(r28) HiggsBb < ATLAS

ATLAS Web>HiggsBb (revision 28) (raw view)~~EditAttach~~
%TOC%

---+ %MAKETEXT{"Introduction"}%

Documenting the setup of Higgsbb analysis code used by [[https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/VHbbBaseLine2012][cern.]]

An overview of the software framework can be found [[https://svnweb.cern.ch/cern/wsvn/atlasusr/mbellomo/ElectroweakBosons/trunk/doc/userguide.pdf][here.]]

The CERN twiki page for [[https://twiki.cern.ch/twiki/bin/view/Main/AtlasCATElectroweakBosons][Diboson studies]] may also be useful.

The latest CERN [[https://twiki.cern.ch/twiki/bin/viewauth/AtlasProtected/VHbbMoriond2013CutBased][ntuples]] may be useful for testing purposes.

(%RED%Note:%ENDCOLOR% If at any stage when setting up an environment or building code you encounter a problem before trying anything else first do =make clean= on anything you have done =make= on then use a clean shell and retry.)

---+ %MAKETEXT{"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.

---+ %MAKETEXT{"Running Locally"}%

---++ %MAKETEXT{"Code Checkout"}%

The latest version of the [[https://svnweb.cern.ch/cern/wsvn/atlasusr/mbellomo/ElectroweakBosons/trunk/AnalysisWZorHbb][code]] can be [[https://twiki.cern.ch/twiki/bin/viewauth/Atlas/SoftwareDevelopmentWorkBookSVN#SVN_Repositories][checked out]] from the correct repository by doing:
<verbatim>
mkdir myVH_research
cd myVH_research
svn co svn+ssh://svn.cern.ch/reps/atlasusr/mbellomo/ElectroweakBosons/trunk</verbatim>

However it is probably best to use the latest tagged version of the code as this should (but wont necessarily) be stable. This can be checked out by doing
<verbatim>
mkdir myVH_research
cd myVH_research
svn co svn+ssh://svn.cern.ch/reps/atlasusr/mbellomo/ElectroweakBosons/tags ElectroweakBosons-xx-xx-xx </verbatim>

Where xx-xx-xx is the tag number.

Note: you may want to set up [[https://twiki.cern.ch/twiki/bin/view/CDS/LinuxTipsKerberos][kerberos]] first.(I did not require the GSSAPITrustDNS yes line).

---++ %MAKETEXT{"Compiling the Code"}%

(%RED%Note:%ENDCOLOR% for more complete instructions see the README file in the trunk subdirectory)

(1) To setup the environment:
<verbatim>
cd myVH_research/trunk
source scripts/setup_lxplus.sh</verbatim>

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

(2) To download and compile and extra software required do

(%RED%Note:%ENDCOLOR% If the extra code fails to compile due to the MET package you need to remove the code and run the 2012 versions of all the scripts)

<verbatim>
./scripts/get_allcode.sh
cd SFrame
source setup.sh
cd ..</verbatim>

(3) Next compile the software by doing
<verbatim>
make</verbatim>

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

(4) For the purposes of analysing H-&gt;bb decays the code is stored in the =AnalysisWZorHbb/= directory.We now need to compile this code before we can do the analysis.
<verbatim>
cd AnalysisWZorHbb
make</verbatim>

---++ %MAKETEXT{"Configuring and Running"}%

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. For example to do a H-&gt;bb analysis involving zero leptons that makes flat ntuples you need the following lines.
<verbatim>
 <UserConfig>
                &setup;
                <Tool Name="BaselineZeroLepton"    Class="WZorHbb">
                        &tool_base;
                                <Item Name="runNominal" Value = "True"/>
                                <Item Name="ntupleName" Value = "Ntuple"/>
                </Tool>
    </UserConfig>

</verbatim>

The "BaselineZeroLepton" option is what sets the analysis type. The string is parsed to determine whether we are doing a 0, 1 or 2 lepton analysis and also if we want to do an electron, muon or nominal analysis. (See line 250ish in WZorHbb.cxx for the code that performs the selection)

(%RED%Note:%ENDCOLOR% every time you open a shell to run the code you need to do steps (1), (3) and (4) from the compilation instructions again. i.e. setup the environment and make the code. It is also a good idea to run =make clean= before you recompile anything.)

(%RED%Note:%ENDCOLOR% 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
<verbatim>

<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>

</verbatim>

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.

(%RED%Note:%ENDCOLOR% The first cycle must be closed with the </Cycle> flag before opening another cycle)
<verbatim>
  <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>


</verbatim>

The [[%ATTACHURL%/paul_test_lepton_cuts.xml][config file]] and the file containing the [[%ATTACHURL%/llbb_local.xml][paths to the montecarlo]] files are attached for reference.

---++ %MAKETEXT{"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
<verbatim>
cd macros
make</verbatim>

to make the required code. To run the code we use the command
<verbatim>
./RunHistMaker  <path to config file> <runMJ> <path to files output by sframe> <output directory>      -- explain better?

e.g.

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


</verbatim>

This will output a .root file containing histograms.

