This tutorial is based on CERN SoftwareTutorialxAODAnalysisInROOT wiki. However, the lessons given below are simplified for a faster start. Also, the last 2 lessons are designed for the ANL cluster that uses condor for job submissions. In addition, we we will test US ATLAS connect as explained at the bottom of this page.

We would like to encourage you all to obtain a computer account already at your local Tier3. That is the recommended way to do the tutorials since, eventually, you may want to run your xAOD analysis at home institutes. If needed, we can also provide you an account at Argonne Tier3.

• Please make sure that your local Tier3 has the usual ATLAS setup environment based on “cvmfs”.
• Several tutorial topics will require the grid access (use voms-proxy-init -voms atlas to check this).

ANL people can use “atlas1.hep.anl.gov” or atlas2.hep.anl.gov.

First, we will setup ATLAS release.

1) Setup kinit if needed: kinit [email protected] where username is your user name on lxplus. This step is normally not needed.

2) Create a bash script to setup ATLAS software. The method below works at ANL:

setup.sh

#!/bin/bash
export ALRB_localConfigDir="/share/sl6/cvmfs/localConfig"
export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh
#asetup 19.1.1.4,slc6,here # setup ATLAS release when needed
setupATLAS

and then do “source setup.sh”. This works at ANL/ASC. Make a similar script when using lxplus or other Tier3 as explained in CERN tutorial.

On LXPLUS:

setup.sh

export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'
setupATLAS

To run tutorials, you can check these requirements (prepared by Asoka De Silva):

• You can check that your computer is ATLAS ready by doing (SL, SLC, CentOS) version 6):

setupATLAS
diagnostics
checkOS

• You will need a valid grid certificate registered with LCG and installed in $HOME/.globus. You can check that your grid credentials are good by doing:

setupATLAS
diagnostics
gridCert

• Available disk space:

You will need 500 MB of free space. It can be $HOME or any other location - note the location as you will be asked for it. If you are running on lxplus, you can request your home dir quota be increased to 10GB or request up to an additional 100GB of workspace. To ask for space, go to (use your lxplus username below)

 
https://resources.web.cern.ch/resources/Manage/AFS/Settings.aspx?login=<your lxplus username>

You may need to request repeatedly to get the full quota (it is granted in increments.). To check how much quota you have on /afs (eg on lxplus), type fs lq; eg.

fs lq /afs/cern.ch/user/d/desilva
fs lq /afs/cern.ch/work/d/desilva # for workspace if you have it

Let's us take a look at a typical xAOD file. You can open it with ROOT TBrowser to study its structure.

mkdir lesson_1
cd ./lesson_1

Now we need to get an example xAOD file. You can do all the checks above plus data for this tutorial as:

setupATLAS
diagnostics
setMeUp anl-oct2014

If you want to get an example xAOD file without running the above command, let's do it slowly:

Method 1. If you are at ANL, copy it:

cp /data/nfs/chakanau/tutorial_xAOD_long/valid2.117050.PowhegPythia_P2011C_ttbar.digit.AOD.e2657_s1933_s1964_r5534_tid01482225_00/AOD.01482225._000140.pool.root.1  AOD.01482225._000140.pool.root

Method 2. Use xrdcp:

localSetupFAX --rootVersion=current-SL6
voms-proxy-init -voms atlas
xrdcp $STORAGEPREFIX/atlas/rucio/valid2:AOD.01482225._000140.pool.root.1 AOD.01482225._000140.pool.root

Method 3: If you work at CERN, use this file:

/afs/cern.ch/atlas/project/PAT/xAODs/r5597/data12_8TeV.00204158.physics_JetTauEtmiss.recon.AOD.r5597/AOD.01495682._003054.pool.root.1
/afs/cern.ch/atlas/project/PAT/xAODs/r5591/mc14_8TeV.117050.PowhegPythia_P2011C_ttbar.recon.AOD.e1727_s1933_s1911_r5591/AOD.01494882._111853.pool.root.1

Method 4: If you work at your Tier3

setupATLAS
diagnostics
setMeUpData anl-oct2014 mydata

The file will appear in “mydata/tutorial/anl-oct2014/database/” directory

Now open this file with TBrowser:

root
TBrowser a

Click the file name using the left panel, Select “CollectionTree” and find a branch with the extension “Aux” (for example, “AntiKt4TruthJetsAux”) and then plot “AntiKt4TruthJetsAux.pt”. See other detail in CERN tutorial

Now we will read the above line in Python and print some values for electron (eta and phi)

First, we setup our environment in the directory “lesson_1” that has the xAOD file:

source setup.sh
rcSetup -u; rcSetup Base,2.0.12

Now you can check what versions of packages are linked:

rc version

that shows a long version of package versions.

