Difference between revisions of "NIKHEF PAT workshop Oct2006"

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==Pre-Tutorial==
 
==Pre-Tutorial==
  
−
*This pre-Tutorial is copy of the one gave by Ketevi A. Assamagan, adapted to work in 12.0.2  
+
*This pre-Tutorial is copy of the one given by Ketevi A. Assamagan, adapted to work in 12.0.2  
  
 
*here is a link to other Tutorials by Ketevi, and other usful PAT links:
 
*here is a link to other Tutorials by Ketevi, and other usful PAT links:
Line 9: Line 9:
  
 
[http://www.nikhef.nl/pub/experiments/atlaswiki/index.php/NIKHEF_PAT_workshop_Oct2006_pre-Tutorial Pre-Tutorial link]
 
[http://www.nikhef.nl/pub/experiments/atlaswiki/index.php/NIKHEF_PAT_workshop_Oct2006_pre-Tutorial Pre-Tutorial link]
 +
 +
During the workshop we'll browse over the code that we've used in the pre-Tutorial to try and uderstand it. Later we'll focused on the TAG and AAN selection.
  
 
==Event Selection==
 
==Event Selection==
Line 19: Line 21:
 
cp ~ordonez/public/Workshop_files/UserAnalysis/AnalysisSkeleton.h UserAnalysis/.
 
cp ~ordonez/public/Workshop_files/UserAnalysis/AnalysisSkeleton.h UserAnalysis/.
 
cd cmt
 
cd cmt
−
gamke
+
gmake
 
cd ..
 
cd ..
 
mkdir run2
 
mkdir run2
Line 34: Line 36:
 
*First we generate our own TAG.
 
*First we generate our own TAG.
  
−
*Still in the new Run directory:
+
*Still in the new run2 directory:
  
 
<pre>
 
<pre>
Line 71: Line 73:
 
</pre>
 
</pre>
 
*And run again. Note that only will run the events that satisfy the query:
 
*And run again. Note that only will run the events that satisfy the query:
−
EventSelector.Query = "NLooseMuon>0 && NLooseMuon<3 && abs(LooseMuonEta1)<2.5 && abs(LooseMuonEta2)<2.5 && LooseMuonPt2>10000 && LooseMuonPt2>10000"
+
EventSelector.Query = "NLooseMuon>0 && NLooseMuon<3 && abs(LooseMuonEta1)<2.5 && abs(LooseMuonEta2)<2.5 && LooseMuonPt1>10000 && LooseMuonPt2>10000"
  
  
Line 92: Line 94:
 
</pre>
 
</pre>
  
−
</pre>
 
 
*Comment out  
 
*Comment out  
 
<pre>
 
<pre>
Line 109: Line 110:
 
</pre>
 
</pre>
  
−
You'll see a new Zmumu_new_AOD.root file has been created
+
You'll see a new Zmumu_new_AOD_withTAGSelection.root file has been created
  
 
==Event Selection using AAN==
 
==Event Selection using AAN==
 
*Follow as in the previous section but useANN=True instead of useTAG=True. In the end you should have the following two files:
 
*Follow as in the previous section but useANN=True instead of useTAG=True. In the end you should have the following two files:
−
 
+
ZmumuOnAOD_withAANSelection.aan.root
−
 
+
Zmumu_new_AOD_withAANSelection.root
  
 
==Interactive Analysis in ATHENA==
 
==Interactive Analysis in ATHENA==
Line 137: Line 138:
 
*Initialize application manager
 
*Initialize application manager
 
<pre>
 
<pre>
−
athena> theApp.initialize()
+
athena>theApp.initialize()
 
</pre>
 
</pre>
 
*Run 1 event
 
*Run 1 event
 
<pre>
 
<pre>
−
athena> theApp.nextEvent()
+
athena>theApp.nextEvent()
 
</pre>
 
</pre>
  
 
*Retrieve Muons from AOD
 
*Retrieve Muons from AOD
 
<pre>
 
<pre>
−
athena> mcon = PyParticleTools.getMuons("MuidMuonCollection")
+
athena>mcon = PyParticleTools.getMuons("MuidMuonCollection")
 
</pre>
 
</pre>
  
 
*Other methods are defined in [http://tmaeno.home.cern.ch/tmaeno/PyParticleTools/index.html PyParticleTools]
 
