Pablo Jacome's Four Tops

More... Close my twisty content

LINKS:

1. Other 4top Analysis:
   1. http://cms.cern.ch/iCMS/jsp/analysis/admin/analysismanagement.jsp
2. https://twiki.cern.ch/twiki/bin/viewauth/CMS/TWikiTopRefEventSel

K) RooStatsCL95

1. https://twiki.cern.ch/twiki/bin/view/CMS/RooStatsCl95
2. https://twiki.cern.ch/twiki/bin/viewauth/CMS/SWGuideCMSDataAnalysisSchoolStatistics2012#Part_4_RooStats
3. http://root.cern.ch/root/html/tutorials/roostats/index.html
4. https://twiki.cern.ch/twiki/bin/view/CMS/StatisticsTools

5. export CVSROOT=:ext:pjacomeh@lxplus.cern.ch:/afs/cern.ch/user/c/cvscmssw/public/CMSSW
   cvs co -r V00-02-06 StatisticalTools/RooStatsRoutines
   cd StatisticalTools/RooStatsRoutines
   

6. Change ~/rootlogon.C

   gSystem -> SetIncludePath( "-I$ROOFITSYS/include" );
   

7. cd StatisticalTools/RooStatsRoutines/root
   root -l
   .L roostats_cl95.C+
   LimitResult mylimit = GetClsLimit(17775.6, 711.0, 0.5, 0.1, 1887.1, 10.0, 1991.0);
   Double_t obs_limit = mylimit.GetObservedLimit();
   cout << obs_limit << endl;
   

J) Simple Limits

1. wget http://mon.iihe.ac.be/~keaveney/CMASDAS2014/roostats_cl95.C

I) SFrame Plotter

1. Copy all .root files to */uscms_data/d3/pjacome/plots/Selection/
2. cp /eos/uscms/store/user/pjacome/Selection/4tops/Muon_2/*.root .
3. 4topsCyclePlots.steer
4. /uscms_data/d3/pjacome/SFrame_new/SFramePlotter/bin/Plots -f 4topsCyclePlots.steer

H) Selection: Results

1. Number of events:

J) Selection: cuts (CONDOR)

1. IMPORTANT: Do not use PROOF here. Trigger selection does not work in PROOF
2. To read: https://twiki.cern.ch/twiki/bin/viewauth/CMS/JECUncertaintySources
3. Cuts:
   1. One good PV.
   2. One good muon: min pt (26 GeV), max eta (2.1) , min reliso (0.12), and muon ID
   3. No loose electron: pt (35 GeV), eta(2.5), iso (0.1)
   4. At least 6 jets: pt (40 GeV), eta (2.4)
   5. At least 2 CSVM b-tagged jets.
   6. Ht (400 GeV)
4. PileUpHistos required:
   1. myPileUpHistoCycle_config.xml
5. Code of Selection in ZprimeSelectionCycle.cxx:

   1. cd /uscms_data/d3/pjacome/sframe
      cd ZprimeAnalysis
      nano src/ZprimeSelectionCycle.cxx
      

6. Before make, remove old library files:

   1. cd ZprimeAnalysis
      rm obj/ZprimeSelectionCycle.o  obj/dep/ZprimeSelectionCycle.d
      rm  ../lib/ZprimeAnalysis.par  ../lib/libZprimeAnalysis.so
      
      make
      

7. Files: multiConfigs_SELECTION_NO-PROOF.sh , sframe_CONDOR_NO-PROOF.sh, mySelectionCycle_config.xml , template.condor

8. wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/multiConfigs_SELECTION_NO-PROOF.sh
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/sframe_CONDOR_NO-PROOF.sh
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/mySelectionCycle_config.xml
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
   bash multiConfigs_NO-PROOF.sh

9. Extracting results: selection_results-NO-PROOF.sh

info

1. Working on number of events and luminosity problems:
   1. The following plot was obtained by using the luminosities from the config file of SFrame-Selection
      1. 
2. Working with SFramePlotter:
   1. Installing the latest version of SFrame: SFrame_Zprime.txt

