• Departmento Física Experimental
• IFIC (Instituto de Física Corpuscular), Valencia - HomePage IFIC
• +34 963543852
• victoria.sanchez@ific.uv.es
• VSM cern twiki
• VSM - ProducedSamples
• Victionary
• VSM Analysis -TRC-TopD3PDBoosted
• VSM - Computing
• VSM - Boosted Charge Asymmetry Group

VictoriaSanchezMartinez - IFIC - ... in construction ...

Preparing your Digital Certificate

~> ssh -X vicsanma@ui06.ific.uv.es            ### ssh -X vsanchez@lxplus.cern.ch
~> cd $HOME
~> mkdir -p .globus
~> cd .globus
~> cp /*/myCertificate.p12 .
~> openssl pkcs12 -in myCertificate.p12 -clcerts -nokeys -out usercert.pem
~> openssl pkcs12 -in myCertificate.p12 -nocerts -out userkey.pem
~> chmod 400 userkey.pem
~> chmod 444 usercert.pem
~> source /afs/cern.ch/project/gd/LCG-share/current/etc/profile.d/grid_env.sh
~> voms-proxy-init -voms atlas

This certificate myCertificate.p12 should be copied across to your laptop and imported into the browser:

• Preferences (or Tools) → Advanced → Encryption → View Certificates → Your Certificates → Import

Athena

The ATLAS software is divided into packages, and these are managed through the use of a configuration management tool, CMT. This is used to copy ("check out") code from the main ATLAS repository and handle linking and compilation.

You can check all the athena's releases here:

~> ssh -X vicsanma@ui06.ific.uv.es  
~> ls $VO_ATLAS_SW_DIR/software/

Athena 15.X.Y

~> ssh -X vicsanma@ui06.ific.uv.es
~> cd $HOME
~> mkdir -p AthenaTestArea/15.X.Y/cmthome
~> cd AthenaTestArea/15.X.Y/cmthome
~> emacs requirements &   ###this file is shown below
~> source $VO_ATLAS_SW_DIR/software/15.X.Y/cmtsite/setup.sh
~> cmt config
~> 
~> cd $HOME
~> source AthenaTestArea/15.X.Y/cmthome/setup.sh -tag=15.X.Y,setup
~> 
~> echo $TestArea
~> cd $TestArea
~> cmt show versions PhysicsAnalysis/AnalysisCommon/UserAnalysis   
~> cmt co -r UserAnalysis-00-15-04 PhysicsAnalysis/AnalysisCommon/UserAnalysis
~> cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt/
~> cmt config
~> source setup.sh
~> cmt make

The requirements file is like this:

#---------------------------------------------------------------------
set CMTSITE STANDALONE #establecer el cmtsite???#
###old###set SITEROOT ${VO_ATLAS_SW_DIR}/prod/releases/rel_15-24/
set SITEROOT ${VO_ATLAS_SW_DIR}/software/15.X.Y/
macro ATLAS_DIST_AREA ${SITEROOT}
macro ATLAS_TEST_AREA ${HOME}/AthenaTestArea

apply_tag projectArea
macro SITE_PROJECT_AREA ${SITEROOT}
macro EXTERNAL_PROJECT_AREA ${SITEROOT}
apply_tag simpleTest

set SVNROOT svn+ssh://vsanchez@svn.cern.ch/reps/atlasoff
apply_tag noSVNROOT

use AtlasLogin AtlasLogin-* $(ATLAS_DIST_AREA)
#set CMTCONFIG i686-slc5-gcc43-opt
#---------------------------------------------------------------------

Every time you close and open the terminal, you must set up Athena, doing:

~> cd $HOME
~> source AthenaTestArea/15.X.Y/cmthome/setup.sh -tag=15.X.Y,setup
~> cd $TestArea
~> cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/run

Athena 16.X.Y

~> cd $HOME
~> source $VO_ATLAS_SW_DIR/local/setup.sh
~> mkdir -p AthenaTestArea/16.X.Y      ###old###export AtlasSetup=${VO_ATLAS_SW_DIR}/prod/releases/rel_16-2/AtlasSetup
~> export AtlasSetup=${VO_ATLAS_SW_DIR}/software/16.X.Y/AtlasSetup
~> alias asetup='source $AtlasSetup/scripts/asetup.sh'
~> asetup 16.X.Y --testarea=$HOME/AthenaTestArea --svnroot=svn+ssh://vsanchez@svn.cern.ch/reps/atlasoff --multitest --dbrelease "<latest>"
~> 
~> cd $TestArea
~> pwd
~> cmt co -r UserAnalysis-00-15-04 PhysicsAnalysis/AnalysisCommon/UserAnalysis
~> cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt/
~> cmt config
~> source setup.sh
~> cmt make
~> 
~> cd ../run
~> get_files AnalysisSkeleton_topOptions_AutoConfig.py   ###equivalent to: cp ../share/AnalysisSkeleton_topOptions_AutoConfig.py .

Every time you close and open the terminal, you must set up Athena, doing:

~> cd $HOME
~> source /lustre/ific.uv.es/sw/atlas/local/setup.sh
~> export AtlasSetup=${VO_ATLAS_SW_DIR}/software/16.X.Y/AtlasSetup
~> alias asetup='source $AtlasSetup/scripts/asetup.sh'
~> asetup 16.X.Y --testarea=$HOME/AthenaTestArea --svnroot=svn+ssh://vsanchez@svn.cern.ch/reps/atlasoff --multitest 
~> cd $TestArea/PhysicsAnalysis/AnalysisCommon/UserAnalysis/run/

MadGraph

• http://madgraph.hep.uiuc.edu/ - The MadGraph homepage.
• arXiv:0809.2410v1 - New Developments in MadGraph/MadEvent (14 Sep 2008).

• MadGraph4 - Generate Code On-Line.

