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+
+
+* Run simulations
+  To run all the simulations, execute the following call:
+  #+NAME: runSim
+  #+CALL: runBW(lat=runLat(nbSens=runNbSensors(nbHop=runNbHop())))
+
+  #+RESULTS: runSim
+
+** Experiments
+   
+*** Sensors Position
+    #+NAME: runSensorsPos
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="SENSORSPOS"
+      for sensorsNumber in $(seq 5 2 15)
+      do
+          for positionSeed in $(seq 1 10)
+          do
+              run
+          done      
+      done
+    #+END_SRC
+
+*** Sensors Send Interval
+    #+NAME: runSendInterval
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="SENDINTERVAL"
+      for sensorsNumber in $(seq 5 2 15)
+      do
+          for sensorsSendInterval in $(seq 10 10 100)
+          do
+              run
+          done      
+      done
+    #+END_SRC
+
+*** Bandwidth
+    #+NAME: runBW
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="BW"
+      for sensorsNumber in $(seq 1 10)
+      do
+          for linksBandwidth in $(seq 10 20 100)
+          do
+              run
+          done      
+      done
+    #+END_SRC
+
+    #+RESULTS: runBW
+
+    #+RESULTS:
+
+*** Latency
+    #+NAME: runLat
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="LATENCY"
+      for sensorsNumber in $(seq 1 10)
+      do
+          for linksLatency in $(seq 1 1 10)
+          do
+              run
+          done      
+      done
+    #+END_SRC
+
+    #+RESULTS: runLat
+
+    #+RESULTS:
+    
+*** Number of sensors
+    #+NAME: runNbSensors
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="NBSENSORS"
+      for sensorsNumber in $(seq 1 15)
+      do
+          run
+      done      
+    #+END_SRC
+
+    #+RESULTS:
+
+*** Number of Hop
+    #+NAME: runNbHop
+    #+BEGIN_SRC bash :noweb yes :results output
+      <<singleRun>>
+      simKey="NBHOP"
+      for sensorsNumber in $(seq 1 10)
+      do
+          for nbHop in $(seq 1 10)
+          do
+              run
+          done
+      done
+    #+END_SRC
+
+    #+RESULTS: runNbHop
+
+
+** Single Run
+   
+   #+NAME: singleRun
+   #+BEGIN_SRC bash :eval never :noweb yes :results output
+     simulator="simulator/simulator"
+     parseEnergyScript="./parseEnergy.awk"
+     parseDelayScript="./parseDelay.awk"
+     logFolder="logs/"
+     export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${NS3_PATH}/build/lib
+
+     # Default Parameters
+     sensorsSendInterval=1 # DON'T GO BELOW 1 SECONDS !!!!!!! Simulator will stay stuck
+     sensorsPktSize=192 # 1 byte temperature (-128 à +128 °C) and 4Byte sensorsId
+     sensorsNumber=5
+     nbHop=10 # Cf paper AC/Yunbo
+     linksBandwidth=10000 # 10Ge links (to be coherent with energy values of ECOFEN/literature)
+     linksLatency=11
+     positionSeed=5
+     simKey="NOKEY"
+
+     run () {
+         # If another function want to handle simulation (tipically used on g5k)
+         type -t handleSim > /dev/null && { handleSim; return; }
+
+         local logFile="${logFolder}/${simKey}_${sensorsSendInterval}SSI_${sensorsPktSize}SPS_${sensorsNumber}SN_${nbHop}NH_${linksBandwidth}LB_${linksLatency}LL_${positionSeed}PS.org"
+         [ -f "$logFile" ] && return
+         local simCMD="$simulator --sensorsSendInterval=${sensorsSendInterval} --sensorsPktSize=${sensorsPktSize} --sensorsNumber=${sensorsNumber} --nbHop=${nbHop} --linksBandwidth=${linksBandwidth} --linksLatency=${linksLatency} --positionSeed=${positionSeed} 2>&1"
+         local log=$(bash -c "$simCMD")
+
+         # Compute some metrics
+         energyLog=$(echo "$log" | $parseEnergyScript)
+         avgDelay=$(echo "$log" | $parseDelayScript)