   2. SFrame_new/SFramePlotter$ ./bin/Plots -f myExampleCyclePlots.steer

   3. NOTE: Production based on tlbsm_53x_v2
3. Number of events for backgrounds from: https://twiki.cern.ch/twiki/bin/view/CMS/B2GZPrime2012SFrameProduction
4. DATA:
   1. dcap://cmsgridftp.fnal.gov:24125/pnfs/fnal.gov/usr/cms/WAX/11/store/user/peiffer/Ntuples_53/
5. Normalization:
   1. Formula for scale factor:
      1. 
   2. Example:
      1. http://cmscvs.cern.ch/cgi-bin/cmscvs.cgi/UserCode/makouski/NtuplePlotter/test/SF.py?revision=1.9&view=markup
6. Working on histograms:
   1. Here's the code: Histos.C

I) Cross Sections and Luminosities

1. DATA:

1. Montecarlo samples:
   1. ttbar, singleTop : http://arxiv.org/pdf/1205.3453v1.pdf
   2. Standard Model Cross sections from: https://twiki.cern.ch/twiki/bin/view/CMS/StandardModelCrossSectionsat8TeV
   3. Background samples: https://twiki.cern.ch/twiki/bin/viewauth/CMS/B2GZPrime2013SFrameProduction
   4. Calculating Luminosity:

H) CONDOR, PROOF for PreSelection

1. CONDOR, No PROOF (OK, recomended for ntuples located at /eos):
   1. Files: multiConfigs_NO-PROOF.sh, sframe_CONDOR_NO-PROOF.sh, myPreSelection_Muo_NO-PROOF.xml, template.condor

   2. wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/multiConfigs_NO-PROOF.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/sframe_CONDOR_NO-PROOF.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/myPreSelection_Muo_NO-PROOF.xml
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
      bash multiConfigs_NO-PROOF.sh

   3. Extracting results for NO-PROOF: preselection_results.sh
2. CONDOR, PROOF (OK, just work for ntuples located at DCACHE):
   1. IMPORTANT: PROOF working/sandbox is NOT able to write to /eos system. For OUTPUT directory there is no problem to write to /eos
      1. ~/.rootrc

         1. Proof.Sandbox: /uscms_data/d3/pjacome/proof

      2. config/myAnalysisSelection.xml

         1. <Cycle Name="FourtopsSelectionCycle" RunMode="PROOF" ProofServer="lite://"  ProofWorkDir="/uscms_data/d3/pjacome/proof/" OutputDirectory="/eos/uscms/store/user/pjacome/Selection/from_Zprime/Muons/" PostFix="" TargetLumi="1.0" >

   2. Put __proof_wd__/ tag where the path of ProofWorkDir
   3. Files: multiConfigs_PROOF.sh, allEOS_no-flag_condorPROOF_SFrame.sh, myPreSelection_Muo_PROOF.xml, template.condor
   4. Preparing PROOF configuration:

      1. cd  ~
         ln -s /eos/uscms/store/user/pjacome/rootrc  .rootrc
         

   5. cd /eos/uscms/store/user/pjacome/preselection/muon/run1
      cp /uscms_data/d3/pjacome/sframe/ZprimeAnalysis/config/JobConfig.dtd  .
      