• arXiv:1106.0522 - MadGraph5: Going Beyond (2 Jun 2011).
• MadGraph5 - Generate processes online using MadGraph 5.
• MadGraph version5 - Welcome to the MadGraph version 5 Wiki.

• pdf graph - Parton Distribution Plotter.
• LHAPDF downloads - HepForge downloads.
• LHAPDF manual - LHAPDF the Les Houches Accord.
• MadGraph5 project files - Several MadGraph5's packages to download.
• KKGluonTopAntiTop - KKGluon top-antitop twiki.
• MadGraphForAtlas - Releases validation twiki.
• How to use MadGraph - An example of how to use MadGraph.
• CTEQ6 - CTEQ6 parton distribution functions.

ToDo MadGraph is a matrix element creator. Given the process, MadGraph automatically creates the amplitudes for all the relevant subprocesses and produces the mappings for the integration over the phase space. This process-dependent information is packaged into MadEvent, and a self containted code is produced that can be downloaded from the web site and allows the user to calculate cross sections and to obtain unweighted events. Alternatively, events can be also generated directly from the web1, by filling a form and letting the code run over our clusters. Once the events have been generated - event information, (e.g. particle id's, momenta, spin, color connections) is stored in the “Les Houches Event Files” (LHEF) format -, may be passed directly to a shower Monte Carlo program (interface is available for Pythia) or be used as inputs for combined matrix element-shower calculations. A series of standard plots and a rootfile contaning the parton level events are also automatically created for events generated over the web. Optionally, rootfiles containing event at pythia or after a generic simulation of a detector (PGS) can be available.

The code is written in Fortran77 and has been developed using the g77 compiler under Linux. The code is parallel in nature and it is optimized to run on a PC farm. At present, the supported PBS batch managing systems are respectively Torque, proPBS and Condor at Italian, American and Belgian clusters. Process specific codes are self contained and therefore do not need any external library. In principle the matrix-element creator can handle any user's request, however, they are limitations of the code are related to the maximum number of final state QCD particles. Currently, the package is limited to ten thousands diagrams per subprocess. So, for example, W+5 jets which has been calculated, is close to its practical limit.

MadGraph4

~> ssh -X vicsanma@evaluQ.ific.uv.es
~> cd $DIRECTORY      ###directory where you want to work
~> gunzip MG4_vX.Y.Z.tar.gz
~> tar -xvf MG4_vX.Y.Z.tar
~> cd MG4_vX.Y.Z/
~> make
~> mkdir myTest
~> cp -a Template/ myTest/
~> cd myTest/
~> emacs Cards/proc_card.dat &      ###put the process which you want
~> bin/newprocess      ###it may take a few minutes...
~> emacs Cards/param_card.dat &      ###modify some properties like mass, width, couplings...
~> emacs Cards/run_card.dat &      ###modify some properties like Nºevents, Ebeam, pdf, scales, cuts...
~> bin/generate_events
     0 
     testName

MadGraph5

~> ssh -X vicsanma@evaluQ.ific.uv.es
~> cd $DIRECTORY      ###directory where you want to work
~> gunzip MadGraph5_vX.Y.Z.tar.gz
~> tar -xvf MadGraph5_vX.Y.Z.tar
~> 
~> cd MadGraph5_vX.Y.Z/
~> mkdir myTest
~> cp -a Template/ myTest/
~> cd myTest/
~> emacs Cards/proc_card.dat &      ###put the process which you want
~> bin/newprocess      ###it may take a few minutes...
~> emacs Cards/param_card.dat &      ###modify some properties like mass, width, couplings...
~> emacs Cards/run_card.dat &      ###modify some properties like Nºevents, Ebeam, pdf, scales, cuts...
~> bin/generate_events
     0 
     testName

2) From bin/mg5

~> ssh -X vicsanma@evaluQ.ific.uv.es
~> cd $DIRECTORY      ###directory where you want to work
~> gunzip MG4_vX.Y.Z.tar.gz
~> tar -xvf MG4_vX.Y.Z.tar
~> 
~> cd MG4_vX.Y.Z/
~> bin/mg5
mg5> import model MODEL   ###you pick the MODEL
mg5> generate p p > t t~   ###PROCESS you want
mg5> output myTest   ###
mg5> exit
~> cd myTest/
~> emacs Cards/param_card.dat &
~> emacs Cards/run_card.dat &
~> bin/generate_events
     0 
     testName

LHApdf

~> cd $DIRECTORY
~> gunzip lhapdf-5.8.8b1.tar.gz
~> tar -xvf lhapdf-5.8.8b1.tar
~> cd lhapdf-5.8.8b1
~> ./configure
~> make
~> sudo make install
~> bin/lhapdf-getdata cteq
~> bin/lhapdf-getdata mstw

~> cd $DIRECTORY/MadGraph5_v1_3_33
~> mkdir myTest
~> cd myTest
~> cp -a Template/ myTest/
~> mv Template/* .
~> rm -r Template/
~> more README.lhapdf       ## Follow these steps to get the libraries which you need
~> emacs Cards/proc_card_mg5.dat &
~> bin/newprocess_mg5
~> emacs Cards/param_card.dat &
~> emacs Cards/run_card.dat &

Table1 - This table compares the cross sections for samples with the same pdf but different center of mass energy. The samples have been generated with MadGraph5.v1.3.33
(the generated process was pp > o1 > tt~, where o1=KKG with m=1TeV):

Table2 - This table shows the matching at different center of mass energy. The samples have been generated with MadGraph5.v1.3.33
(the generated process was pp > o1 > tt~ (+) pp > o1 > tt~g, where o1=KKG with m=1TeV):

KKgluon with MSTW2008

Table3.1

Table3.2 - This table shows some information obtained in the generation at 7TeV and 8TeV (ptj,pta,ptl=0 and ptjmax,ptamax,ptlmax=infinity):

Table3.3 - This table shows some information obtained in the generation of pp > o1 > tt~ process with pdf=mstw2008 (ptj,pta,ptl=0 and ptjmax,ptamax,ptlmax=infinity):