*Other methods are defined in [http://tmaeno.home.cern.ch/tmaeno/PyParticleTools/index.html PyParticleTools]
−
 
−
*Number of Muons
 
−
<pre>
 
−
athena> econ.size()
 
−
</pre>
 
  
 
*Get the first muon
 
*Get the first muon
 
<pre>
 
<pre>
−
athena> m = mcon[0]
+
athena>m = mcon[0]
 
</pre>
 
</pre>
  
 
*Get a list of methods
 
*Get a list of methods
 
<pre>
 
<pre>
−
athena> dir(m)
+
athena>dir(m)
 
</pre>
 
</pre>
  
 
*See pT
 
*See pT
 
<pre>
 
<pre>
−
athena> m.pt()
+
athena>m.pt()
 
</pre>
 
</pre>
  
 
*Get TrackParticle via ElementLink
 
*Get TrackParticle via ElementLink
 
<pre>
 
<pre>
−
athena> tp = m.track()
+
athena>tp = m.track()
−
athena> dir(tp)
+
athena>dir(tp)
 +
athena>tp.pt()
 
</pre>
 
</pre>
  
 
*Retrieve the MC Truth
 
*Retrieve the MC Truth
 
<pre>
 
<pre>
−
athena> mcc = PyTruthTools.getMcEvents("TruthEvent")
+
athena>mcc = PyTruthTools.getMcEvents("TruthEvent")
−
athena> mc = mcc[0]
+
athena>mc = mcc[0]
−
athena> mc.alphaQCD()
+
athena>mc.alphaQCD()
 
</pre>
 
</pre>
  
 
*Dump Data Store
 
*Dump Data Store
 
<pre>
 
<pre>
−
athena> dumpSG()
+
athena>dumpSG()
−
</pre>
 
−
 
 
−
*Run your own Python script
 
−
<pre>
 
−
athena> emacs test.py
 
−
</pre>
 
−
*put your python code:
 
−
<pre>
 
−
x = (1234*GeV, 3456*GeV)
 
−
import math
 
−
xx = math.sqrt(x[0])
 
−
 
 
−
it  = mc.particles_begin()
 
−
itE = mc.particles_end()
 
−
while (it != itE):
 
−
    p = it.next()
 
−
    print p.pdg_id()
 
−
   
 
−
print "Done"
 
 
</pre>
 
</pre>
−
*e.g., test.py. Then Ctrl+XC to close emacs
 
  
 
*Run next event
 
*Run next event
 
<pre>
 
<pre>
−
athena> theApp.nextEvent()
+
athena>theApp.nextEvent()
 
</pre>
 
</pre>
  
 
Rewind event counter
 
Rewind event counter
 
<pre>
 
<pre>
−
athena> theApp.seek(0)
+
athena>theApp.seek(0)
 
</pre>
 
</pre>
−
 
  
 
*See pT distribution of muons
 
*See pT distribution of muons
−
 
+
<pre>
 
athena> plot("MuonContainer#MuidMuonCollection","$x.pt()",nEvent=5)
 
athena> plot("MuonContainer#MuidMuonCollection","$x.pt()",nEvent=5)
 +
</pre>
  
−
==Monte Carlo Truth Tools on AOD==
 
−
*In this exercise, we will look MC Truth Tools on AOD. Follow the link below, but skip the configuration part since it pertains to the release 11.0.5 while we are using the release 12.0.1 here and we have already done the configuration for 12.0.1 in the Introduction above. You will also need to make the following changes for 12.0.1: everywhere where application, replace the following
 
−
<pre>
 
−
#include "TruthParticleAlgs/McVtxFilterTool.h"
 
−
#include "TruthParticleAlgs/TruthParticleCnvTool.h"
 
−
#include "AnalysisUtils/McVtxFilter.h"
 
−
#include "ParticleEvent/TruthParticle.h"
 
−
#include "ParticleEvent/TruthParticleContainer.h"
 
−
</pre>
 
−
*with the following:
 
−
<pre>
 
−
#include "McParticleTools/McVtxFilterTool.h"
 
−
#include "McParticleTools/TruthParticleCnvTool.h"
 