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/myPreSelection_Muo_PROOF.xml
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/multiConfigs_PROOF.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/allEOS_no-flag_condorPROOF_SFrame.sh
      bash multiConfigs_PROOF.sh

   6. Extract results for PROOF selections/preselections: preselection_results-PROOF.sh

G) PreSelection

1. Reference:
   1. https://twiki.cern.ch/twiki/bin/view/Main/FYumicevaSFrameFwk#Skimmed_Analysis_ntuples_Presele
      1. At least one good muon: min pt (26 GeV), max eta (2.1) , min reliso (0.12), and muon ID
      2. No loose electron: pt (35 GeV), eta(2.5), iso (0.1)
      3. At least 6 jets: pt (40 GeV), eta (2.4)
2. Changes made in ZprimeAnalysis/src/ZprimePreSelectionCycle.cxx:
   1. See available Selection modules in: SFrameAnalysis/src/SelectionModules.cxx
   2. See available Cleaner modules in: SFrameAnalysis/src/Cleaner.cxx

   3. source fullsetup.sh
      cd ZprimeAnalysis
      rm obj/ZprimePreSelectionCycle.o  obj/dep/ZprimePreSelectionCycle.d
      rm  ../lib/ZprimeAnalysis.par  ../lib/libZprimeAnalysis.so
      

   4. nano src/ZprimePreSelectionCycle.cxx
      1. More... Close

             Selection* preselection = new Selection("preselection");
             if(m_Electron_Or_Muon_Selection=="Electrons" || m_Electron_Or_Muon_Selection=="Electron" || m_Electron_Or_Muon_Selection=="Ele" || m_Electron_Or_Muon_Selection=="ELE") {
                 preselection->addSelectionModule(new NElectronSelection(1,int_infinity(),35,2.5));//at least one electron
                 preselection->addSelectionModule(new NMuonSelection(0,0));//no muons
             } else if(m_Electron_Or_Muon_Selection=="Muon" || m_Electron_Or_Muon_Selection=="Muons" || m_Electron_Or_Muon_Selection=="Mu" || m_Electron_Or_Muon_Selection=="MU") {
                 preselection->addSelectionModule(new NElectronSelection(0,0));//no electron
                 preselection->addSelectionModule(new NMuonSelection(1,int_infinity(),26,2.1));//at least one muon
             } else {
            m_logger << ERROR << "Electron_Or_Muon_Selection is not defined in your xml config file --- should be either `ELE` or `MU`" << SLogger::endmsg;
             }
             preselection->addSelectionModule(new NJetSelection(6,int_infinity(),40,2.4));//at least two jets
             RegisterSelection(preselection);
         
         ## . . . 
         
             //clean collections here
         
             if(bcc->muons) cleaner.MuonCleaner(26,2.1,0.12);
                 // MuonCleaner(double ptmin, double etamax, double relisomax)
             if(bcc->electrons) cleaner.ElectronCleaner(35,2.5,0.1,m_reversed_electron_selection,false,true);
                 // ElectronCleaner(double ptmin, double etamax, double relisomax, bool reverseID, bool reverseIso, bool egmId)
             if(bcc->jets) cleaner.JetLeptonSubtractor(m_corrector,false);
             if(!bcc->isRealData && bcc->jets) cleaner.JetEnergyResolutionShifter();
             if(bcc->jets) cleaner.JetCleaner(40,2.4,true);
                 // JetCleaner(double ptmin, double etamax, bool doPFID)
         
         
         

   5. make
      

3. PreSelection requirements:
   1. JEC is required when using DATA
      1. /eos/uscms/store/user/peiffer/JECFiles
      2. /eos/uscms/store/user/peiffer/LumiFiles
      3. /eos/uscms/store/user/peiffer/PileUpHistos
   2. Francisco added code:
4. Notes:
   1. Check: ElectronCleaner: reverseID =m_reversed_electron_selection, reverseIso =false, egmId =true
   2. Check: JetCleaner: doPFID = true
5. Config file:

   1. <Item Name="JECDataGlobalTag" Value="FT_53_V21_AN6" />
      <Item Name="JECMCGlobalTag" Value="START53_V27" />
      <Item Name="JECJetCollection" Value="AK5PFchs" /> 