NEW Matching Study

Table4.1 - This table shows the different processes generated:

Table4.2 - This table shows the MATCHING STUDY using different initial process, for a KKG mass=500GeV, Ecm=8TeV and xqcut=10GeV. The param_card.dat used is the same for all the samples (param_card.dat). At MadGraph, jet has been defined as j = g u c d s u~ c~ d~ s~:

OLD Matching Study

Table5.1 - This table shows the different initial process used:

Table5.2 - This table shows the MATCHING STUDY using different initial process, for a KKG mass=1600GeV and Ecm=7TeV. The param_card.dat used is the same for all the samples (param_card.dat). At MadGraph, jet has been defined as j = g u c d s u~ c~ d~ s~:

Table5.3 - This table shows the MATCHING STUDY using different initial process, for a KKG mass=1600GeV and Ecm=8TeV. The param_card.dat used is the same for all the samples (param_card.dat). At MadGraph, jet has been defined as j = g u c d s u~ c~ d~ s~:

Table5.4 - This table shows the MATCHING STUDY using different initial process, for a KKG mass=500GeV and Ecm=8TeV. The param_card.dat used is the same for all the samples (param_card.dat). At MadGraph, jet has been defined as j = g u c d s u~ c~ d~ s~:

To obtain the Truth Jets with pT>20GeV plot, you have to get both files classTRUTH.C and classTRUTH.h, and run them over the my.truth.ntup.root file as follow:

~> cd FOLDER   ###this folder contains my.truth.ntup.root and classTRUTH.*
~> root -l -q classTRUTH.C+
~> root
root> .L classTRUTH.C+
root> classTRUTH* t = new classTRUTH; t->Loop();
root> ### save canvas3.C
root> ### save canvas4.C

KKG's codes:

• MadGraph: 6000048.
• Pythia: 5100021.

Validation process (mc12)

To generate the new JOs files: get this two files (script and template) and run "source New_JO_cambiarNombre.sh". Thus, you'll obtain all the JOs files for the kkg.

README:

~> Beware!!! log in to @lxplus440 (it works with SL5)
~> Download the package validation_MC12_vsm.tar and untar it.
~> Copy JobOptions file, group file (with extension .events and .tar.gz) inside the validation folder (this will be your work directory).
~> Be sure inside the folder the following files exist:
         parse_evgen_log.py
         MC12JobOpts-00-04-85_v0.tar.gz 
            (http://atlas-computing.web.cern.ch/atlas-computing/links/kitsDirectory/EvgenJobOpts/)
            (more /cvmfs/atlas.cern.ch/repo/sw/Generators/MC12JobOptions/tag   -->   MC12JobOptions-00-10-78/)
~> Open runGenerationValidation.sh file and choose the suitable variables:
         Athena's release (17.2.4.8 for these files and scripts)
         (ls /cvmfs/atlas.cern.ch/repo/sw/software/x86_64-slc6-gcc47-opt/17.8.0/AtlasProduction/17.8.0.3/)
         Mass ($MASS)
         RunNumber ($RUNNUMBER)
         JobOptions name ($JOBOPTIONS)
         GroupFile name ($GroupFile)
         Work directory name ($WORKdirectory)
~> Inside the work directory execute "source runGenerationValidation.sh"
~> Finally, you'll obtain several plots...

~> ls /cvmfs/atlas.cern.ch/repo/sw/software/17.2.4/AtlasProduction/17.2.4.8/Generators/EvgenJobTransforms/scripts/
### Generate_trf.py
~> ls /cvmfs/atlas.cern.ch/repo/sw/software/17.2.4/AtlasProduction/17.2.4.8/Generators/MC12JobOptions/
### TODO  bin  cmt   common   gencontrol  i686-slc5-gcc43-opt  share
~> ls /cvmfs/atlas.cern.ch/repo/sw/software/17.2.4/AtlasProduction/17.2.4.8/InstallArea/jobOptions/MC12JobOptions/
### Pythia8_AU2_MSTW2008LO_Common.py ...
~> ls /cvmfs/atlas.cern.ch/repo/sw/software/x86_64-slc5-gcc43-opt/17.2.4/AtlasProduction/17.2.4.8/InstallArea/share/bin/Generate_trf.py
~> ls /cvmfs/atlas.cern.ch/repo/sw/software/x86_64-slc5-gcc43-opt/17.2.4/AtlasProduction/17.2.4.8/InstallArea/share/bin/Reco_trf.py
~> 
      JOBOPTSEARCHPATH=/cvmfs/atlas.cern.ch/repo/sw/Generators/MC12JobOptions/latest/common:$JOBOPTSEARCHPATH
      JOBOPTSEARCHPATH=/cvmfs/atlas.cern.ch/repo/sw/Generators/MC12JobOptions/latest/gencontrol:$JOBOPTSEARCHPATH
      JOBOPTSEARCHPATH=/cvmfs/atlas.cern.ch/repo/sw/Generators/MC12JobOptions/latest/share/DSID182xxx:$JOBOPTSEARCHPATH

README for SLC6: for now it doesn't work!!! The only supported MC12 evgen release is 17.2.X.Y. Also, for MC12 reco it is 17.2.X.Y again or 17.3.X.Y for upgrade samples...

MC & DATA - produced samples

MC11 - KKgluon

• MG_ME_V4.4.57
• PDF set = cteq6l1
• Ecm=7TeV
• ptj=20; pta,ptl=10 and ptjmax,ptamax,ptlmax=infinity (1d5)

Table6.1 - This table shows some features about the KKgluon samples generated with MadGraph4.

These the produced KKgluon-MC-samples have these features:

• MadGraph5_v1.3.33
• PDF set = cteq6l1
• Ecm=7TeV
• ptj=20; pta,ptl=10 and ptjmax,ptamax,ptlmax=infinity (1d5)

Table6.2 - This table shows some features about the KKgluon samples. The control_card.dat is a summary about the proc_card.dat, param_card.dat and run_card.dat used in the production. You can run this script (script) to get all the samples.

