Very quick ATLAS software tutorial

1

• Very quick ATLAS software tutorial
• Iacopo Vivarelli (not an expert, just a user)
• INFN Pisa
• What you find here
• - How to use CMT and run Athena
• - How to use ATLFAST
• - Useful (at least, I hope) informations about
  instructions,
• HowTo, tutorials
• Conventions
• red commands for the prompt
• blue hyperlinks
• violet The OS answer

2
Athena - where?

• If one has an account on lxplus, that is the
  right place to start
• Athena kit can be downloaded and installed
  anywhere. Only executables and libraries are
  there, but the sources can be checked out from a
  repository (e.g. CERN)
• Many and many useful information are on the ATLAS
  computing page and in the ATLAS WiKi page
• For the computing http//atlas.web.cern.ch/Atlas
  /GROUPS/SOFTWARE/OO/Applications/
• For the Wiki https//uimon.cern.ch/twiki/bin/view
  /Atlas/AtlasComputing
• Most of the informations you might need are there

3
ATLFAST

• In the following I will explain how to generate
  events and use ATLFAST (fast parametrized
  response of the detector)
• I won't go through the Full ATLAS simulation and
  reconstruction, I will give just references about
  it
• The final strategy in ATLAS will be to make
  analysis inside Athena on Analysis Object Data
  (AOD) (and Event Summary Data, ESD).
• Instead, I will show how to produce a ROOT (or
  PAW) ntuple. Refer to the computing page to know
  more about AODs and the Analysis Tools for them.
• ATLFAST is a particle level simulation. It is
  extremely useful if one wants to generate quickly
  a huge number of events (it takes about 1-2 hours
  to generate (PYTHIA) and simulate/reconstruct 100
  K tt events on my Pentium 4 2.5 Ghz single
  processor machine). One can easily (and quickly)
  get millions of events.
• It is not accurate the response of tracker,
  calorimeters, muon spectrometer is only
  parametrized (from the full simulation). An
  analysis is robust if its key points are
  certified with the full simulation

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How to run ATLFAST

• Everything I will say refers to lxplus at CERN.
  Minor changes needed if you want to run on your
  Athena at home.
• Good reference (actually this is for interactive
  athena. I won't talk about this. Anyway, most of
  the commands and the jobOptions are the same)
  http//stavrop.home.cern.ch/stavrop/Generators/tut
  orial/generators.html
• I will go step by step

5
Setting up a main CMT directory (more
informations)

• Create an empty directory (e.g. main_cmt)
• Go into it and edit a file named requirements. It
  should be as follow

Set the site where you are working. For CERN
set set CMTSITE CERN
For portables set CMTSITE EXTSITE Other
possible values are LBNL, BNL Set the base
location of all release for your site macro
ATLAS_DIST_AREA "/afs/cern.ch/atlas/software/dist"
Set release number, here it is 9.0.4 (which
is a good release for atlfast) macro
ATLAS_RELEASE "9.0.4" // The ATLAS
version you want to use, 9.0.4 is fine for
Atlfast the AtlasSettings package centralizes
the setting of basic environment variables use
AtlasSettings v (ATLAS_DIST_AREA) Set the
location of your prefered development area, where
packages will be checked out, (change
"HOME/MyTest" to be any directory path or
soft link under your home directory) macro
devarea "HOME/MyTest //
This is the place where you are going to use
packages Add dev area to the front of your
CMTPATH (but first remove any previously
defined devarea which is under your home
directory) macro home_dir "HOME/scratch0/Atlas
Work/Athena9.0.4" path_remove CMTPATH
"home_dir" path_prepend CMTPATH "(devarea)"
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Setting up the CMT

• Check here which version of CMT you have to use.
• Then, for 9.0.4 it is v1r16p20040901
• From the main_cmt directory type
• source /afs/cern.ch/sw/contrib/CMT/v1r16p20040901/
  mgr/setup.sh
• cmt config
• source setup.sh -tagopt // This any time you
  login and you want to use Athena
• The CMT should be set. To check, verify that the
  enviroment variable CMTPATH has your installation
  directory (MyTest in the previous slide) as the
  first directory and that CMTROOT is defined to
  the right CMT version
• The -tagopt option means that you don't want to
  run the debugger on the compiled packages (see
  later). Leave it there if you want only to use
  Athena, remove it if you plan to develop software

This only the first time
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Checking out packages

• Now you have to check out a package
• The software tree can be browsed here
• Use RecExCommon fine for ATLFAST and ready for
  the full reconstruction
• Check which is the tag of the wanted package in
  the release you want
• ls /afs/cern.ch/atlas/software/dist/9.0.4/Reconstr
  uction/RecExample/RecExCommon/
• RecExCommon-00-03-02-11
• Then we want the tag 00-03-02-11 of RecExCommon
• Go into the MyTest directory
• Then, check it out
• cmt co -r RecExCommon-00-03-02-11
  Reconstruction/RecExample/RecExCommon
• This produces a Reconstruction/RecExample/RecExCom
  mon/RecExCommon-00-03-02-11 directory in your
  MyTest. Go there.