+         totalEnergy=$(echo "$energyLog" | awk 'BEGIN{power=0;FS=","}NR!=1{power+=$2}END{print(power)}')
+         sensorsEnergy=$(echo "$energyLog" |awk -F',' 'BEGIN{sumW=0}$1<0{sumW+=$2}END{print sumW}')
+         networkEnergy=$(echo "$energyLog" |awk -F',' 'BEGIN{sumN=0}$1>=0{sumN+=$2}END{print sumN}')
+         nbPacketCloud=$(echo "$log"|grep -c "CloudSwitch receive")
+         nbNodes=$(echo "$log"|awk '/Simulation used/{print($3)}')
+         ns3Version=$(echo "$log"|awk '/NS-3 Version/{print($3)}')
+
+         # Save logs
+         echo -e "#+TITLE: $(date) ns-3 (version ${ns3Version}) simulation\n" > $logFile
+         echo "* Environment Variables" >> $logFile
+         env >> $logFile
+         echo "* Full Command" >> $logFile
+         echo "$simCMD" >> $logFile
+         echo "* Output" >> $logFile
+         echo "$log" >> $logFile
+         echo "* Energy CSV (negative nodeId = WIFI, 0 = AP (Wireless+Wired), positive nodeId = ECOFEN" >> $logFile
+         echo "$energyLog" >> $logFile
+         echo "* Metrics" >> $logFile
+         echo "-METRICSLINE- sensorsSendInterval:${sensorsSendInterval} sensorsPktSize:${sensorsPktSize} sensorsNumber:${sensorsNumber} nbHop:${nbHop} linksBandwidth:${linksBandwidth} linksLatency:${linksLatency} totalEnergy:$totalEnergy nbPacketCloud:$nbPacketCloud nbNodes:$nbNodes avgDelay:${avgDelay} ns3Version:${ns3Version} simKey:${simKey} positionSeed:${positionSeed} sensorsEnergy:${sensorsEnergy} networkEnergy:${networkEnergy}" >> $logFile
+     }
+
+   #+END_SRC
+
+** Grid 5000
+*** Master Node Script
+    This code generate and distribute simulation argument to the slave worker nodes and
+    run start their simulations processes:
+    #+BEGIN_SRC sh :tangle ./g5k-root.sh :shebang "#!/bin/bash" :noweb yes
+      ##### Arguments #####
+      nHost=20 # At least 20 host x)
+      nProcesses=3 # Max number of parrallel simulations (don't go too high, your process will be killed (arround 8))
+      nHours=4 # Reservation duration
+      simArgsLoc=~/args/ # Don't change this path witouth changing it in workder scripts
+      finishedFile="$simArgsLoc/finished-microBenchmarks.txt"
+      logsFinalDst=~/logs/
+      #####################
+
+      # Check
+      [ "$1" == "subscribe" ] && subscribe=1 ||subscribe=0
+      [ "$1" == "deploy" ] && deploy=1 || deploy=0
+      [ "$1" == "-p" ] && progress=1 || progress=0
+
+      handleSim () {
+          [ -z "${argId}" ] && argId=1 || argId=$(( argId + 1 ))
+          outF="$simArgsLoc/${argId}.sh" # Args file based on host name (avoid conflict)
+
+          # Add Shebang
+          echo '#!/bin/bash' > $outF
+          echo "finishedFile=\"$finishedFile\"" >> $outF
+          echo "nProcesses=$nProcesses" >> $outF
+          echo "logsFinalDst=\"$logsFinalDst\"" >> $outF
+          # Save arguments
+          echo "sensorsSendInterval=${sensorsSendInterval}" >> $outF
+          echo "sensorsPktSize=${sensorsPktSize}" >> $outF
+          echo "nbHop=${nbHop}" >> $outF
+          echo "simKey=\"${simKey}\"" >> $outF
+          echo "sensorsNumber=${sensorsNumber}" >> $outF
+          echo "linksLatency=${linksLatency}" >> $outF
+          echo "sensorsNumber=${sensorsNumber}" >> $outF
+          echo "linksBandwidth=${linksBandwidth}" >> $outF
+          echo "positionSeed=${positionSeed}" >> $outF
+      }
+
+
+      # Start subscribe/deploy
+      if [ $subscribe -eq 1 ]
+      then
+          echo "Starting oarsub..."
+          oarsub -l host=$nHost,walltime=$nHours 'sleep "10d"' # Start reservation
+          echo "Please join your node manually when your reservation is ready by using oarsub -C <job-id>"
+          exit 0
+      elif [ $deploy -eq 1 ]
+      then
+          echo "Starting deployment..."