MC12 - KKgluon

• MadGraph5_v1.3.33
• lhapdf_5.8.8b1(pdf=mstw2008 - lhapdf=21000)
• Ecm=8TeV
• ptj,pta,ptl=0 and ptjmax,ptamax,ptlmax=infinity

Table7.1 - This table shows some features about the KKgluon samples. The ControlCard.txt is a summary about the proc_card.dat, param_card.dat and run_card.dat used in the production. You can run these two scripts (script1 and script2) to get all the samples, but you need to use these templates (KKG_run_card_template.dat and KKG_param_card_template.dat):

Table7.2 - This table contains some samples of KKgluon with different widths. The KKGancho_proc_card_mg5.dat is the same for all. You can run this script to get all the samples, but you need to use these templates (KKGancho_run_card_template.dat and KKGancho_param_card_template.dat):

Table7.3 - This table contains some samples of nominal KKgluon with 1TeV mass. The generated process contains the semileptonic final state
(p p > o1 > t t~, (t > b w+, w+ > l+ vl), (t~ > b~ w-, w- > j j)). Here you can find the cards.dat used (proc_card.dat, run_card.dat & param_card.dat). The produced samples have these features:

• MadGraph5_v1.3.33
• lhapdf_5.8.8b1(pdf=mstw2008 - lhapdf=21000)
• Ecm=8TeV
• ptj,pta,ptl=0 and ptjmax,ptamax,ptlmax=infinity

KKgluon

Graviton

Running the Full Chain

You can short circuit the Full Chain by using Atlfast, which provides a fast simulation of the whole chain by taking the generated events and smearing them to produce AOD directly. Atlfast can in fact take input from any of the event generator, simulation, digitization, or Event Summary Data (ESD) files.

Here are some commands to run the Full Chain step by step (at IFIC). This example is fot Athena's release 15.6.14.13:
Preparing the work environment:

~> ssh -X vicsanma@ui06.ific.uv.es   
~> source AthenaTestArea/15.6.14.13/cmthome/setup.sh -tag=AtlasProduction,15.6.14.13,setup            ###setup Athena  
~> get_files Evgen_trf.py         ### if you want Atlfast use EvgenCorrAtlfast_trf.py
~> get_files MC10.115554.Pythia_MadGraph_KKGluonTTbar_1000.py         ### here, the jobOptions which you need
~> get_files AtlasG4_trf.py
~> get_files Digi_trf.py
~> get_files Reco_trf.py

1. GENERATION: If you need to know what means every argument, you can run ~> Evgen_trf.py -h and then see all the options.

~> Evgen_trf.py --omitvalidation=testEventMinMax ecmEnergy=7000. runNumber=115554 firstEvent=1 maxEvents=10 randomSeed=1324354657 jobConfig=MC10.115554.Pythia_MadGraph_KKGluonTTbar_1000.py outputEvgenFile=pythia.pool.root inputgeneratorfile=group10.phys-gener.madgraph.115554.KKGluonTTbar1000.TXT.v1._00001.tar > athena_gen.out 2>&1

2. SIMULATION:

~> AtlasG4_trf.py inputEvgenFile=pythia.pool.root outputHitsFile=g4hits.pool.root maxEvents=10 skipEvents=0 randomSeed=1234 geometryVersion=ATLAS-GEO-16-00-00 conditionsTag=OFLCOND-SIM-BS7T-02  > athena_sim.out 2>&1

3. DIGITIZATION:

~> Digi_trf.py inputHitsFile=g4hits.pool.root outputRDOFile=g4digi.pool.root maxEvents=10 skipEvents=0 geometryVersion=ATLAS-GEO-16-00-00 conditionsTag=OFLCOND-DR-BS7T-ANom-16  > athena_digi.out 2>&1

4. RECONSTRUCTION:

~> Reco_trf.py  inputRDOFile=g4digi.pool.root outputESDFile=esd.pool.root maxEvents=10 skipEvents=0 geometryVersion=ATLAS-GEO-16-00-00 conditionsTag=OFLCOND-DR-BS7T-ANom-16 autoConfiguration='everything'  > athena_rec.out 2>&1

5. PRODUCTION-AOD:

~> Reco_trf.py  inputESDFile=esd.pool.root outputAODFile=aod.pool.root maxEvents=10 skipEvents=0 geometryVersion=ATLAS-GEO-16-00-00 conditionsTag=OFLCOND-DR-BS7T-ANom-16 autoConfiguration='everything' > athena_aod.out 2>&1

Creating a dataset

1. Changing the particles's code. You have to replace all the KKG's codes in the file.lhe. You can do it in two ways:

• From an editor:

         ~> emacs test_kkg_unweighted_events.lhe &   
         ### Edit -> Search -> Replace
         ### 6000048 EnterKey 5100021 EnterKey !key
         ### close emacs

• From a shell:

         ~> sed 's/6000048/5100021/' test_kkg_unweighted_events.lhe > new_test_kkg_unweighted_events.lhe
         ~> rm test_kkg_unweighted_events.lhe
         ~> mv new_test_kkg_unweighted_events.lhe test_kkg_unweighted_events.lhe

2. Changing the file's name and extension. The following steps should be performed.

~> mv test_kkg_unweighted_events.lhe group10.phys-gener.madgraph.115554.KKGluonTTbar1000.TXT.v1._00001.events
   ###this last name is inside the jobOptions MC10.115554.Pythia_MadGraph_KKGluonTTbar_1000.py
~> tar -cvf group10.phys-gener.madgraph.115554.KKGluonTTbar1000.TXT.v1._00001.tar group10.phys-gener.madgraph.115554.KKGluonTTbar1000.TXT.v1._00001.events
   ###be careful:   tar -cvf NAME.tar NAME.events   (no NAME.events.tar)