−
#include "McParticleUtils/McVtxFilter.h"
 
−
#include "McParticleEvent/TruthParticle.h"
 
−
#include "McParticleEvent/TruthParticleContainer.h"
 
−
</pre>
 
−
*Also in your requirements file, you may need to add the following lines and redo cmt config and gmake:
 
−
<pre>
 
−
cmt co -r McParticleTools    McParticleTools-00-*      PhysicsAnalysis/TruthParticleID
 
−
cmt co -r McParticleUtils      McParticleUtils-00-*      PhysicsAnalysis/TruthParticleID
 
−
cmt co -r McParticleEvent    McParticleEvent-00-*    PhysicsAnalysis/TruthParticleID
 
−
</pre>
 
  
−
*Now follow this link, McTrtuh on AOD, make sure that you make the above modifications before running.
 
  
 
==Analysis with the EventView==
 
==Analysis with the EventView==
−
*Follow this link: EventView. However, I would suggest that you do the specific exercises above on ESD/AOD/TAG first: that provides the background for understanding the ESD/AOD/TAG before proceeding to the EventView.
+
*Due to the time I won't cover this section during the Workshop. But now you should have the basic knowledge requiered to understand it. You can learn about the [https://twiki.cern.ch/twiki/bin/view/Atlas/EventView Event View] here
  
 
== Analysis on the GRID ==
 
== Analysis on the GRID ==
Line 285: Line 238:
 
</pre>
 
</pre>
  
−
*For job estatus monitoring visit: [http://gridui02.usatlas.bnl.gov:25880/server/pandamon/query Monitoring]
+
*For job status monitoring visit: [http://gridui02.usatlas.bnl.gov:25880/server/pandamon/query Monitoring]
  
−
==GANGA==
 
−
*For further details vistit [https://twiki.cern.ch/twiki/bin/view/Atlas/DistributedAnalysisUsingGanga ganga wiki]
 
−
*A very simple example of how to use panda move to your ${HOME} directory and do:
 
−
<pre>
 
−
export PATH=$PATH:/afs/cern.ch/sw/ganga/install/slc3_gcc323/4.2.0-beta7/bin/
 
  
−
or
 
  
−
setenv PATH /afs/cern.ch/sw/ganga/install/slc3_gcc323/4.2.0-beta7/bin/:${PATH}
+
==DQ2 Tools==
−
</pre>
+
*For furhter details visit [https://twiki.cern.ch/twiki/bin/view/Atlas/UsingDQ2 DQ2 wiki]
−
 
+
*This tools make your life easier when working on the GRID
−
*Generate a ${HOME}/.gangarc with
 
 
<pre>
 
<pre>
−
ganga -g
+
dq2_ls *Zmumu*AOD*
 
</pre>
 
</pre>
  
−
*Edit $HOME/.gangarc as follows:
+
*Have a look at the files contained in one of the sets
−
 
 
−
1. In the section labelled [Configuration] add the line:
 
−
<pre>
 
−
      RUNTIME_PATH = GangaAtlas
 
−
</pre>
 
−
2. In the section labelled [LCG] add the line:
 
 
<pre>
 
<pre>
−
      VirtualOrganisation = atlas
+
dq2_ls -f <datasetname>
 
</pre>
 
</pre>
  
−
*Now move to the run directory again and try this:
+
*change user.GustavoOrdonezSanz.00008.AAN.root for your own
 
<pre>
 
<pre>
−
ganga
+
dq2_get -rv -d . user.GustavoOrdonezSanz.00008.AAN.root
 
</pre>
 
</pre>
  
−
*Inside the Python interpreter:
+
==Ganga==
−
<pre>
+
We're not going to cover Ganga in this tutorial. But for reference look at:[https://twiki.cern.ch/twiki/bin/view/Atlas/DistributedAnalysisUsingGanga Ganga link]
−
j = Job()
 
−
j.application=Athena()
 
−
j.application.prepare()
 
−
j.application.option_file='$HOME/scratch0/Workshop/12.0.2/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run/ZmumuOnAOD_jobOptions.py'
 
−
j.inputdata=DQ2Dataset()
 
−
j.inputdata.type='DQ2_LOCAL'
 
−
j.inputdata.dataset='csc11.005145.PythiaZmumu.recon.AOD.v11004103'
 