The let's create a new directory and put this file:

xAODPythonMacro.py

#!/usr/bin/env python
 
# Set up ROOT and RootCore:
import ROOT
ROOT.gROOT.Macro( '$ROOTCOREDIR/scripts/load_packages.C' )
 
ROOT.xAOD.Init() # Initialize the xAOD infrastructure
 
fileName="AOD.01482225._000140.pool.root" # Set up the input files
treeName = "CollectionTree" # default when making transient tree anyway
 
f = ROOT.TFile.Open(fileName)
t = ROOT.xAOD.MakeTransientTree( f, treeName) # Make the "transient tree"
 
# Print some information:
print( "Number of input events: %s" % t.GetEntries() )
for entry in xrange( t.GetEntries() ):
   t.GetEntry( entry )
   print( "Processing run #%i, event #%i" % ( t.EventInfo.runNumber(), t.EventInfo.eventNumber() ) )
   print( "Number of electrons: %i" % len( t.ElectronCollection ) )
   for el in t.ElectronCollection:  # loop over electron collection
      print( "  Electron trackParticle eta = %g, phi = %g" %  ( el.trackParticle().eta(), el.trackParticle().phi() ) )
      pass # end for loop over electron collection
   pass # end loop over entries
f.Close()   

If you copy this script, correct indentation (the lines should start from the column position 0). This is a good for your to learn this code! Then run it as:

chmod +x xAODPythonMacro.py
./xAODPythonMacro.py

Using this code, one can fill histograms. But the code runs slow. Below we will show how to use C++/ROOT compiled code to run over this file.

How do you know about methods of “el.trackParticle()”? You can print methods of this object as:

print dir(el.trackParticle())

How will you find xAOD variables without using ROOT TBrowser? Try this code:

asetup 19.1.1.1,slc6,gcc47,64,here
checkSG.py AOD.01482225._000140.pool.root

Now you can fill a histogram in this Python code. You should create a histogram before the event loop:

from ROOT import *
h1=TH1D("eta","eta",20,-4,4)

Then fill it in the event loop as h1.Fill( el.trackParticle().eta() ). Then we will write this histogram in a file as:

hfile=TFile("test.root","RECREATE","ANL tutorial")
h1.Write()
hfile.Close()

Here the code that write a ROOT histogram:

xAODPythonMacro_histo.py

#!/usr/bin/env python
 
import ROOT
ROOT.gROOT.Macro( '$ROOTCOREDIR/scripts/load_packages.C' )
 
ROOT.xAOD.Init() # Initialize the xAOD infrastructure
 
fileName="AOD.01482225._000140.pool.root" # Set up the input files
treeName = "CollectionTree" # default when making transient tree anyway
 
f = ROOT.TFile.Open(fileName)
t = ROOT.xAOD.MakeTransientTree( f, treeName) # Make the "transient tree"
 
from ROOT import *
h1=TH1D("eta","eta",20, -4,4)
 
# Print some information:
print( "Number of input events: %s" % t.GetEntries() )
for entry in xrange( t.GetEntries() ):
   t.GetEntry( entry )
   print( "Processing run #%i, event #%i" % ( t.EventInfo.runNumber(), t.EventInfo.eventNumber() ) )
   print( "Number of electrons: %i" % len( t.ElectronCollection ) )
   for el in t.ElectronCollection:  # loop over electron collection
      h1.Fill( el.trackParticle().eta() )
      pass # end for loop over electron collection
 
   pass # end loop over entries
 
hfile=TFile("test.root","RECREATE","ANL tutorial")
h1.Write()
f.Close()
hfile.Close()

Now open the root file and look at the histogram.