3. Creating a dataset. To create our dataset we are going to use DQ2, so we need to set up:

~> ssh -X vicsanma@ui06.ific.uv.es
~> voms-proxy-init -voms atlas   ### or    voms-proxy-init -voms atlas:/atlas/phys-gener/Role=production
~> source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh 

We change the value of local_site variable to store the dataset in IFIC's disk:

~> echo $DQ2_LOCAL_SITE_ID      ### probably is CERN-PROD_SCRATCHDISK
~> export DQ2_LOCAL_SITE_ID=IFIC-LCG2_SCRATCHDISK   ### IFIC-LCG2_LOCALGROUPDISK

To make tasks easier, let's create some variables:

~> NAME="group.phys-gener.${GENERATOR}.${DATASETNUMBER}.${DESCRIPTION}.TXT.${mcXY}_${VERSION}"
~> DATASET=${NAME}_i11
~> CONTAINER=${NAME}/
~> directory=/lustre/ific.uv.es/grid/atlas/t3/vicsanma/ALLsamples
~> uploaddirectory=${directory}/samples_kkg

We create the dataset in this way:

~> dq2-put -s ${uploaddirectory} ${DATASET}

To ensure that there is no problems with the file's names and datasets, we have to run a validation file (the file can be downloaded here here):

~> python validate_ds2eos.py ${NAME}

If all went fine, we can freeze the dataset (Make sure that when the dataset had been freezed, it must be like COMPLETE):

~> dq2-freeze-dataset ${DATASET}

Now we should register the dataset and the container (the latter is optional):

~> dq2-register-subscription ${DATASET} CERN-PROD_PHYS-GENER
~> dq2-register-container ${CONTAINER}
~> dq2-register-datasets-container ${CONTAINER} ${DATASET}

• If you want to add others datasets inside the container above:

~> dq2-register-datasets-container ${CONTAINER} Dataset_1 Dataset_2 Dataset_3

• If you need to remove a dataset from only a site:

~> dq2-delete-replicas DatasetName Site

• If you need to completely erase a dataset:

~> dq2-delete-replicas DatasetName Site

• If you need to change the dataset name you should do the following (beware, this step don't remove the old dataset, it creates a new one):

~> dq2-put -D OLDdatasetName NEWdatasetName
~> 0-20   ###here you have to put the files what you want (In this case, there are 20files and I want 20files)
~> y   ### yes
~> y   ###yes

Using a Good Run List to handle real DATA and MC samples

Getting the suitable GRL

For example, if you are working with quark tops, you can "download" the GRL from:

YourUserName@ui06.ific.uv.es~> /afs/cern.ch/user/a/atlasdqm/www/grlgen/Top/

Setting up CMT

~> ssh -X vsanchez@lxplus.cern.ch
~> cd $HOME
~> mkdir -p GoodRunList/cmthome
~> cd GoodRunList/cmthome

2. Make your login requirements file - use your favorite editor to create a file called requirements and paste these lines within it:

#---------------------------------------------------------------------
set CMTSITE CERN
set SITEROOT /afs/cern.ch
set ATLAS_DIST_AREA ${SITEROOT}/atlas/software/dist
macro ATLAS_TEST_AREA ${HOME}/GoodRunList/scratch0/15.6.4
apply_tag 32
apply_tag AtlasOffline
apply_tag setupCMT
apply_tag setup
apply_tag oneTest
apply_tag simpleTest
use AtlasLogin AtlasLogin-* $(ATLAS_DIST_AREA)
#---------------------------------------------------------------------

Note: Line 4 (macro ATLAS_TEST_AREA): Change the path so that it points to wherever you want to work. If you have scratch space (by default at CERN this is called scratch0) it is recommended that you work in there. Of course if you want to make a new directory inside this space, that is fine.

Save and exit this file

3. Now set up CMT as follows:

~> source /afs/cern.ch/sw/contrib/CMT/v1r20p20090520/mgr/setup.sh
~> cmt config

4. And then make a working directory:

~> mkdir -p $HOME/GoodRunList/scratch0/15.6.4

You only have to do this once.

5. Now you can setup release 15.6.4

~> cd $HOME
~> source GoodRunList/cmthome/setup.sh -tag=15.6.4,32

This you will have to do every time you want to use your new release. See also the next section.

Now check your environment:

~> echo $CMTPATH

Then:

~> echo $TestArea

6. Go into your $TestArea, now we can install the good run list package(s).

Setting up the good run list package(s)

~> cd $HOME
~> source GoodRunList/cmthome/setup.sh -tag=15.6.4,32
~> cd $TestArea

2. Now we check out the recommended version of the good run list and related packages. If you are working on a remote installation, do not forget to get a Kerberos ticket:

~> kinit -5 CernUserName      ###put the password once.

~> cmt co -r GoodRunsListsUser-00-00-12 DataQuality/GoodRunsListsUser
~> cmt co -r GoodRunsLists-00-00-96 DataQuality/GoodRunsLists
~> cmt co -r LumiBlockComps-00-02-11 LumiBlock/LumiBlockComps
~> cmt co -r CoolRunQuery-00-03-35 Database/CoolRunQuery

3. Now we can compile:

~> cd $TestArea/Database/CoolRunQuery/cmt/
~> cmt make; source setup.sh
~> cd $TestArea/DataQuality/GoodRunsLists/cmt/
~> cmt make; source setup.sh
~> cd $TestArea/LumiBlock/LumiBlockComps/cmt/
~> cmt make; source setup.sh
~> cd $TestArea/DataQuality/GoodRunsListsUser/cmt/
~> cmt make; source setup.sh

4. It is useful to make the script init.sh. Open your favorite editor to create init.sh, and insert the lines:

~> echo $TestArea
~> source $HOME/GoodRunList/cmthome/setup.sh -tag=15.6.4,32
~> source $TestArea/Database/CoolRunQuery/cmt/setup.sh
~> source $TestArea/DataQuality/GoodRunsLists/cmt/setup.sh
~> source $TestArea/LumiBlock/LumiBlockComps/cmt/setup.sh
~> source $TestArea/DataQuality/GoodRunsListsUser/cmt/setup.sh
~> cd $TestArea

5. You are now ready to use the good run list tools!

t-tbar asymmetries

• Workshop@CERN - Top physics: from charge asymmetry to the boosted regime (from 02/05/2012 to 04/05/2012).
• Summary of the article A charge asymmetry measurement for high mass t-tbar pairs (ATL-COM-PHYS-2012-786, not yet published) - slides in English or Spanish.