+
+          ##### Usefull Variables #####
+          wai=$(dirname "$(readlink -f $0)") # Where Am I ?
+          hostList=($(cat $OAR_NODE_FILE | uniq))
+          #############################
+
+          # Initialize logsFinalDst
+          mkdir -p $logsFinalDst
+          rm -rf $logsFinalDst/* # Clean log dst just in case (it is dangerous but avoid conflict)
+          mkdir -p $simArgsLoc
+          rm -rf $simArgsLoc/* # Clean old args
+
+          # Add your simulation code block here
+          <<runNbSensors>>
+          <<runSendInterval>>
+          <<runSensorsPos>>
+
+          # Distribute argument according to subsribed nodes
+          cd $simArgsLoc
+          curHostId=0
+          for file in $(find ./ -type f)
+          do
+              [ $curHostId -eq $nHost ] && curHostId=0  
+              mv -- ${file} ${hostList[$curHostId]}-$(basename ${file})
+              curHostId=$(( curHostId + 1 ))
+          done
+          cd -
+
+
+          # Run simulations
+          echo "Host who finished their work:" > $finishedFile
+          for host in ${hostList[@]}
+          do
+              echo "Start simulations on node $host"
+              oarsh lguegan@$host bash g5k-worker.sh &
+          done
+
+          exit 0
+      elif [ $progress -eq 1 ]
+      then
+          alreadyFinished=$(cat $finishedFile| tail -n +2| wc -l)
+          percent=$(echo $alreadyFinished $nHost| awk '{print $1/$2*100}')
+          echo "Progression: " $alreadyFinished/$nHost "(${percent}%)"
+      else
+          echo "Invalid arguments, make sure you know what you are doing !"
+          exit 1
+      fi
+    #+END_SRC
+*** Worker Node Script
+    Almost like the [[microBenchmarksSingle][single run script]] but with additionnal code to handle g5k simulation platform (arguments,logs etc..).
+    #+BEGIN_SRC sh :tangle ./g5k-worker.sh :shebang "#!/bin/bash" :noweb yes
+      export NS3_PATH=~/.bin/ns-3/ns-3.29/
+      g5kLogFolder="/tmp/logs/"
+      mkdir -p $g5kLogFolder # Create log folder just in case
+      rm -rf $g5kLogFolder/* # Clean previous logs just in case
+
+      hostname=$(hostname)
+
+      # Run simulations with sourced arguments :D
+      simArgsLoc=~/args/ # Don't change this path without changing it in root scripts
+
+      argsId=0
+      argsFile="$simArgsLoc/${hostname}-args-${argsId}.sh" # Arguments generated by Root Node
+      curNProcesses=0 # Start with no processes
+      for argsFile in $(find $simArgsLoc -type f -name "$hostname*")
+      do
+          <<singleRun>>
+          logFolder=$g5kLogFolder # Don't forget override default g5kLogFolder
+          source  $argsFile # Fetch argument
+          run & # Run async 
+          ((curNProcesses+=1)) # Increase by 2           
+          [ $curNProcesses -ge $nProcesses ] && { curNProcesses=0; wait; }
+      done
+      wait # Wait until the end of all simulations
+
+      cp -r $g5kLogFolder/* "$logsFinalDst" # Fetch log from tmp into nfs
+      echo $(hostname) >> $finishedFile # Just say I finished
+    #+END_SRC
+
+* Logs Analysis
+  To Generate all the plots, please execute the following line:
+  #+NAME: runAnalysis
+  #+CALL: plotToPDF(plots=genAllPlots(data=logToCSV()))
+
+  #+RESULTS: runAnalysis
+
+** R Scripts
+*** Generate all plots script
+    Available variables:
+    |---------------------|
+    | Name                |
+    |---------------------|
+    | sensorsSendInterval |
+    | sensorsPktSize      |
+    | sensorsNumber       |
+    | nbHop               |
+    | linksBandwidth      |
+    | linksLatency        |
+    | totalEnergy         |
+    | nbPacketCloud       |
+    | nbNodes             |
+    | avgDelay            |
+    | simKey              |
+    |---------------------|
+
+    #+NAME: genAllPlots
+    #+BEGIN_SRC R :noweb yes :results output
+      <<RUtils>>
+#      easyPlotGroup("linksLatency","totalEnergy", "LATENCY","sensorsNumber")
+#      easyPlotGroup("linksBandwidth","totalEnergy", "BW","sensorsNumber")
+      easyPlot("sensorsNumber","totalEnergy", "NBSENSORS")
+      easyPlotGroup("positionSeed", "totalEnergy","SENSORSPOS","sensorsNumber")
+      easyPlotGroup("positionSeed", "avgDelay","SENSORSPOS","sensorsNumber")
+      easyPlotGroup("sensorsSendInterval","sensorsEnergy","SENDINTERVAL","sensorsNumber")
+      easyPlotGroup("sensorsSendInterval","networkEnergy","SENDINTERVAL","sensorsNumber")
+
+    #+END_SRC
+
+    #+RESULTS: genAllPlots
+
+*** R Utils
+    RUtils is intended to load logs (data.csv) and providing
+    simple plot function for them.
