Code setup

Initial setup

• Connect to pc2012 and obtain CERN kerberos ticket for SVN authentication:

    $ ssh -XY pc2012.hep.manchester.ac.uk
    $ kinit -f -r7d -A YOUR_CERN_USER_NAME@CERN.CH

• Commands to check out and compile code for the first time:

    $ mkdir -p /pc2012-data3/${USER}/testarea/MPhysProject
    $ cd /pc2012-data3/${USER}/testarea/MPhysProject

    $ svn co svn+ssh://svn.cern.ch/reps/manc/PhysicsNtuple/PhysicsProject/trunk/macros/setup
    $ source setup/setup_code_first_time.sh
    $ ln -s PhysicsNtuple/PhysicsProject/macros/setup/setup_atlas_release_cvmfs.sh .

Setup on higgs.hep.manchester.ac.uk

• Replace "pc2012-data3" with "higgs-data4"
• Replace "pc2012 with "higgs"
• Use this data path when running code below: /higgs-data4/rustem/data/tth/v4_mc_data

Run analysis example

• Setup release:

    $ cd /pc2012-data3/${USER}/testarea/MPhysProject
    $ source setup_atlas_release_cvmfs.sh

• Run over 100k ttbar events to select simple analysis regions and make plots:

    $ tag="410000"; python $TestArea/PhysicsNtuple/PhysicsProject/macros/runMPhys.py /pc2012-data1/rustem/data/tth/25ns_MC_v2/${tag}.root -n 100000 -o hist_${tag}.root

• old Ntuples:

    $ tag="410000"; python $TestArea/PhysicsNtuple/PhysicsProject/macros/runMPhys.py /pc2012-data3/rustem/data/tth/v4_mc_data/${tag}.root -n 100000 -o hist_${tag}.root

• To run on a different sample replace input file with a required process id:
  • ttbar: 410000.root
  • Z to ee: 361106.root
  • Z to mumu: 361107.root
  • Z to tautau: 361108.root
• List of all MC processes and cross-sections
• Brief description for some of available variables: docs/MPhys_variables.txt
• Print all available variables:

    $ python $TestArea/PhysicsNtuple/PhysicsProject/macros/runMPhys.py /pc2012-data3/rustem/data/tth/v4_mc_data/410000.root -n 50 --print-vars

• How to make plots
  • Double click on canvas to advance to advance to a next plot
  • Plotting command:

       $ python macros/plotHists.py hist_410000.root --rkey=.*nocut -o plots -s -w

Analysis flow

• PhysicsProject - software package for this project

• Top level module is ReadNtuple class
  • Reads ROOT ntuple
  • Creates RecoEvent which contains raw reconstructed objects: muons, electrons, jets and hadronic tau candidates
  • Creates and executes children algorithms that are described next
  • It should not be necessary to modify this class

• PrepCand class creates candidate event
  • Select reconstructed objects using kinematic and particle identification information
  • Apply overlap removal between objects (eg electrons should not overlap with particle jets)
  • Create CandEvent to represent candidate event containing selected objects
  • It should not be necessary to modify this class

• PrepTopEvent class computes analysis variables
  • Code for new CandEvent variables should be added here

• PlotCand class plots variables stored with candidate event in a selected analysis region
  • Select candidate events with desired properties, for example: "2 leptons" OR "1 lepton and 1 hadronic tau"
  • Plot event variables defined in histogram files
  • It should not be necessary to modify this class

• Analysis job is configured in python module python/PhysicsProjectMPhys.py
  • Mapping between variables in ROOT ntuples and variables used by this analysis code
  • Define flow of algorithms that will be executed for every event
  • Configuration for object selection to create CandEvent
  • Configuration for event selection to plot CandEvent variables
  • Changes to object and event selection should go here

How to create and plot a new event variable

• Main analysis package is PhysicsProject - this is where all work should be done
  • Use "NJet" and "Mll" variables as an example.

