Clean repo, update paper

1 files changed, 0 insertions, 466 deletions

diff --git a/ns3-simulations/simulate.org b/ns3-simulations/simulate.org
deleted file mode 100644
index c110e5f..0000000
--- a/ns3-simulations/simulate.org
+++ /dev/null
@@ -1,466 +0,0 @@
-
-
-
-* 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 5 20)
-      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 5 20)
-      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 10)
-      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}:${NS3_PATH}/build/lib
-
-     # Default Parameters
-     sensorsSendInterval=10 # DON'T GO BELOW 1 SECONDS !!!!!!! Simulator will stay stuck
-     sensorsPktSize=5 # 1 byte temperature (-128 à +128 °C) and 4Byte sensorsId
-     sensorsNumber=10
-     nbHop=10 # Cf paper AC/Yunbo
-     linksBandwidth=10
-     linksLatency=2
-     positionSeed=5
-     simKey="NOKEY"
-
-     run () {
-         # If another function want to handle simulation (tipically used on g5k)
-         type -t handleSim > /dev/null && { handleSim; return; }
-
-         local logFile="${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]]