At hadron colliders, perturbative QCD predicts that the top quark will be emitted preferentialy in the direction of the incoming valence quark and the antitop in the direction of the incoming sea antiquark. Although ttbar production is predicted to be symmetric under charge conjugation at leading order (LO), at next-to-leading order (NLO) the processes q qbar → t tbar g (FSR) and q g → t tbar q (ISR) exhibit a small asymmetry in the differential distributions of the top and antitop, due to interference between initial (ISR) and final (FSR) state gluon emission (negative contribution to our signal, ttbar+1jet). The q qbar → t tbar process also possesses an asymmetry due to the interference between the Born and box diagrams (positive contribution, ttbar+0jet).

To compute the charge asymmetry, is necessary to count tops (or leptons) with specific properties (i.e, rapidity positive or negative, high transverse momentum...). If this count is done at central region of detector, it arises a net charge asymmetry called central charge asymmetry. This is defined as follows:

However, ATLAS and CMS collaboration use the charge asymmetry:

If we want to measure the lepton charge asymmetry, using leptons produced at top decay, we must take care because the central charge asymmetry can only be measured in dileptonic final states.

More... ToDo

Handling real data samples

MakeClass

~> cd folderSamples/
~> root data_K_mu.ntuple_all.root
root [1] t2->MakeClass("ClassVIKI");         ### ClassVIKI.C and ClassVIKI.h are the files created by this function
root [2] .L ClassVIKI.C
root [3] ClassVIKI* t = new ClassVIKI;
root [4] t->Loop();
root [5] .q

~> emacs ClassVIKI.C &
~> emacs ClassVIKI.h &
~> root -l -q ClassVIKI.C+
~> 
~> root
root [1] .L ClassVIKI.C
root [2] ClassVIKI* t = new ClassVIKI; t->Loop();

Running Ganga locally

~> ssh -X vicsanma@ui06.ific.uv.es
~> cd /lustre/ific.uv.es/grid/atlas/t3/vicsanma/Asymmetries
~> root data_K_mu.ntuple_all.root
root [1] t2->MakeClass("ClassVIKIui");         ### ClassVIKIui.C and ClassVIKIui.h are the files created by this function
root [2] .L ClassVIKIui.C
root [3] ClassVIKIui* t = new ClassVIKIui;
root [4] t->Loop();
root [5] .q

~> emacs ClassVIKIui.C &     
   ### let's save the histogram/canvas at the end of the file:
      c1->Write();///LNA
      c1->Update();  
      c1->SaveSource("canvas_ASYMMETRYhistui.C");
~> emacs ClassVIKIui.h &
~> root -l -q ClassVIKIui.C+

~> root
root [1] .L ClassVIKIui.C
root [2] ClassVIKIui* t = new ClassVIKIui; t->Loop();

Inside the ClassVIKI.h the following lines should be modified:
TFile f = (TFile)gROOT->GetListOfFiles()->FindObject("/lustre/ific.uv.es/grid/atlas/t3/sgonzale/elena/data_E_mu.ntuple_all.root");
if (f) {
f = new TFile("/lustre/ific.uv.es/grid/atlas/t3/sgonzale/elena/data_E_mu.ntuple_all.root");
}

Is necessary to create a Root and Ganga scripts, called ClassVIKI.h and ClassVIKI.h, for instance.

The ejecutar.C file is like this:

###---------------------------------------------------------------------
#include <iostream>
#include <string>

void ejecutar()
{
  gROOT->ProcessLine(".L ClassVIKIui.C");
  ClassVIKIui* t = new ClassVIKIui; t->Loop();                 
}
###---------------------------------------------------------------------

The LocalRoot.py file is like this:

###---------------------------------------------------------------------
j = Job()
j.name='Exercice Root'

j.application=Root()
j.application.script='ejecutar.C'
j.application.version='5.30.01'
j.inputsandbox=['ClassVIKIui.C','ClassVIKIui_C.so','ClassVIKIui_C.d','ClassVIKIui.h']

j.outputsandbox=['output.test.root']

j.backend=Local()

j.submit()
###---------------------------------------------------------------------

Now we are able to run our scripts, doing the following:

### set up Root
~> source /lustre/ific.uv.es/sw/ific/sw/root/5.30.01/slc5_amd64_gcc41/root/bin/thisroot.sh

### set up Ganga
~> source /afs/ific.uv.es/project/atlas/software/ganga/install/etc/setup-atlas.sh  
~> export GANGA_CONFIG_PATH=GangaAtlas/Atlas.ini

~> root -l -q ClassVIKI.C+
~> ganga LocalRoot.py

~> ganga
In [1]: jobs
In [2]: jobs(XYZ).peek('stderr','more')      ###to see the out errors
In [3]: jobs(XYZ).peek('stdout','more')      ###to see the screen output
In [4]: jobs(XYZ).peek('output.test.root','root -l')
In [5]: ctrl+D
 
~> cd /afs/ific.uv.es/user/v/vicsanma/gangadir/workspace/vicsanma/LocalXML/XYZ/output/
~> root output.test.root
root [1] TBrowser V;

If we've run several jobs with differents inputs (data samples), we can merge all the outputs output.test.root as follow:

~> cd DirectoryChoosed
~> hadd output.ALLtest.root $HOME/gangadir/workspace/vicsanma/LocalXML/*/output/output.test.root

