./RunPlotMaker -config ./configs/MyFirstSystematic.config -MJScales 

Where in the config file you replace the MCMJ, DataElMJ and DataMuMJ files with their systematic versions.

A little about the plot.config file

The plot.Config file will look something like the following

VersionMC           20140515_LimitFile_v5.3
TagMJ               True
CDI_CALIB           ttbar_all
DataType            Data12
YearName            2012
#ScaleFitRegion      MJFit
ScaleFitRegion      2BTag
#ScaleFitRegion      MJFit2BTag
ScaleFitVar         met
#ScaleFitVar         mtw
#ScaleFitVar         lep1Pt
UseEOS              True
#OutTag              2BTagScales

Blind               True

#                   MergedLepton, Electron or Muon
LepFlavour          MergedLepton
SplitCharge         False

# Directory to store input plot outputs - could do to make this nicer to you don't need to input username
FitDirectory        /afs/cern.ch/work/p/pmullen/analysis/FitInputs/

#DataMETFile         
#DataMETMJFile       
DataElFile          AnalysisManager.data12_8TeV.OneLepton.Electron.Hists.root
DataElMJFile        AnalysisManager.data12_8TeV.OneLepton.Electron.Hists.MJ.SysMJShapeDo.root
DataMuFile          AnalysisManager.data12_8TeV.OneLepton.Muon.Hists.root
DataMuMJFile        AnalysisManager.data12_8TeV.OneLepton.Muon.Hists.MJ.root
MCFile              AnalysisManager.mc12_8TeV_p1328.OneLepton.Hists.root
MCMJFile            AnalysisManager.mc12_8TeV_p1328.OneLepton.Hists.MJ.root

LimitFileVersion    v5.3

If you want to look at the MJ template and its electroweak contamination you can make DataElFile and DataElMJFile be the MJ template, comment out the MCMJ file and make the MC file the MC MJ template.

 source scripts/tar_area.sh SomeName_v0.0 

This creates a directory of that name in ~/work. You then do

 source scripts/submit2012.sh 

. This file can be edited to decide which systematics to inclue. For none just set the systematic to Nominal. This will submit all the jobs to the batch and will return the output to your eos directory named something like /eos/atlas/user/p/pmullen/Hbb/Pub2014/histMaker/2012.

 ./RunPlotMaker -config ./configs/plot.config -MJScales 

 ./RunPlotMaker -config ./configs/plot.config -CheckForFiles 

to make sure all the required files are present.(Note: This will not check the files are of a reasonable size so if something went wrong but the file was returned as empty it will think nothing is wrong)

 ./RunPlotMaker -config ./configs/plot.config -MJScales 

to calculate the scale factory then run

 ./RunPlotMaker -config ./configs/plot.config -CheckForFiles 

Using RunPlotMaker

Making an Input File

To use RunPlotMaker to make an input file do the following.

Get a file named listMCFiles.lst that lists all the montecarlo background input files to RunHistMaker. This can usually be found on eos. (I got it from /eos/atlas/user/g/gfacini/Hbb/Pub2014/SFrame/2012/NTuple_20140119/listMCFiles.lst)

The run

 source scripts/tar_area.sh SomeName_v0.0 

 source scripts/setup2012.sh 

 ./RunPlotMaker -config ./configs/plot.config -MJScales 

 ./RunPlotMaker -config ./configs/plot.config -CheckForFiles 

Next we do

source scripts/tar_area.sh SomeName_v0.0_LimitFile
source scripts/submitInputFile.sh plot.config datestamp_SomeName_v0.0_LimitFile

This tars the files and sends them off to the batch to scale the plots using the calculated scale factors. (Note: You do not need configs/plot.config just plot.config as the bash script that untars the file on the batch will take care of prepending configs/)

When thi is done you can do

./RunPlotMaker -config ./config/plot.config -NominalLimitFile
./RunPlotMaker -config ./config/plot.config -LimitFile

Adding Extra Plots

Adding Extra Stacked Plots

Adding the Variable to The Output Tree

For the variable to be written to the TTree in the SFrame section of the code we must create an output variable. To do this first add a variable of the correct type to the Algorithms header file. Now go to the Algorithms source file and use DeclareVariable in the BeginInputData() function to declare a branch in the output tree. Make sure to also clear() the variable in the ResetNtupleVars() function. You can now fill this variable in the fillNTuple() function probably using push_back.