+
+    #+NAME: RUtils
+    #+BEGIN_SRC R :eval never
+      library("tidyverse")
+
+      # Fell free to update the following
+      labels=c(nbNodes="Number of nodes",sensorsNumber="Number of sensors",totalEnergy="Total Energy (J)",
+        nbHop="Number of hop (AP to Cloud)", linksBandwidth="Links Bandwidth (Mbps)", avgDelay="Average Application Delay (s)",
+        linksLatency="Links Latency (ms)", sensorsSendInterval="Sensors Send Interval (s)", positionSeed="Position Seed",
+        sensorsEnergy="Sensors Wifi Energy Consumption (J)", networkEnergy="Network Energy Consumption (J)")
+
+      # Load Data
+      data=read_csv("logs/data.csv")
+
+      # Get label according to varName
+      getLabel=function(varName){
+        if(is.na(labels[varName])){
+          return(varName)
+        }
+        return(labels[varName])
+      }
+
+      easyPlot=function(X,Y,KEY){
+        curData=data%>%filter(simKey==KEY)
+        stopifnot(NROW(curData)>0)
+        ggplot(curData,aes_string(x=X,y=Y))+geom_point()+geom_line()+xlab(getLabel(X))+ylab(getLabel(Y))
+        ggsave(paste0("plots/",KEY,"-",X,"_",Y,".png"))
+      }
+
+      easyPlotGroup=function(X,Y,KEY,GRP){
+        curData=data%>%filter(simKey==KEY) %>% mutate(!!GRP:=as.character(UQ(rlang::sym(GRP)))) # %>%mutate(sensorsNumber=as.character(sensorsNumber))
+        stopifnot(NROW(curData)>0)
+        ggplot(curData,aes_string(x=X,y=Y,color=GRP,group=GRP))+geom_point()+geom_line()+xlab(getLabel(X))+ylab(getLabel(Y)) + labs(color = getLabel(GRP))
+        ggsave(paste0("plots/",KEY,"-",X,"_",Y,".png"))
+      }
+    #+END_SRC
+
+** Plots -> PDF
+   Merge all plots in plots/ folder into a pdf file.
+   #+NAME: plotToPDF
+   #+BEGIN_SRC bash :results output :noweb yes
+     orgFile="plots/plots.org"
+     <<singleRun>> # To get all default arguments
+
+     # Write helper function
+     function write {
+         echo "$1" >> $orgFile
+     }
+
+     echo "#+TITLE: Analysis" > $orgFile
+     write "#+LATEX_HEADER: \usepackage{fullpage}"
+     write "#+OPTIONS: toc:nil"
+     # Default arguments
+     write '\begin{center}'
+     write '\begin{tabular}{lr}'
+     write 'Parameters & Values\\'
+     write '\hline'
+     write "sensorsPktSize & ${sensorsPktSize} bytes\\\\"
+     write "sensorsSendInterval & ${sensorsSendInterval}s\\\\"
+     write "sensorsNumber & ${sensorsNumber}\\\\"
+     write "nbHop & ${nbHop}\\\\"
+     write "linksBandwidth & ${linksBandwidth}Mbps\\\\"
+     write "linksLatency & ${linksLatency}ms\\\\"
+     write '\end{tabular}'
+     write '\newline'
+     write '\end{center}'
+
+     for plot in $(find plots/ -type f -name "*.png")
+     do
+         write "\includegraphics[width=0.5\linewidth]{$(basename ${plot})}"
+     done
+
+     # Export to pdf
+     emacs $orgFile --batch -f org-latex-export-to-pdf --kill  
+   #+END_SRC
+
+   #+RESULTS:
+
+** Log -> CSV
+   logToCSV extract usefull data from logs and put them into logs/data.csv.
