NODELIST
-nodes=$SLURM_JOB_NUM_NODES
+codeDir="/Codes/build"
+execDir="/Exec"
+ResultsDir="/Results"
 
-if [ $# -lt 1 ]
+if [ $# -lt 2 ]
 then
   echo "Not enough arguments. Usage:"
-  echo "singleRun.sh config.ini [outFileIndex] [Qty] [Output path]"
+  echo "bash singleRun.sh config.ini [outFileIndex] [Qty] [Use extrae] [Output path]"
   exit 1
 fi
 
-echo "START TEST"
-
 #$1 == configFile
 #$2 == outFileIndex
 #$3 == Qty of repetitions
-#$4 == Output path
+#$4 == Use extrae NO(0) YES(1)
+#$5 == Output path
 
-configFile=$1
-outFileIndex=$2
+config_file=$1
+outFileIndex=0
 qty=1
+use_extrae=0
 
 if [ $# -gt 2 ]
+then
+  outFileIndex=$2
+fi
+if [ $# -gt 3 ]
 then
   qty=$3
-  if [ $# -gt 3 ]
-  then
-    output=$4
-  fi
+fi
+if [ $# -gt 4 ]
+then
+  use_extrae=$4
+fi
+if [ $# -gt 5 ]
+then
+  output=$5
 fi
 
-aux=$(grep "\[resize0\]" -n $configFile | cut -d ":" -f1)
-read -r ini fin <<<$(echo $aux)
-diff=$(( fin - ini ))
-numP=$(head -$fin $configFile | tail -$diff | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
-
-echo "Nodes=$SLURM_JOB_NODELIST"
-for ((i=0; i<qty; i++))
+#1 - Obtain maximum number of processes for the run
+max_numP=-1
+total_groups=$(grep Total_Resizes config2.ini | cut -d '=' -f2)
+for ((j=0; j<total_groups; j++)); 
 do
-  echo "Iter $i -- numP=$numP"
-  mpirun -np $numP $dir$codeDir/a.out $configFile $outFileIndex $nodelist $nodes 
+  resize_info=$(grep "\[resize$j\]" -n $config_file | cut -d ":" -f1)
+  first_line=$(echo $resize_info | cut -d " " -f1)
+  last_line=$(echo $resize_info | cut -d " " -f2)
+  range_lines=$(( last_line - first_line ))
+  numP=$(head -$last_line $config_file | tail -$range_lines | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
+  if [ "$numP" -gt "$max_numP" ];
+  then
+    max_numP=$numP
+  fi
 done
 
-echo "END TEST"
-sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
-sed -i 's/Abort(-100)/shrink cleaning/g' slurm-$SLURM_JOB_ID.out
+#2 - Obtain needed nodes for the number of processes
+node_qty=$(($max_numP / $cores))
+if [ "$node_qty" -eq "0" ];
+then
+  node_qty=1
+fi
 
-if [ $# -gt 3 ]
+#3 - Run with the expected amount of nodes
+sbatch -p $partition --exclude=$exclude -N $node_qty $dir$execDir/generalRun.sh $dir $config_file $use_extrae $outFileIndex $qty
+
+if ! [ -z "$output" ]
 then
+  mkdir -p $output
   echo "Moving data to $output\nMoved files:"
   ls R${outFileIndex}_G*
   mv R${outFileIndex}_G* $output
+  if [ "$use_extrae" -eq 1 ]
+  then
+    mv a.out.* $output
+    mv TRACE* $output
+    mv set-0/ $output
+  fi
 fi

Exec/singleRunCostum.sh

+#!/bin/bash
+
+dir="/home/martini/malleability_benchmark"
+
+# Executes a given configuration file
+# Parameter 1: Configuration file name for the emulation.
+# Parameter 2(Optional): Index to use for the output files. Must be a positive integer.
+# Parameter 3(Optional): Number of repetitions to perform. Must be a positive integer.
+# Parameter 4(Optional): Use Extrae(1) or not(0).
+# Parameter 5(Optional): Path where the output files should be saved. 
+#====== Do not modify these values =======
+
+codeDir="/Codes/build"
+execDir="/Exec"
+ResultsDir="/Results"
+
+if [ $# -lt 2 ]
+then
+  echo "Not enough arguments. Usage:"
+  echo "singleRunCostum.sh config.ini [outFileIndex] [Qty] [Use Extrae] [Output path]"
+  exit 1
+fi
+
+echo "START TEST"
+
+#$1 == configFile
+#$2 == outFileIndex
+#$3 == Qty of repetitions
+#$4 == Use extrae NO(0) YES(1)
+#$5 == Output path
+
+config_file=$1
+outFileIndex=0
+qty=1
+use_extrae=0
+
+if [ $# -gt 2 ]
+then
+  outFileIndex=$2
+fi
+if [ $# -gt 3 ]
+then
+  qty=$3
+fi
+if [ $# -gt 4 ]
+then
+  use_extrae=$4
+fi
+if [ $# -gt 5 ]
+then
+  output=$5
+fi
+
+bash $dir$execDir/generalRunCostum.sh $dir $config_file $use_extrae $outFileIndex $qty
+
+if ! [ -z "$output" ]
+then
+  mkdir -p $output
+  echo "Moving data to $output\nMoved files:"
+  ls R${outFileIndex}_G*
+  mv R${outFileIndex}_G* $output
+  if [ "$use_extrae" -eq 1 ]
+  then
+    mv a.out.* $output
+    mv TRACE* $output
+    mv set-0/ $output
+  fi
+fi