As an example lets say we want to output the jet_WIDTH variable from the previous section. We would first add std::vector pauls_jet_WIDTH; in the header file. In the source file we would go to the BeginInputData() function and add DeclareVariable(pauls_jet_WIDTH, "pauls_jet_WIDTH", treename); where pauls_jet_WIDTH is the name of the branch in our output tree and treename is our output tree; Also add pauls_jet_WIDTH.clear(); in the fillNTuple() function. To fill this variable we would then add pauls_jet_WIDTH.push_back(ev.jet_WIDTH->at(i)); to the fillNTuple() function.

Adding D3PD variables to our Algorithm

In order to use D3PD variables that are not already used by the CERN code you must first find the details of the variable. To do this it is easiest to load the root file in CINT (root -l myfile.root) then use the MakeClass function of root to produce a header file that could be used to read the tree. This can be done on the CINT command line by doing treename->MakeClass("MyClassName"). This will write out a MyClassName.C and a MyClassName.h file. The details of how to read the variable you want can then be found in these files.

Once you have the details of the variable we can now add it to the AnalysisBase/include/EventBase.h and the AnalysisBase/include/Event.h file so that any code that inherits from this code is aware of the variable(the AnalysisWZorHbb code inherits from this as does all the code that comes from the CERN SVN package)

Now that we have done this we can add our variable to our function. In the case of the AnalysisWZorHbb code we would go to /AnalysisWZorHbb/src/WZorHbb.cxx and add ConnectVariable("MyD3PDVariableName") to the BeginInputFile function.

For instance for the jet_AntiKt4TopoEM_WIDTH variable we would find in MyClassName.h the line vector   *jet_AntiKt4TopoEM_WIDTH;. We would then go to AnalysisBase/include/EventBase.h and add this line there. We would then go to /AnalysisWZorHbb/src/WZorHbb.cxx and add ConnectVariable("jet_WIDTH"). Note that we have removed the name of the algorithm from the variable name. This is the convention used. The algorithm name is added by the ConnectVariable function. We must also add vector *jet_WIDTH to AnalysisBase/include/Event.h .

mkdir myVH_research
cd myVH_research
svn co svn+ssh://svn.cern.ch/reps/atlasusr/mbellomo/ElectroweakBosons/tags ElectroweakBosons-xx-xx-xx 

Where xx-xx-xx is the tag number.

Compiling the Code

Configuring and Running

(Note: It is advisable to use BaselineOneLepton for both the 1 lepton and 2 lepton analysis then diffirentiate between the two in the config file that is passed to RunHistmaker.C)

In order to do a full analysis with the whole CERN framework this code must produce three files. One for montecarlo, one for electrons and one for muons. To do this three separate "cycles" must be defined in the .xml file. A cycle is defined as follows

<Cycle Name="AnalysisManager" RunMode="LOCAL" ProofServer="lite://" ProofWorkDir="/afs/cern.ch/user/p/pmullen/tag-tmp/" ProofNodes="-1" UseTreeCache="True" TreeCacheSize="30000000" TreeCacheLearnEntries="10" OutputDirectory="/afs/cern.ch/user/p/pmullen/tag-tmp/" PostFix="" TargetLumi="1.0">

    <InputData Lumi="1.0" NEventsMax="-1" Type="mc12_8TeV" Version="OneLepton.Nominal" Cacheable="True" SkipValid="True">

        &pauls_mc;
       <InputTree Name="physics" />
                 <OutputTree Name="Ntuple" />
    </InputData>

<UserConfig>


                &setup;
                <Item Name="CorrectFatJet"  Value="False"/>

                <Tool Name="BaselineOneLepton"    Class="WZorHbb">
                        &tool_base;
                                <Item Name="runNominal" Value = "True"/><!--true-->
                                <Item Name="ntupleName" Value = "Ntuple"/>

                </Tool>
    </UserConfig>
  </Cycle>

Where &pauls_mc is a file with paths to the montecarlo files being input. For contrast another cycle configuration is shown below; this time for an electron analysis in data.