8
Set up and compile packages

• There are some important directories here
• cmt directory to set up CMT of the package, to
  compile....
• share - the jobOptions (see later) of the package
  are here
• doc some scripts and maybe documentation
• If instead of RecExCommon one checks out another
  package
• cmt co -r JetRec-00-03-33 Reconstruction/JetRec
• then there are two more directories
• JetRec (the headers directory)
• src (the sources directory)
• Go into the cmt directory. Then
• cmt config
• source setup.sh // This also has to be done
  each time you login
• gmake

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Almost done.....

• If no error messages appear, then Athena should
  be ready to run. One can check that athena.py is
  in the PATH
• which athena.py
• /afs/cern.ch/atlas/software/dist/9.0.4/InstallArea
  /share/bin/athena.py
• You are in the cmt directory go into the ../run
  directory and type RecExCommon_links.sh. This
  produces a number of files in the run directory
• Be sure that the file PDGTABLE.MeV is there
• To summarize, after the setting up of everything,
  each time you login you have to do the following
• In the main_cmt directory source setup.sh
  -tagopt
• In the MyTest directory
• cd Reconstruction/RecExample/RecExCommon/RecExComm
  on-ltTaggt/cmt
• source setup.sh

10
Setting up a jobOption

• In the following I assume to run Pythia (with the
  default settings) and to use ATLFAST on the
  events produced.
• A jobOption is an input file for Athena. The
  jobOptions specifies what you are going to do.
• It uses python
• You can use the following skeleton (let's name it
  my_atl_job.py)

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This job options file runs Atlfast in the
Athena framework theApp.setup( MONTECARLO )
// The App is the main application of
Athena include( "PartPropSvc/PartPropSvc.py" )
load relevant libraries // The following
commands load the libraries for Pythia, Atlfast,
Gaudi (the core of Athena) theApp.Dlls
"Pythia_i" theApp.Dlls
"GaudiAlg" theApp.Dlls "AtlfastAlgs" theApp
.Dlls "RootHistCnv" theApp.ExtSvc
"AtRndmGenSvc" --------------------------------
------------------------------ Persistency
services ----------------------------------------
---------------------- you should not need to
change this EventPersistencySvc.CnvServices
"McCnvSvc"