My study

• ClassVIKIui.C
• ClassVIKIui.h
• ejecutar.C
• LocalRoot.py
• output.test.root
• ejecutarGrid.C
• GridRoot.py
• macro_allCanvas.C

TopRootCore & TopD3PDBoosted - 2011

To download the TopRootCore package (release 11-00-00-05) we are going to work at lxplus. The necessary steps are:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh   ### This script is below
~> export CERN_USER=vsanchez
~> mkdir TopRootCore-2011 && cd TopRootCore-2011
~> svn co svn+ssh://$CERN_USER@svn.cern.ch/reps/atlasoff/PhysicsAnalysis/TopPhys/TopRootCoreRelease/tags/TopRootCoreRelease-11-00-00-05/ TopRootCoreRelease-11-00-00-05
~> cd
~> cd TopRootCore-2011/TopRootCoreRelease-11-00-00-05/share
~> ./build-all.sh
~> exit

Every time you want to use TopRootCore for data and mc 2011, you must set up this one:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> cd TopRootCore-2011/
~> cd RootCore/scripts/
~> source setup.sh
~> cd ../../

To check TRC works correctly, we are going to run a litle example. I prefer to run code in a separate run directory, which we will need to setup with links to the data files and the binaries:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> cd TopRootCore-2011/
~> mkdir run && cd run
~> ln -s ../RootCore/data .
~> ln -s ../TopD3PDAnalysis/control .
~> ln -s ../TopD3PDAnalysis/bin .
~> cd ../
~> source RootCore/scripts/setup.sh  
~> 
~> cd PackageToCompile/
~> cd /cmt
~> make -f Makefile.RootCore

We need to put the input file at file_list.txt.

~> cd TopRootCore-2011/run/   ###VERY IMPORTANT!!! Be sure you are at run/ directory when you run the cut-flow
~> cp control/file_list.txt .
~> emacs file_list.txt &   ### add the NTUP*.root name and NEW LINE!!!
~> 
~> DATASET=mc11_7TeV.105200.T1_McAtNlo_Jimmy.merge.NTUP_TOPBOOST.e835_s1272_s1274_r3043_r2993_p841_tid706226_00
~> FILE=NTUP_TOPBOOST.706226._000961.root.1
~> dq2-get -f $FILE $DATASET
~> 
~> mkdir OUT_mc11_$FILE
~> 
~> CutFlow -f file_list.txt -o OutputHistos_CutFlow.root -mcType mc11c -p control/settings.txt > outTable_CutFlow.txt
~> CutFlowCorr -f file_list.txt -o OutputHistos_CutFlowCorr.root -mcType mc11c -p control/settings.txt > outTable_CutFlowCorr.txt
~> 
~> mv OutputHistos_CutFlow.root OUT_mc11_$FILE/
~> mv outTable_CutFlow.txt OUT_mc11_$FILE/
~> mv OutputHistos_CutFlowCorr.root OUT_mc11_$FILE/
~> mv outTable_CutFlowCorr.txt OUT_mc11_$FILE/

To download the TopD3PDBoosted-11-00-15 package (see the official twiki page and the releases), we have to run:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> export CERN_USER=vsanchez
~> cd TopRootCore-2011
###~> svn co svn+ssh://$CERN_USER@svn.cern.ch/reps/atlasoff/PhysicsAnalysis/TopPhys/TopD3PDBoosted/tags/TopD3PDBoosted-11-00-15/ TopD3PDBoosted
~> svn co svn+ssh://$CERN_USER@svn.cern.ch/reps/atlasoff/PhysicsAnalysis/TopPhys/TopD3PDBoosted/tags/TopD3PDBoosted-11-00-15/ TopD3PDBoosted-11-00-15
~> 
~> cd
###~> cd TopRootCore-2011/TopD3PDBoosted/FilesToReplace
~> cd TopRootCore-2011/TopD3PDBoosted-11-00-15/FilesToReplace
~> cd seedToolRelated_TopD3PDCorr
~> source cp.sh
~> cd ../TopAnalysisBase
~> source cp.sh
~> cd ../TopD3PDSelection
~> source cp.sh
~> 
~> cd
~> cd TopRootCore-2011/TopRootCoreRelease-11-00-00-05/share
~> ./build-all.sh
~> 
~> exit

Running BoostedCutFlow 2011

To run locally an example, you can get a file and save it at your lxplus' /tmp/:

~> ssh -Y vsanchez@lxplus303.cern.ch
~> cd /tmp/vsancehz/samples/MC
~> FILE=NTUP_TOPBOOST.706226._000961.root.1
~> DATASET=mc11_7TeV.105200.T1_McAtNlo_Jimmy.merge.NTUP_TOPBOOST.e835_s1272_s1274_r3043_r2993_p841_tid706226_00 
~> CONTAINER=mc11_7TeV.105200.T1_McAtNlo_Jimmy.merge.NTUP_TOPBOOST.e835_s1272_s1274_r3043_r2993_p841/
~> dq2-get -f $FILE $DATASET
           ### ~> FILE=NTUP_TOP.00993413._000001.root.1
           ### ~> DATASET=mc12_8TeV.105200.McAtNloJimmy_CT10_ttbar_LeptonFilter.merge.NTUP_TOP.e1193_s1469_s1470_r3542_r3549_p1230_tid00993413_00
           ### ~> CONTAINER=

Every time you do some change in the files, you should compile the package: [@lxplus303]~>

~> cd TopRootCore-2011/
~> ./RootCore/scripts/compile.sh   ###to compile all the packages
~> 
~> cd TopRootCore-2011/FOLDERtoCOMPILE/cmt/
~> make -f Makefile.RootCore

Running MC (NO correction) 2011:

~> BoostedCutFlow -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger
                            ### BoostedCutFlow -f mc_ch_file.txt -mcType mc12 -boost -rndmType debug

• Debug will operate with SeedTool, due to the replace of files. (no correction)
• When jetTrigger is not specify then lepTrigger is the default one.