F) SFrame Installation

1. References:
   1. https://twiki.cern.ch/twiki/bin/viewauth/CMS/B2GZprimeSFrameInstall
   2. https://twiki.cern.ch/twiki/bin/viewauth/CMS/B2GZprimeHighmassSemilep2012
   3. https://twiki.cern.ch/twiki/bin/view/Main/FranciscoYumiceva
   4. https://github.com/yumiceva/FITAnalysis
2. Installing SFrame + ZprimeAnalysis in cmslpc:
   1. installing_sframe.sh
3. After installation you could automatize your bash session:
   1. nano ~/.bashrc 1 my.bashrc

E) NTuples

1. References:
   1. https://twiki.cern.ch/twiki/bin/viewauth/CMS/B2GZprimeSFrameInstall#Installation_of_sframe_ntuple_wr
   2. https://twiki.cern.ch/twiki/bin/view/Main/FYumicevaSFrameFwk#Production_of_Analysis_ntuples
   3. Useful for tobtecfakefilters: https://github.com/jiafulow/HLTrigger-HLTanalyzers-test-openHLT/blob/master/addpkg_5_3_14.csh
   4. https://github.com/jiafulow/HLTrigger-HLTanalyzers-test-openHLT/blob/master/addpkg_5_3_11.csh
   5. Some reported errors: https://github.com/cms-sw/cmssw/pull/2363
2. Installing required packages:
   1. Post-Moriond: install-postMoriond.sh
   2. NtupleWriter: install_NtupleWriter.sh
3. Send jobs: D_Ntuples.sh , myNtupleWriter_cfg.py.txt

   1. cd /eos/uscms/store/user/pjacome/ntuples
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/D_Ntuples.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/cmsrun_condor.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/myNtupleWriter_cfg.py.txt
      mv myNtupleWriter_cfg.py.txt myNtupleWriter_cfg.py
      nano D_Ntuples.sh
      ./D_Ntuples.sh

4. Count Ntuple events in xml files from TTBSM53:
   1. count_xml_Ntuples_events_CONDOR.sh
   2. DATA and BACKGROUND number of events: Samples_TTBSM53_FNAL_Ntuples_count
   3. Generating bad_files list:

      1. cd /eos/uscms/store/user/pjacome/count_ntuple
         grep -v "_x_OK"  list_*.xml > bad_files

   4. Removing bad files: removing_bad_files.sh

      1. cd /uscms_data/d3/pjacome/sframe/SFrameAnalysis/config/Samples_TTBSM53_FNAL
         cp /eos/uscms/store/user/pjacome/count_ntuple/bad_files .
         wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/removing_bad_files.sh
         bash removing_bad_files.sh

   5. Final Sample list: final_Samples_TTBSM53_FNAL.zip
5. Creating XML list of the signal ntuples: creating_XMLs_for_signal.sh

D) PatTuples OLD, do not use until check, go directly to Ntuples

1. References:
   1. https://twiki.cern.ch/twiki/bin/viewauth/CMS/B2GTopLikeBSM53X#Version_2_53x_pre_Moriond_versio
2. Installing required packages:
   1. Pre-Moriond: install-preMoriond.sh ( Old, using CVS PatTuples_setup.sh )
   2. Post-Moriond: install-postMoriond.sh
3. Use the config file: my_pat.py.txt, C_PATtuples.sh
   1. Based on:

      1. cp /uscms_data/d3/pjacome/CMSSW_5_3_3/src/TopQuarkAnalysis/TopPairBSM/test/ttbsm_cfg.py   my_pat.py
         ##  USAGE: cmsRun my_pat.py useData=0 runOnFastSim=1  usePythia8=1  2>err 1> log 

   2. cd /eos/uscms/store/user/pjacome/pattuples
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/C_PATtuples.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/cmsrun_condor.sh
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/my_pat.py.txt
      mv my_pat.py.txt  my_pat.py
      nano C_PATtuples.sh
      ./C_PATtuples.sh
      