Setting the Pythia seeds AtRndmGenSvc Service(
"AtRndmGenSvc" ) AtRndmGenSvc.Seeds
"PYTHIA_INIT 237662 57728382", "PYTHIA 29311444
566058" //random seeds
This is the name of the file where your
histograms will be created. theApp.HistogramPers
istency"ROOT" HistogramPersistencySvc
Service( "HistogramPersistencySvc"
) HistogramPersistencySvc.OutputFile
"ArtemisAtlfastJob.rz" NtupleSvc Service(
"NtupleSvc" ) NtupleSvc.Output "FILE1
DATAFILE'ttH.root' TYP'ROOT' OPT'NEW'" ------
--------------------------------------------------
------ Event related parameters ---------------
-----------------------------------------------
Number of events to be processed (default is
10) theApp.EvtMax 50000 // maximum number of
events
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-------------------------------------------------
------------- Private Application Configuration
options -----------------------------------------
--------------------- OUTPUT PRINTOUT LEVEL
Set output level threshold (2DEBUG, 3INFO,
4WARNING, 5ERROR, 6FATAL ) you can override
this for individual modules if necessary MessageSv
c.OutputLevel 5 Execution of
algorithms given in sequencer theApp.TopAlg
"Sequencer/TopSequence" // the main
application is a sequence of algorithm TopSequence
Algorithm( "TopSequence" ) TopSequence.Members
"Sequencer/Generator","Sequencer/Atlfast" //
The algorithms that belong to the
sequence GENERATORS SETUP (select by
uncommenting/commenting) ---------------- Genera
tor.Members "Isajet" Generator Algorithm(
"Generator" ) Generator.Members "Pythia"
uncomment this option if you want top
contribution to cross sections Pythia Service(
"Pythia" ) include( "ttH.inc" ) // all the
settings of Pythia are here, see the next slide
include( "AtlfastAlgs/AtlfastStandardOptions.py"
) // All the Atlfast settings are here
Have a look at the ATLFAST webpage for more
informations
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Pythia.PythiaCommand "pyinit pylisti
12",\ "pysubs msel 0",\ "pysubs msub 121
1",\ "pysubs msub 122 1",\ "pypars mstp 82
4",\ "pydat1 mstj 22 2",\ "pydat1 mstj 11
3",\ "pydat1 parj 54 -0.07",\ "pydat1 parj 55
-0.006",\ "pypars parp 82 2.2",\ "pypars mstp 128
0"
This is the content of the ttH.inc file. Of
course it can be put directly into the jobOptions
The syntax is - name of the pythia routine -
name of the pythia variable (vector) - number of
the component - value
Let's have a look at the Atlfast Options. We need
the AtlfastAlgs/AtlfastStandardOptions.py
file To get a jobOption from the distributions,
one can use the get_joboptions command get_jobopt
ions AtlfastStandardOptions.py
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The first lines set some algorithms that can be
executed
Atlfast.members "AtlfastTrackMaker/TrackMake
r" Atlfast Algorithm( "Atlfast"
) Atlfast.members "AtlfastMonitor/Monitor"
Atlfast.members "AtlfastTrackNtupleMaker/Trac
kNtupleMaker" Atlfast.members
"AtlfastStandardNtupleMaker/StandardNtupleMak
er" //uncomment this Atlfast.members
"AtlfastExampleAnalysis/ExampleAnalysis"
Atlfast.members "AtlfastAtlfastProtoJetMaker/
AtlfastProtoJetMaker"
If one uncomment the marked line (and change the
syntax to python), one will get the standalone
atlfast ntuple. Then, one changes the last line
of the jobOption. Change include(
"AtlfastAlgs/AtlfastStandardOptions.py" ) into
include( "AtlfastStandardOptions.py" ) to use
your local AtlfastStandardOptions.py
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Then run. This should produce an root
ntuple athena.py my_atl_job.py If you don't
get error messages and at the end you have a file
called ttH.root in your directory, then the first
job has been run.
Into AtlfastStandardOptions.py there are most of
the parameters for the ATLFAST simulation/reconstr
uction The minimum PT for electrons, photons,
isolated and non-isolated muons, reconstruction,
the reconstruction cone for clusters and jets,
the value for the b-tagging and tau-tagging
efficiency and many other options are there. The
Atlfast manual is useful to understand the
meaning of the options (it is the manual for the
fortran version, but there are no big
differencies) Something about the options can be
found also on the http//www.hep.ucl.ac.uk/atlas/a
tlfast/
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What is in the ntuple
Look here to get more informations about the
atlfast ntuple There are a number of blocks, with
similar structure. PLEPTONS ? Isolated electrons
and muons. Available variables
nele,pxele,pyele,pzele,eeele,kfele (the pdg code
of the reconstructed electron) the same for
muons. PPHOTONS? Isolated photons. Available
variables the same PMUXS?Non-isolated muons.
Available variables the same PPJETS? Jets and
AtlfastB jets. Available variables the same for
jets plus PTcalo,PTbjet,Ptujet (PT of all the
jets, of the true bjet, of the true ujet), then
the same for AtlfastB jets. PHISTORY? Parton
level informations PMISSING?Missing ET
informations
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• Be careful pxjetb IS NOT the px of b-jets. The b
  flag at the end of the jet variable name means
  that those are the variables obtained running
  AtlfastB.
• What is AtlfastB it is a simple routine that
  provides
• b-jet and tau-jet identification according to
  the tagging and mistagging efficiencies set in
  the AtlfastStandardOptions.py files. If you use
  the default, the b-tagging efficiency is 50 with
  pt dependent mistagging for c and u jets. Then, a
  random number is thrown and it is compared with
  the tagging probability according to the true
  identifier (KFJET).
• After the jet tagging, calibration constants for
  the out of cone energy are applied.
• One should use the jetb variables (pxjetb,pyjetb
  etc.) if he/she is interested in reconstructed id
  and calibrated jets.

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Some further information

• Instructions for downloading and installing
  athena somewhere you need a machine with rh7.3
  or SLC3 installed (I dont know what happens with
  different OS). It needs about 5 GB on the hard
  disk (maybe more for the installation). Then
  follow the instructions InstallingAtlasSoftware
  lt Atlas lt Twiki
• Running Herwing / How to interface external
  events (generated with Alpgen, AcerMC, CompHep,
  MC_at_NLO etc.) with pythia/ATLFAST or
  Herwig/ATLFAST index
• Running the ATLAS reconstruction on full
  simulated eventsReconstruction in Athena
• Trigger simulation (LVL1 and HLT) see Atlas UK
  Simulation - Level2

For any question you can contact me
iacopo.vivarelli_at_pi.infn.it Either I can answer
or I can redirect the question.