Now we will create a C++/ROOT analysis program and run over this input xAOD file. Use the same setup file as above.

source setup.sh
mkdir lesson_3; cd lesson_3
rcSetup -u; rcSetup Base,2.0.12
rc find_packages  # find needed packages
rc compile        # compiles them

This takes some time to compile. Next we will us a simple example code that runs over multiple files located in some directory

curl http://atlaswww.hep.anl.gov/asc/xaod_tutor_oct2014/MyAnalysis_lesson3.tgz | tar -xz; 
rc find_packages    # find this package
rc compile          # compiles it
cd MyAnalysis/util  # go to the analysis code

We are ready to run the code, which is “testRun.cxx” But we first should define a list with input data. This example reads file “inputdata.txt” with location of xAOD files. You can create it as:

python Make_input <directory with xAOD files>

In case if you need xAOD data, do this:

mkdir data
cd data
localSetupFAX --rootVersion=current-SL6
voms-proxy-init -voms atlas
xrdcp $STORAGEPREFIX/atlas/rucio/valid2:AOD.01482225._000140.pool.root.1 .
xrdcp $STORAGEPREFIX/atlas/rucio/valid2:AOD.01482225._000141.pool.root.1 .
xrdcp $STORAGEPREFIX/atlas/rucio/valid2:AOD.01482225._000142.pool.root.1 .

and run:

cd ..
python Make_input data

Now inputdata.txt should pick up your xAOD files.

Now the input file is ready and we run the example as:

testRun submitDir   # runs over all files inside inputdata.txt  

We pass “submitDir” which will be the output directory with ROOT file. You must delete it every time you run the code (or use different output). The actual analysis should be put to “Root/MyxAODAnalysis.cxx” (will come back to this later). The output histogram is ““submitDir/hist-sample.root” (which is almost empty).

Now we will make a number of changes to the above program. We will fill 2 histograms with pT of jets and muons. To do this we will need a number of changes:

1) We need to link several ATLAS packages (it's done already, just look what is inside of the package prepared for this lesson).

 PACKAGE_DEP = EventLoop xAODRootAccess xAODEventInfo GoodRunsLists xAODJet xAODTrigger xAODEgamma JetSelectorTools JetResolution xAODMuon

in “cmt/Makefile.RootCore”. We linked more packaged than needed to illustrate what can be linked. Use “rc version” to check their versions.

2) Then we need to modify 2 places to put histograms (it's done already in the example shown below)

MyAnalysis/MyxAODAnalysis.h # used to define pointers to histograms
Root/MyxAODAnalysis.cxx     # initialized histograms and our analysis code that loops over jets and muons

Let us run this code to see how it works:

source setup.sh
mkdir lesson_4; cd lesson_4

rcSetup -u; rcSetup Base,2.0.12
rc find_packages  # find needed packages
rc compile        # compiles 

Next we will us a simple example code that runs over multiple files located in some directory.

curl http://atlaswww.hep.anl.gov/asc/xaod_tutor_oct2014/MyAnalysis_lesson4.tgz | tar -xz; 
wget http://atlaswww.hep.anl.gov/asc/xaod_tutor_oct2014/data12_8TeV.periodAllYear_DetStatus-v61-pro14-02_DQDefects-00-01-00_PHYS_StandardGRL_All_Good.xml
rc find_packages    # find this package
rc compile          # compiles it
cd MyAnalysis/util  # go to the analysis code 

Now prepare an input file with data from a directory with xAOD files:

python Make_input <directory with xAOD files>

and run the analysis:

testRun submitDir   # runs over all files inside inputdata.txt  

How does this work? Your analysis code is testRun.cxx. We pass “submitDir” which will be the output directory with ROOT file. The actual analysis should be put to “Root/MyxAODAnalysis.cxx” as explained above. This example has an access to muon and jet containers, plus it reads goodrunlist.

The output of this example is in “submitDir/hist-sample.root”. Open it with ROOT:

root
TBrowser a

and look at the histograms with jet and muon pT.

— Sergei Chekanov 2014/10/28 07:49