C) GEN,FASTSIM,HLT

1. References:
   1. https://twiki.cern.ch/twiki/bin/view/CMSPublic/SWGuideFastSimulation
2. Installing, generating config files: generate_GEN-FASTSIM-HLT_config_file.sh

   1. ./generate_GEN-FASTSIM-HLT_config_file.sh

3. Dowload the following scripts: B2_GEN_FASTSIM_HLT.sh , cmsrun_condor.sh , template.condor , (B_GEN_FASTSIM_HLT.sh)

4. cd /eos/uscms/store/user/pjacome/fastsim
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/B2_GEN_FASTSIM_HLT.sh
   wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/cmsrun_condor.sh
   ./B2_GEN_FASTSIM_HLT.sh

5. Counting the number of events in every output file: count_FASTSIM_events.sh
6. Explore output file:

   1.  edmDumpEventContent  /eos/uscms/store/user/pjacome/fastsim/SM_tttt_8TeV_10000ev_r01.root

   2. Another option: Use EdAnalizer: https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookWriteFrameworkModule
   3. To print particles information for every event use the following HistoAnalyzer code: HistoAnalyzer.cc.GenParticleDUMP , histoanalyzer_cfg.py.GenParticleDUMP
   4. Histograms and GenMatch : generateGenParticleHisto.sh , histoanalyzer_cfg.py.template , HistoAnalyzer.cc

B) MadGraph

1. MonteCarlo signals:
2. Scripts: A_SM_Madgraph.sh , A2_GH_Madgraph.sh

   1. cd /eos/uscms/store/user/pjacome/mg5
      wget --no-check-certificate https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/template.condor
      wget  --no-check-certificate  https://twiki.cern.ch/twiki/pub/Sandbox/FourTopAnalysisPabloJacomeV2/A2_GH_Madgraph.sh
      cond_f='gh_mg'
      cp template.condor  ${cond_f}.condor
      sed -i 's|__script__|'${PWD}'/'A2_GH_Madgraph.sh'|g'  ${cond_f}.condor
      sed -i 's|__name__|'${cond_f}'|g'  ${cond_f}.condor
      sed -i 's|__config__| |g'  ${cond_f}.condor
      condor_submit ${cond_f}.condor
      

3. | Sample name | Nevents | XSec [pb] | uncert |

1. Plot LHE file with MadAnalysis:*RECOMENDATION:* Convert to root instead of using MadAnalysis

   1. cd /uscms_data/d3/pjacome/MadGraph5_v1_5_9/madanalysis5
      ./bin/ma5
      

   2. pp to tttt to 1mu j j: madanalysis5_plot_commands.txt , Output file: tttt_to_1mu_jets.pdf
   3. pp to tttt : ttttONLY_madanalysis5_plot_commands.txt , Output file: tttONLY_madanalysis_plots.pdf
   4. IMPORTANT: Problems with definitions, for example, to plot muon_PT define mu = mu+ mu- is required. But for top antitop we get different output PT(t t~) , PT( top) where top = t t~
2. Convert .LHE to .root

   1. cd  ExRootAnalysis
      ExRootLHEFConverter  my.LHE out.root
      

   2. To plot use this ROOT macro Pt_histo.C

A) Basics

1. To Access LPC Fermilab: http://uscms.org/uscms_at_work/physics/computing/getstarted/uaf.shtml
2. GIT: https://twiki.cern.ch/twiki/bin/view/Sandbox/ASmallGitCMSSWTutorial
3. CONDOR commands:

   • condor_q  <usr>
     condor_q  -analyze <usr>
     condor_rm _proc_id_

4. Reading output using ROOT:

   • _file0->ls();
     TDirectory*  Event_Postsel = _file0->GetDirectory("Event_Postsel;1");
     Event_Postsel->ls();
     TH1F * HT = (TH1F*)Event_Postsel->Get("HT;1");
     # HT->Scale(0.1); ## example
     HT->Draw();
     
     TTree *myTree = (TTree*)_file0->Get("AnalysisTree;1");