+
+   #+NAME: logToCSV
+   #+BEGIN_SRC bash :results none
+     csvOutput="logs/data.csv"
+
+     # First save csv header line
+     aLog=$(find logs/ -type f -name "*.org"|head -n 1)
+     metrics=$(cat $aLog|grep "\-METRICSLINE\-"|sed "s/-METRICSLINE-//g")
+     echo $metrics | awk '{for(i=1;i<=NF;i++){split($i,elem,":");printf(elem[1]);if(i<NF)printf(",");else{print("")}}}' > $csvOutput
+
+     # Second save all values
+     for logFile in $(find logs/ -type f -name "*.org")
+     do
+         metrics=$(cat $logFile|grep "\-METRICSLINE\-"|sed "s/-METRICSLINE-//g")
+         echo $metrics | awk '{for(i=1;i<=NF;i++){split($i,elem,":");printf(elem[2]);if(i<NF)printf(",");else{print("")}}}' >> $csvOutput
+     done
+   #+END_SRC
+
+
+
+   
+   
+   
+** Custom Plots
+
+   #+NAME: ssiNet
+   #+BEGIN_SRC R :noweb yes :results graphics :file plots/sensorsSendInterval-net.png
+     <<RUtils>>
+
+     data%>%filter(simKey=="SENDINTERVAL",sensorsNumber==20) %>% ggplot(aes(x=sensorsSendInterval,y=networkEnergy))+xlab(getLabel("sensorsSendInterval"))+ylab(getLabel("networkEnergy"))+
+     geom_line()+labs(title="For 20 sensors")
+     ggsave("plots/sensorsSendInterval-net.png",dpi=80)
+   #+END_SRC
+
+   #+RESULTS:
+   [[file:plots/sensorsSendInterval-net.png]]
+
+   
+   #+NAME: ssiWifi
+   #+BEGIN_SRC R :noweb yes :results graphics :file plots/sensorsSendInterval-wifi.png
+     <<RUtils>>
+     data%>%filter(simKey=="SENDINTERVAL",sensorsNumber==20) %>% ggplot(aes(x=sensorsSendInterval,y=sensorsEnergy))+xlab(getLabel("sensorsSendInterval"))+ylab(getLabel("sensorsEnergy"))+
+     geom_line() +     geom_line()+labs(title="For 20 sensors")
+     ggsave("plots/sensorsSendInterval-wifi.png",dpi=80)
+   #+END_SRC
+
+   #+RESULTS: ssiWifi
+   [[file:plots/sensorsSendInterval-wifi.png]]
+
+   #+RESULTS:
+   [[file:plots/sensorsSendInterval.png]]
+
+
+
+
+
+
+    #+BEGIN_SRC R :results graphics  :noweb yes  :file plot-final.png :session *R*
+      <<RUtils>>
+      simTime=1800
+
+      # Network
+      data=read_csv("logs/data.csv")
+      data=data%>%filter(simKey=="NBSENSORS")
+      dataC5=data%>%filter(sensorsNumber==5)%>% mutate(energy=networkEnergy/simTime) %>%select(energy,sensorsNumber)
+      dataC10=data%>%filter(sensorsNumber==10)%>%mutate(energy=networkEnergy/simTime) %>%select(energy,sensorsNumber)
+      dataNet=rbind(dataC5,dataC10)%>%mutate(type="Network")
+
+      # Network
+      dataS5=data%>%filter(sensorsNumber==5)%>% mutate(energy=sensorsEnergy/simTime) %>%select(energy,sensorsNumber) 
+      dataS10=data%>%filter(sensorsNumber==10)%>%mutate(energy=sensorsEnergy/simTime) %>%select(energy,sensorsNumber) 
+      dataS=rbind(dataS5,dataS10)%>%mutate(type="Sensors")
+      
+      data=rbind(dataNet,dataS)%>%mutate(sensorsNumber=as.character(sensorsNumber))
+
+      ggplot(data)+geom_bar(aes(x=sensorsNumber,y=energy,fill=type),stat="identity")+xlab("Sensors Number")+ylab("Power Consumption (W)")+guides(fill=guide_legend(title="Part"))
+      ggsave("plot-final.png",dpi=80)
+
+    #+END_SRC
+
+    #+RESULTS:
+    [[file:plot-final.png]]
+