(Note: The first cycle must be closed with the flag before opening another cycle)

  <Cycle Name="AnalysisManager" RunMode="LOCAL" ProofServer="lite://" ProofWorkDir="/afs/cern.ch/user/p/pmullen/tag-tmp/" ProofNodes="-1" UseTreeCache="True" TreeCacheSize="30000000" TreeCacheLearnEntries="10" OutputDirectory="/afs/cern.ch/user/p/pmullen/tag-tmp/" PostFix="" TargetLumi="1.0">


    <InputData Lumi="1.0" NEventsMax="-1" Type="data12_8TeV" Version="OneLepton.Electron" Cacheable="True" SkipValid="True">    

        &pauls_data;
       <InputTree Name="physics" />
                 <OutputTree Name="Ntuple" />
    </InputData>
    <UserConfig>

                &setup;
                <Item Name="CorrectFatJet"  Value="False"/>

                <Tool Name="OneLepton"    Class="WZorHbb">
                        &tool_base;
                                <Item Name="runNominal" Value = "True"/>
                                <Item Name="ntupleName" Value = "Ntuple"/>
                </Tool>


    </UserConfig>

  </Cycle>

The config file and the file containing the paths to the montecarlo files are attached for reference.

./RunPlotMaker -Data12 -llbb -NominalLimitFile -Indir $HOME/out/

It expects to find 6 files in the $HOME/out/ folder.

AnalysisManager.data12_8TeV.OneLepton.Electron.Hists.MJ.root
AnalysisManager.data12_8TeV.OneLepton.Electron.Hists.root
AnalysisManager.data12_8TeV.OneLepton.Muon.Hists.MJ.root
AnalysisManager.data12_8TeV.OneLepton.Muon.Hists.root
AnalysisManager.mc12_8TeV.OneLepton.Nominal.Hists.MJ.root
AnalysisManager.mc12_8TeV.OneLepton.Nominal.Hists.root

Note the "OneLepton" in all the file names. This is because I have yet to change the hard coded file name format in the script. The "MJ" files(Multijet) were produced from the RunHistMaker program by changing the RunMJ parameter to True. If you do not want to have to rename your files before using this program then simply edit your sframe .xml config file as follows

     

<InputData Lumi="1.0" NEventsMax="-1" Type="mc12_8TeV" Version="OneLepton.Nominal" Cacheable="True" SkipValid="True">

        <input data files here>
       <InputTree Name="physics" />
                 <OutputTree Name="Ntuple" />
    </InputData>

For the data files change the Type to "data12_8TeV". This does not change the analysis type, only the output file name.

• RunPlotMaker.C: plotting script

Stacking Plots

Stacked plots can be produced using the RunPlotMaker.C program. This uses the plotter.cpp class. This is problematic as the current implementation of plotter.cpp has hard coded references to "BaselineOneLepton" when it looks for tree/branches in the root file provided. This need to be changed depending on what you had in your .xml file. TheRunPlotMaker program itself has hard coded links to a home directory that need to be changed. Choosing what systematics etc. you want to run is done with command line flags. My current version of the edited RunPlotMaker.C can be found here.

cd myVH_research/trunk
source scripts/setup_lxplus.sh
source scripts/setup_pod_lxplus.sh
make
cd AnalysisWZorHbb
make

However our .xml file will look different from our non-PROOF analysis. We must change the RunMode option to be RunMode="PROOF" and the ProofServer option must also be changed. It must look like ProofServer="username@host:portnumber" where the port number, host and username are those output from the pod-server start command or the pod-info -c. For example ProofServer="pmullen@lxplus438.cern.ch:21002"

./RunHistMaker configs/zerolepton.config false $HOME/out/AnalysisManager.mc11_7TeV.ZeroLepton.Nominal.root ./

 <UserConfig>
                &setup;
                <Tool Name="BaselineZeroLepton"    Class="WZorHbb">
                        &tool_base;
                                <Item Name="runNominal" Value = "True"/>
                                <Item Name="ntupleName" Value = "Ntuple"/>
                </Tool>
    </UserConfig>

Then create a file called $HOME/.PoD/user_xpd.cf and put the line xpd.rootd allow in it.

DEPRECATED?----------------------------------------------------------------------------------------------------------

Using PROOF

To start the proof server we can do pod-server start. You can now request worker nodes. To do this we use the pod-submit command. For example to request 20 worker nodes we would do

pod-submit -r lsf -q 1nh -n 20

Running Using PROOF on Demand(PoD)

Proof is a framework for running many root analyses in parallel. It can be run locally using PROOF-lite which will utilise multiple cores on one machine or it can be run on many machines usind the PoD framework.