−
j.outputdata=DQ2OutputDataset()
 
−
j.outputdata.outputdata=['ZmumuOnAOD.aan.root']
 
−
j.backend=LCG()
 
−
j.submit()
 
−
</pre>
 
  
−
==DQ2 Tools==
+
==Final Exercice==
−
*For furhter details visit [https://twiki.cern.ch/twiki/bin/view/Atlas/UsingDQ2 DQ2 wiki]
+
To conclude the workshop we're going to try to make our own Higgs to four muon analysis. Taking as an example the ZmumuOnAOD algorithm, make a H4mu one. The purpose of this, is to dig into the Phisics Analysis Tools used in ZmumuOnAOD, and try to have a realistic approach of how is like to make Analyis in Athena.
−
*This tools make your life easier when working on the GRID
 
−
<pre>
 
−
dq2_ls *Zmumu*AOD*
 
−
</pre>
 
  
−
*change user.GustavoOrdonezSanz.00008.AAN.root for your own
+
Good luck!
−
<pre>
 
−
dq2_get -rv -d . user.GustavoOrdonezSanz.00008.AAN.root
 
−
</pre>
 

Latest revision as of 09:08, 25 October 2006

Pre-Tutorial

  • This pre-Tutorial is copy of the one given by Ketevi A. Assamagan, adapted to work in 12.0.2
  • here is a link to other Tutorials by Ketevi, and other usful PAT links:

PAT

  • Please follow the following pre-Tutorial before the date of the Workshop. It is a very straight forward, tutorial and will help to set up the athena enviroment for the workshop, so we can focus our time in more interested things

Pre-Tutorial link

During the workshop we'll browse over the code that we've used in the pre-Tutorial to try and uderstand it. Later we'll focused on the TAG and AAN selection.

Event Selection

First we're going to generate a new AAN that we'll use later for selection. 

cd ~scratch0/Workshop/
source setup.sh -tag=12.0.2,opt
cd 12.0.2/PhysicsAnalysis/AnalysisCommon/UserAnalysis
cp ~ordonez/public/Workshop_files/src/AnalysisSkeleton.cxx src/.
cp ~ordonez/public/Workshop_files/UserAnalysis/AnalysisSkeleton.h UserAnalysis/.
cd cmt
gmake
cd ..
mkdir run2
cd run2
cp ~ordonez/public/Workshop_files/run2/AnalysisSkeleton_jobOptions.py .
cp ~ordonez/public/Workshop_files/data2/PoolFileCatalog.xml .
cp ~ordonez/public/Workshop_files/data2/mc11.004202.ZmumuJimmy.recon.AOD.v11000401.py .
athena AnalysisSkeleton_jobOptions.py | tee athenaOut_AnalysisSkeleton.log

This will generate the file AnalysisSkeleton.aan.root.

Event Selection using TAG

  • First we generate our own TAG.
  • Still in the new run2 directory:
cp ~ordonez/public/Workshop_files/run2/Main_topOptions.py .
  • Edit Main_topOptions.py and uncomment the line
### Create TAG file
doWriteTAG=True

athena Main_topOptions.py | tee athenaOut.log
  • This will generate the file called ZmumuOnAOD_TAG.root
  • Now we are ready to run our algorithms with a TAG selection on the fly. Edit Main_topOptions.py again comment out:
#doWriteTAG=True
  • and uncomment
doRunAODwithSelection=True

and

useTag=True
  • Copy:
cp ~ordonez/public/Workshop_files/run2/ZmumuOnAOD_new_jobOptions.py .
  • And run again. Note that only will run the events that satisfy the query:

EventSelector.Query = "NLooseMuon>0 && NLooseMuon<3 && abs(LooseMuonEta1)<2.5 && abs(LooseMuonEta2)<2.5 && LooseMuonPt1>10000 && LooseMuonPt2>10000" 


athena Main_topOptions.py | tee athenaOut.log
  • As an output you have ZmumuOnAOD_withTAGSelection.aan.root. You can have a look at it in root to make sure that the query has been satisfied
  • Now we'll rewrite our own AOD containeing only the events selected. We'll do it for only 50 events to gain some time
  • Edit again Main_topOptions.py and change:
TheApp.EvtMax = 500

to

TheApp.EvtMax = 50
  • Comment out
#doRunAODwithSelection=True
  • uncomment:
doRewriteAOD=True

and run once more 

athena Main_topOptions.py | tee athenaOut.log

You'll see a new Zmumu_new_AOD_withTAGSelection.root file has been created

Event Selection using AAN

  • Follow as in the previous section but useANN=True instead of useTAG=True. In the end you should have the following two files:

