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 – hyperlinksviolet – The OS answer

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

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

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/tutorial/generators.html

● I will go step by step

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 variablesuse 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/AtlasWork/Athena9.0.4"path_remove CMTPATH "${home_dir}"path_prepend CMTPATH "$(devarea)"

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 -tag=opt // 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 -tag=opt 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

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/Reconstruction/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/RecExCommon/RecExCommon-00-03-02-11 directory in your MyTest. Go there.

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

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 -tag=opt

In the MyTest directory:

cd Reconstruction/RecExample/RecExCommon/RecExCommon-<Tag>/cmt

source setup.sh

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)

# This job options file runs Atlfast in the Athena frameworktheApp.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 thisEventPersistencySvc.CnvServices = [ "McCnvSvc" ]; # Setting the Pythia seedsAtRndmGenSvc = 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.HistogramPersistency="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

#--------------------------------------------------------------# Private Application Configuration options#--------------------------------------------------------------# OUTPUT PRINTOUT LEVEL# Set output level threshold (2=DEBUG, 3=INFO, 4=WARNING, 5=ERROR, 6=FATAL )# you can override this for individual modules if necessaryMessageSvc.OutputLevel = 5# Execution of algorithms given in sequencer#theApp.TopAlg = ["Sequencer/TopSequence"] // the main application is a sequence of algorithmTopSequence = Algorithm( "TopSequence" )TopSequence.Members = ["Sequencer/Generator","Sequencer/Atlfast"] // The algorithms that belong to the sequence##GENERATORS SETUP (select by uncommenting/commenting)#----------------#Generator.Members = {"Isajet"};Generator = Algorithm( "Generator" )Generator.Members = ["Pythia"]# uncomment this option if you want top# contribution to cross sectionsPythia = 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

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_joboptions AtlfastStandardOptions.py

The first lines set some algorithms that can be executed

#Atlfast.members +={"Atlfast::TrackMaker/TrackMaker"};Atlfast = Algorithm( "Atlfast" )Atlfast.members +=["Atlfast::Monitor/Monitor"]#Atlfast.members +={"Atlfast::TrackNtupleMaker/TrackNtupleMaker"};# Atlfast.members +={"Atlfast::StandardNtupleMaker/StandardNtupleMaker"}; //uncomment this# Atlfast.members +={"Atlfast::ExampleAnalysis/ExampleAnalysis"};# Atlfast.members +={"Atlfast::AtlfastProtoJetMaker/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

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/reconstruction

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/atlfast/

What is in the ntupleLook 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

PMUXSNon-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

PMISSINGMissing ET informations

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.

Some further information-Instructions for downloading and installing athena somewhere: you need a machine with rh7.3 or SLC3 installed (I don’t 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 < Atlas

< Twiki

- Running Herwing / How to interface external events (generated with Alpgen, AcerMC, CompHep, MC@NLO etc.) with pythia/ATLFAST or

Herwig/ATLFAST: index

- Running the ATLAS reconstruction on full simulated events:Reconstruction in Athena

-Trigger simulation (LVL1 and HLT): see Atlas UK Simulation - Level2

For any question you can contact me: iacopo.vivarelli@pi.infn.it

Either I can answer or I can redirect the question……….