Installing and Building

To Install PROOF on Demand first we must get and unpack the code.

cd $HOME
wget http://pod.gsi.de/releases/pod/3.10/PoD-3.10-Source.tar.gz
tar -xzvf PoD-3.10-Source.tar.gz

To build the code do

cd $HOME/PoD-3.10-Source
mkdir build
cd build
cmake -C ../BuildSetup.cmake ..
make
make install
cd
source myVH_research/ElectroweakBosons/trunk/scripts/setup_pod_lxplus.sh
cd PoD/3.10/
source PoD_env.sh

To change the working directory PoD uses along with many other settings just edit $HOME/.PoD/PoD.cfg

Now create a file called $HOME/.PoD/user_worker_env.sh and put the following settings in it

#! /usr/bin/env bash
echo "Setting user environment for workers ..."
export LD_LIBRARY_PATH=/afs/cern.ch/sw/lcg/external/qt/4.4.2/x86_64-slc5-gcc43-opt/lib:\
/afs/cern.ch/sw/lcg/external/Boost/1.44.0_python2.6/x86_64-slc5-gcc43-opt//lib:\
/afs/cern.ch/sw/lcg/app/releases/ROOT/5.30.01/x86_64-slc5-gcc43-opt/root/lib:\
/afs/cern.ch/sw/lcg/contrib/gcc/4.3.5/x86_64-slc5-gcc34-opt/lib64:\
/afs/cern.ch/sw/lcg/contrib/mpfr/2.3.1/x86_64-slc5-gcc34-opt/lib:\
/afs/cern.ch/sw/lcg/contrib/gmp/4.2.2/x86_64-slc5-gcc34-opt/lib
echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"

Then create a file called $HOME/.PoD/user_xpd.cf and put the line xpd.root allow in it.

allXSecs.push_back(xsection(dataset, cross-section, k factor, 1, "sample name"));  -- find out what 1 is.

e.g.

allXSecs.push_back(xsection(109351, 4.0638E-05, 1, 1,"ZHnunu"));

Atlas twiki pages can be used to find the cross-section for 7TeV data, 8 TeV data and for general datasets.

For a 2012 event InitCrossSection2012() pulls the information from a file called configs/2012_cross_sections.txt which can be edited to add the information for your particular dataset

To setup the environment:

here.

Running Mode

The code can be run in two different modes. Locally or using PROOF(Parallel ROOT Facility). PROOF allows analysis of a large number of ROOT files in parallel using multiple machines or processor cores.

Running Locally

Code Checkout

Compiling And Using The Code

(Note: for more complete instructions see the README file in the trunk subdirectory) To setup the environment:

cd myVH_research/ElectroweakBosons/trunk
source scripts/setup_lxplus.sh

This will setup the required environment variables, the Gnu C++ compiler and ROOTCORE.

To download and compile and extra software required do

./scripts/get_allcode.sh
cd SFrame
source setup.sh
cd ..

Next compile the software by doing

make

(You can also clean up by doing make clean and make distclean)

For the purposes of analysing H->bb decays the code is stored in the AnalysisWZorHbb/ directory.We now need to compile this code before we can do the analysis.

cd AnalysisWZorHbb
make

Now we can run our analysis by doing sframe_main config/WZorHbb_config_mc_nu_2011.xml for example. The .xml file is where the input files and settings are all defined(e.g. what corrections to apply to the data) and can be modified or written to suit the needs of the analysis.

Producing Plots

The output from running sframe is stored in .root files as common ntuples. To produce plots from these output files we need to use HistMaker by doing

cd macros
make

to make the required code. To run the code we use the command

./RunHistMaker  <path to config file> <runMJ> <path to files output by sframe> <output directory>      -- explain better?

Introduction

Documenting the setup of Higgsbb analysis code used by cern.

Code Checkout

The code can be checked out from the correct repository by doing:

mkdir myVH_research cd myVH_research svn co svn+ssh://svn.cern.ch/reps/atlasusr/mbellomo/ElectroweakBosons/trunk/AnalysisWZorHbb/

Note: you may want to set up kerberos first.(I did not require the GSSAPITrustDNS yes line).

Using The Code