ZmumuOnAOD_withAANSelection.aan.root Zmumu_new_AOD_withAANSelection.root

Interactive Analysis in ATHENA

  • In this exercise, we will see how to do interactive analysis in ATHENA, how to browse the Raw Data in the AOD. Proceed as follows:
get_files Interactive_topO.py
  • Edit Interactive_topO.py and replace this line
EventSelector.InputCollections = [ "AOD.pool.root" ]
  • with this line:
include ( "mc11.004202.ZmumuJimmy.recon.AOD.v11000401.py" )
  • run
athena -i Interactive_topO.py
  • Initialize application manager
athena>theApp.initialize()
  • Run 1 event
athena>theApp.nextEvent()
  • Retrieve Muons from AOD
athena>mcon = PyParticleTools.getMuons("MuidMuonCollection")
  • Get the first muon
athena>m = mcon[0]
  • Get a list of methods
athena>dir(m)
  • See pT
athena>m.pt()
  • Get TrackParticle via ElementLink
athena>tp = m.track()
athena>dir(tp)
athena>tp.pt()
  • Retrieve the MC Truth
athena>mcc = PyTruthTools.getMcEvents("TruthEvent")
athena>mc = mcc[0]
athena>mc.alphaQCD()
  • Dump Data Store
athena>dumpSG()
  • Run next event
athena>theApp.nextEvent()

Rewind event counter 

athena>theApp.seek(0)
  • See pT distribution of muons
athena> plot("MuonContainer#MuidMuonCollection","$x.pt()",nEvent=5)


Analysis with the EventView

  • Due to the time I won't cover this section during the Workshop. But now you should have the basic knowledge requiered to understand it. You can learn about the Event View here

Analysis on the GRID

  • In the following examples we'll run on Zmumu datasets.
  • This will be a brief introduction to GRID tools for those of you who already went through the trouble of getting a GRID certificate.
  • First we should set up DQ2 tools:
source /afs/usatlas.bnl.gov/Grid/Don-Quijote/dq2_user_client/setup.csh.CERN

PANDA/PATHENA

  • For further details visit panda wiki
  • Setup PATHENA :
cd ~/scratch0/Workshop/12.0.2/PhysicsAnalysis/AnalysisCommon/UserAnalysis
cvs update -r UserAnalysis-00-08-13 -A python
cvs update -r UserAnalysis-00-08-13 -A share/pathena
cvs update -r UserAnalysis-00-08-13 -A share/pathena_util
cvs update -r UserAnalysis-00-08-13 -A share/ConfigExtractor.py
cd cmt
source setup.sh
gmake
cd ../run
  • run pathena

Note: change user.GustavoOrdonezSanz.00008.AAN.root with an appropiate name!! 

pathena ZmumuOnAOD_jobOptions.py --inDS 'csc11.005145.PythiaZmumu.recon.AOD.v11004103' --outDS \
'user.GustavoOrdonezSanz.00008.AAN.root'


DQ2 Tools

  • For furhter details visit DQ2 wiki
  • This tools make your life easier when working on the GRID
dq2_ls *Zmumu*AOD*
  • Have a look at the files contained in one of the sets
dq2_ls -f <datasetname>
  • change user.GustavoOrdonezSanz.00008.AAN.root for your own
dq2_get -rv -d . user.GustavoOrdonezSanz.00008.AAN.root

Ganga

We're not going to cover Ganga in this tutorial. But for reference look at:Ganga link

Final Exercice

To conclude the workshop we're going to try to make our own Higgs to four muon analysis. Taking as an example the ZmumuOnAOD algorithm, make a H4mu one. The purpose of this, is to dig into the Phisics Analysis Tools used in ZmumuOnAOD, and try to have a realistic approach of how is like to make Analyis in Athena.

Good luck!

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