• Add enum corresponding to the name of a new variable to these files:
  • PhysicsProject/CutVars.h
  • src/CutVars.cxx

• Compute value for new variables in PrepTopEvent class:
  • PrepTopEvent.cxx
  • New variables need to be added to CandEvent object

• Add histogram definition for candidate plots:
  • config/mphys/PlotCand.xml

Brief framework documentation

• Framework design: slides
• Python configuration for selections: PhysicsProjectMPhys.py
• Histogram definitions: histograms

How to update code after initial setup

• Check SVN status - make sure that there no conflicts (C):

    $ source $TestArea/setup_atlas_release_cvmfs.sh status

• Update to server SVN:

    $ source $TestArea/setup_atlas_release_cvmfs.sh update

• Recompile code (if no new files are added):

    $ source $TestArea/setup_atlas_release_cvmfs.sh light-compile

• When new files are added, packages have to be rebuilt from scratch:

    $ source $TestArea/setup_atlas_release_cvmfs.sh compile

How to download new ntuples from CERN

• Ntuples are stored on EOS mass storage at CERN
• Latest version is v4 with small changes with respect to previous version
• MC ntuples are organised by process id - described here
• First copy ntuples to tmp area on lxplus and then copy them to Manchester

    $ ssh lxplus.cern.ch
    $ eos ls root://eospublic.cern.ch//eos/escience/UniTexas/HSG8/multileptons_ntuple_run2/25ns_v4/Nominal/
    $ eos cp root://eospublic.cern.ch//eos/escience/UniTexas/HSG8/multileptons_ntuple_run2/25ns_v4/Nominal/410000.root /tmp/$USER/

To-do items

Analysis at CERN

Introduction

• This section describes to how analysis jobs at CERN using LXBATCH batch system
• This uses python helper scripts which need to be checked out independently
• Batch jobs run this macro to make plots:
  • PhysicsProject/macros/run2Plot.py
• Python configuration for plotting jobs is defined here:
  • PhysicsProject/python/PhysicsProjectRun2Plot.py
• These jobs run over these input files:
  • run2/input_cern_tth_data_v04.txt
  • run2/input_cern_tth_siml_v04.txt
  • run2/input_cern_tth_siml_v04_priority2.txt
• Please make sure to have created this 100 GB work area using CERN IT website:

    $ JOBPATH=/afs/cern.ch/work/${USER:0:1}/$USER/jobs
    $ mkdir -p $JOBPATH
    $ ls -al $JOBPATH

Batch commands

• LXBATCH is made of tens of thousand computers managed using Platform Load Sharing Facility (LSF) software
• Users can submit commands to these computers using special batch commands
• User priority is balanced by LSF software - more jobs you run, less priority you get
• These are simple batch commands

    $ ssh -XY lxplus.cern.ch
    $ bqueues -u $USER
    $ bsub /bin/ls -al
    $ bjobs 

Initial code setup

• Setup usual PhysicsProject code on lxplus at this path: $HOME/testarea/MPhysProject
• Check out batch helper scripts and auxiliary data:

    $ cd $TestArea/PhysicsNtuple/PhysicsProject
    $ svn co svn+ssh://svn.cern.ch/reps/manc/PhysicsNtuple/PhysicsLight/trunk/macros/batch
    $ svn co svn+ssh://svn.cern.ch/reps/manc/PhysicsNtuple/PhysicsLight/trunk/data/run2 
    $ svn co svn+ssh://svn.cern.ch/reps/atlasphys-hsg8/Physics/Higgs/HSG8/AnalysisCode/multileptons/xAOD/ttHMultiAna/trunk/util XsectionInput_tth_run2
    $ rm XsectionInput_tth_run2/update_xsection.cxx

Submit analysis jobs

• Commands to submit analysis jobs ("--submit" actually submits jobs)

    $ source macros/sub_batch_jobs.sh "" "-n 100000" "-first-plots"
    $ source macros/sub_batch_jobs.sh "--submit" "-n 100000" "-first-plots"
    $ bjobs

Merge data files

• Make sure that all jobs are completed: output of "bjobs" command should be empty
• Merge data files:

    $ python batch/addFiles.py $JOBPATH/hists-2016-03-16-first-plots/plots-data_v04

Make plots

• Python command to make data and MC plots for "NJet" plots:

   $ source macros/plot_stack.sh "$JOBPATH/hists-2016-03-16-first-plots" "--hkey=NJet.* --rkey=.* -w"

Paper references

• ATLAS measurement of top quark branching ratios with 7 TeV data
• LEP WW Electroweak Measurements

ATLAS references

• Tau working group recommendations