If RunHistMaker crashes saying it did not find the cross-section(xsec) for a given number(correlating to a data set) you may need to edit the function =InitCrossSections2011()=  in the file =macros/src/process.cpp=. You will need to add the following code
<verbatim>

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"));</verbatim>

Atlas twiki pages can be used to find the cross-section for [[https://twiki.cern.ch/twiki/bin/view/LHCPhysics/CERNYellowReportPageAt7TeV][7TeV data,]] [[https://twiki.cern.ch/twiki/bin/view/LHCPhysics/CERNYellowReportPageAt8TeV][8 TeV data]] and for [[https://ami.in2p3.fr/AMI/servlet/net.hep.atlas.Database.Bookkeeping.AMI.Servlet.Command][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
---+++ %MAKETEXT{Adding Extra Plots}%
---++ %MAKETEXT{"Stacking Plots"}%

Stacked plots can be produced using the RunPlotMaker.C program.(This uses the plotter.cpp class) The current implementation of the program expects input files to follow a naming convention that contains "OneLepton" in the root file name. This need to be changed depending on what you had in your .xml file. It also 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 [[%ATTACHURL%/RunPlotMaker.C][here]]. It has been edited so that you can give it the path to a folder containing your files as a command line argument. It can be run as follows
<verbatim>
./RunPlotMaker -Data12 -llbb -NominalLimitFile -Indir $HOME/out/</verbatim>

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

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

<verbatim>     

<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>

</verbatim>

For the data files change the =Type= to "data12_8TeV" and the =Version= to "OneLepton.Muon" or "OneLepton.Electron". This does not change the analysis type, only the output file name.

To change the Analysis type you change the =Tool Name="BaselineTwoLepton"= to BaselineTwoLeptonElectron or BaselineTwoLeptonMuon
---+++ %MAKETEXT{Adding Extra Stacked Plots}%
---+ %MAKETEXT{"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.

---++ %MAKETEXT{"Installing and Building"}%

To Install PROOF on Demand first we must get and unpack the code.
<verbatim>
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</verbatim>

To build the code do
<verbatim>
cd $HOME/PoD-3.10-Source
mkdir build
cd build
cmake -C ../BuildSetup.cmake ..
make
make install
cd
cd myVH_research/ElectroweakBosons/trunk
source scripts/setup_pod_lxplus.sh
cd
cd PoD/3.10/
source PoD_env.sh</verbatim>

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

(%RED%Note:%ENDCOLOR% For those using an afs directory you [[http://pod.gsi.de/doc/nightly/Known_Issues.html#PoDonAFS][need]] to change your =[server] work_dir= parameter to something like /tmp/$USER/PoD)

Now create a file called =$HOME/.PoD/user_worker_env.sh= and put the line =source /afs/cern.ch/sw/lcg/contrib/gcc/4.3.5/x86_64-slc5-gcc43-opt/setup.sh= in it

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

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

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

#! /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"

</verbatim>

END---------------------------------------------------------------------------------------------------------------------------------------

---++ %MAKETEXT{"Using PROOF"}%

We now have PROOF installed but before doing any analysis we must first setup the correct environment. It is advised that after installing PROOF you start from a clean shell then do

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

(%RED%Note:%ENDCOLOR% It is advisable to delete your ~/.proof and /tmp/$USER directories before starting 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
<verbatim>
pod-submit -r lsf -q 1nh -n 20</verbatim>

Where =1nh= is the name of a que we are submitting the jobs to and =lsf= is the name of the resource management system.

Now that we have set up our environment and requested worker nodes we can use the nodes for our analysis. To run analysis we use the same comand as before; =sframe_main config/proof_WZorHbb_config_mc_nu_2011.xml=.

(%RED%Note:%ENDCOLOR% It is advisable to use =nohup sframe_main config/proof_WZorHbb_config_mc_nu_2011.xml &&gt; output.txt &= so that terminal crashes will not kill your job)

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"=

---+ %MAKETEXT{"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-&gt;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<float>   *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<float> *jet_WIDTH= to AnalysisBase /include/Event.h .

---+ %MAKETEXT{"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<float> 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-&gt;at(i));= to the =fillNTuple()= function.


---+ %MAKETEXT{"Using RunPlotMaker"}%

---++ %MAKETEXT{"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 <verbatim> source scripts/tar_area.sh SomeName_v0.0 </verbatim> 
This creates a directory of that name in ~/work. You then do <verbatim> source scripts/setup2012.sh </verbatim>. 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.

(%RED%Note:%ENDCOLOR% When the directory is tarred it creates a file called scripts/run_now.txt that has Some_Name_v0.0 in it and the Submit2012.sh script looks in this text file for the name of the tarball to use for the submission)


The next step is to calculate the MJ scale factors and scale the plots accordingly. To do this run <verbatim> ./RunPlotMaker -config ./configs/plot.config -MJScales </verbatim> 
(%RED%Note:%ENDCOLOR% To make a basic set of plots now do =./RunPlotMaker -config ./configs/plot.config=)

to calculate the scale factory then run <verbatim> ./RunPlotMaker -config ./configs/plot.config -CheckForFiles </verbatim> to make sure all the required files are present.(%RED%Note:%ENDCOLOR% 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)

Next we do 
<verbatim>
source scripts/tar_area.sh SomeName_v0.0_LimitFile
source scripts/submitInputFile.sh plot.config datestamp_SomeName_v0.0_LimitFile
</verbatim>

This tars the files and sends them off to the batch to scale the plots using the calculated scale factors. 
(%RED%Note:%ENDCOLOR% 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
<verbatim>
./RunPlotMaker -config ./config/plot.config -NominalLimitFile
./RunPlotMaker -config ./config/plot.config -LimitFile
</verbatim>

This will produce a limit file.


   * [[%ATTACHURL%/RunPlotMaker.C][RunPlotMaker.C]]: plotting script
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
c	RunPlotMaker.C	r2 r1	manage	35.1 K	2013-02-22 - 12:32	PaulMullen	plotting script
xml	llbb_local.xml	r1	manage	4.2 K	2013-02-22 - 12:50	PaulMullen	Path to montecarlo files
xml	paul_test_lepton_cuts.xml	r1	manage	4.5 K	2013-02-22 - 12:50	PaulMullen	SFrame configuration file
Topic revision: r28 - 2014-02-24 - PaulMullen
ATLAS