Added Exec scripts for performing Extrae Runs

Exec/extrae.xml

+<?xml version='1.0'?>
+
+<trace enabled="yes"
+ home="/home/martini/extrae-mpich-3.4.1-noucx"
+ initial-mode="detail"
+ type="paraver"
+>
+
+  <mpi enabled="yes">
+    <counters enabled="yes" />
+    <comm-calls enabled="yes" />
+  </mpi>
+
+  <openmp enabled="no" ompt="no">
+    <locks enabled="no" />
+    <taskloop enabled="no" />
+    <counters enabled="yes" />
+  </openmp>
+
+  <pthread enabled="no">
+    <locks enabled="no" />
+    <counters enabled="yes" />
+  </pthread>
+
+  <callers enabled="yes">
+    <mpi enabled="yes">1-3</mpi>
+    <sampling enabled="no">1-5</sampling>
+    <dynamic-memory enabled="no">1-3</dynamic-memory>
+    <input-output enabled="no">1-3</input-output>
+    <syscall enabled="no">1-3</syscall>
+  </callers>
+
+  <user-functions enabled="no" list="/home/bsc41/bsc41273/user-functions.dat" exclude-automatic-functions="no">
+    <counters enabled="yes" />
+  </user-functions>
+
+  <counters enabled="yes">
+    <cpu enabled="yes" starting-set-distribution="1">
+      <set enabled="yes" domain="all" changeat-time="0">
+        PAPI_TOT_INS,PAPI_TOT_CYC
+      </set>
+    </cpu>
+    <network enabled="no" />
+    <resource-usage enabled="no" />
+    <memory-usage enabled="no" />
+  </counters>
+
+
+  <storage enabled="no">
+    <trace-prefix enabled="yes">TRACE</trace-prefix>
+    <size enabled="no">5</size>
+    <temporal-directory enabled="yes">/scratch</temporal-directory>
+    <final-directory enabled="yes">/gpfs/scratch/bsc41/bsc41273</final-directory>
+  </storage>
+
+  <buffer enabled="yes">
+    <size enabled="yes">5000000</size>
+    <circular enabled="no" />
+  </buffer>
+
+  <trace-control enabled="no">
+    <file enabled="no" frequency="5M">/gpfs/scratch/bsc41/bsc41273/control</file>
+    <global-ops enabled="no"></global-ops>
+  </trace-control>
+
+  <others enabled="yes">
+    <minimum-time enabled="no">10M</minimum-time>
+    <finalize-on-signal enabled="yes" 
+      SIGUSR1="no" SIGUSR2="no" SIGINT="yes"
+      SIGQUIT="yes" SIGTERM="yes" SIGXCPU="yes"
+      SIGFPE="yes" SIGSEGV="yes" SIGABRT="yes"
+    />
+    <flush-sampling-buffer-at-instrumentation-point enabled="yes" />
+  </others>
+
+  <bursts enabled="no">
+    <threshold enabled="yes">500u</threshold>
+    <mpi-statistics enabled="yes" />
+  </bursts>
+
+  <sampling enabled="no" type="default" period="50m" variability="10m" />
+
+  <dynamic-memory enabled="no">
+    <alloc enabled="yes" threshold="32768" />
+    <free  enabled="yes" />
+  </dynamic-memory>
+
+  <pebs-sampling enabled="no">
+    <loads enabled="no" frequency="100" minimum-latency="10" />
+    <stores enabled="no" frequency="50">
+    <offcore-l3-misses enabled="no" /> <!-- Read together with stores samples. -->
+    </stores>
+    <load-l3-misses enabled="no" frequency="25" />
+  </pebs-sampling>
+
+  <input-output enabled="no" internals="no"/>
+
+  <syscall enabled="no" />
+
+  <merge enabled="yes" 
+    synchronization="default"
+    tree-fan-out="16"
+    max-memory="512"
+    joint-states="yes"
+    keep-mpits="yes"
+    translate-addresses="yes"
+    sort-addresses="yes"
+    translate-data-addresses="yes"
+    overwrite="yes"
+  />
+
+</trace>

Exec/generalRun.sh

+#!/bin/bash
+#This script should only be called by others scripts, do not call it directly
+
+#SBATCH --exclude=c02,c01,c00
+#SBATCH -p P1
+codeDir="/Codes/build"
+
+echo "START TEST"
+
+#$1 == baseDir
+#$2 == configFile
+#$3 == use_extrae
+#$4 == outFileIndex
+
+echo $@
+if [ $# -lt 3 ]
+then
+  echo "Internal ERROR generalRun.sh - Not enough arguments were given"
+  exit -1
+fi
+
+dir=$1
+configFile=$2
+use_extrae=$3
+outFileIndex=$4
+
+aux=$(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"
+if [ $use_extrae -ne 1 ]
+then
+  mpirun -np $numP $dir$codeDir/a.out $configFile $outFileIndex $SLURM_JOB_NODELIST $SLURM_JOB_NUM_NODES 
+else
+  # EXTRAE Configuration
+  export EXTRAE_CONFIG_FILE=./extrae.xml
+  export LD_PRELOAD=${EXTRAE_HOME}/lib/libmpitrace.so
+  srun -n$numP --mpi=pmi2 $dir$codeDir/a.out $configFile $outFileIndex $SLURM_JOB_NODELIST $SLURM_JOB_NUM_NODES
+fi
+
+
+echo "END TEST"
+sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out

Exec/runTrace.sh

+dir="/home/martini/malleability_benchmark"
+#procs=(2 10 20 40 80 120 160)
+procs=(2)
+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.xml .
+    cp ../../$config_file .
+
+    #pwd
+    sbatch -p P1 -N $node_qty $dir$execDir/generalRun.sh $dir $config_file $use_extrae $outFileIndex
+    cd ..
+  done
+  cd ..
+
+done
+echo "End"