Running Data (NO correction) 2011:

~> BoostedCutFlow -f mc_ch_file.txt -boost -jetTrigger

Running D3PD2MiniSLBoost 2011

~> ./D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger

• Debug will operate with SeedTool, due to the replace of files. (no correction)
• When jetTrigger is not specify then lepTrigger is the default one.

Running Data 2011:

~> ./D3PD2MiniSLBoost -f Data_file_list.txt -boost -jetTrigger

• This will produce a mini NTUP
• Same as running on the grid.
• Too add new variables go you, do it al a Root/MiniSLBoosted.cxx

VIKI

TopRootCore & TopD3PDBoosted - 2012

To download the TopRootCore package we are going to work at lxplus. The necessary steps are:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh   ### This script is below
~> export CERN_USER=vsanchez
~> mkdir TopRootCore-2012 && cd TopRootCore-2012
~> TRCR=TopRootCoreRelease-12-01-17
~> svn co svn+ssh://$CERN_USER@svn.cern.ch/reps/atlasoff/PhysicsAnalysis/TopPhys/TopRootCoreRelease/tags/$TRCR/ $TRCR
~> cd
~> cd TopRootCore-2012/$TRCR/share
~> ./build-all.sh
~> exit

The startRoot5-32.sh (or setRoot.sh) script is like this:
###---------------------------------------------------------------------
#!/bin/bash/

cd $HOME

source /afs/cern.ch/sw/lcg/contrib/gcc/4.3/x86_64-slc5/setup.sh
cd /afs/cern.ch/sw/lcg/app/releases/ROOT/5.32.00/x86_64-slc5-gcc43-opt/root/
source bin/thisroot.sh
#source /afs/cern.ch/sw/lcg/app/releases/ROOT/5.32.00/x86_64-slc5-gcc43-opt/root/bin/thisroot.sh

export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
export PATH=$ROOTSYS/bin:$PATH

cd $HOME
###---------------------------------------------------------------------

Every time you want to use TopRootCore, you must set up this one:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> cd TopRootCore-2012/
~> source RootCore/scripts/setup.sh

Every time you download a new package, you must compile it as:

ssh -Y vsanchez@lxplus303.cern.ch
~> cd cd TopRootCore-2012/PackageToCompile/
~> cd /cmt
~> make -f Makefile.RootCore

To check TRC works correctly, we are going to run a litle example. I prefer to run code in a separate run directory, which we will need to setup with links to the data files and the binaries:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> cd TopRootCore-2012/
~> mkdir run && cd run
~> ln -s ../RootCore/data .
~> ln -s ../TopD3PDAnalysis/control .
~> ln -s ../TopD3PDAnalysis/bin .
~> cd ../
~> source RootCore/scripts/setup.sh  
~> 
~> 
~> cd TopRootCore-2012/run/   ###VERY IMPORTANT!!! Be sure you are at run/ directory when you run the cut-flow
~> cp control/file_list.txt .
~> emacs file_list.txt &   ### add the NTUP*.root name and NEW LINE!!!
~> 
~> mkdir SAMPLES && cd SAMPLES/
~> DATASET=mc12_8TeV.105200.McAtNloJimmy_CT10_ttbar_LeptonFilter.merge.NTUP_TOP.e1193_s1469_s1470_r3542_r3549_p1230_tid00993413_00
~> FILE=NTUP_TOP.00993413._000001.root.1
~> dq2-get -f $FILE $DATASET
~> 
~> cd ../
~> mkdir OUT_CutFlow_mc12_$FILE
~> 
~> CutFlow -f file_list.txt -o OutputHistos_CutFlow.root -mcType mc12 -p control/settings.txt > outTable_CutFlow.txt
~> mv OutputHistos_CutFlow.root OUT_CutFlow_mc12_$FILE/
~> mv outTable_CutFlow.txt OUT_CutFlow_mc12_$FILE/
~> 
~> CutFlowCorr -f file_list.txt -o OutputHistos_CutFlowCorr.root -mcType mc12 -p control/settings.txt > outTable_CutFlowCorr.txt
~> mv OutputHistos_CutFlowCorr.root OUT_CutFlow_mc12_$FILE/
~> mv outTable_CutFlowCorr.txt OUT_CutFlow_mc12_$FILE/

The TopD3PDBoosted package provides a single-lepton cut flow for the Boosted ttbar (%NTUPBOOST% D3PD's) event selection along with the reconstruction of the selected event to build the ttbar system. The package can be used by packing the D3PD information into the mini-EDM (event data model) defined in BoostedElectronSelection, BoostedMuonSelection, BoostedJetSelection and FatJetSelection classes.

Works!!! 11-Dec-2012 To download the TopD3PDBoosted-12-00-08 package (see the official twiki page and the releases), we have to run:

ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
### If you are using TopRootCoreRelease-12-01-04, TopD3PDBoosted-12-00-08 is INSIDE the package!
###~> cd TopRootCore-2012
###~> svn co svn+ssh://vsanchez@svn.cern.ch/reps/atlasoff/PhysicsAnalysis/TopPhys/TopD3PDBoosted/tags/TopD3PDBoosted-12-00-09 TopD3PDBoosted
###~> cd
###~> cd TopRootCore-2012/TopD3PDBoosted/FilesToReplace
###~> cd 2012/
###~> cd seedToolRelated_TopD3PDCorr
###~> source cp.sh
###~> cd ../TopAnalysisBase
###~> source cp.sh
###~> cd ../TopD3PDSelection2
###~> source cp.sh
###~> cd
~>
~> cd TopRootCore-2012/TopD3PDBoosted/FilesToReplace/2012/
~> source cpall.sh  ### WhichPeriod.cxx and WhichPeriodSvn.cxx must not be replaced. If these files are replaced, go into the folder which it contains, remove them and run "svn update"
~> cd 
~> 
~> cd TopRootCore-2012/TopRootCoreRelease-12-01-04/share
~> cp $HOME/TopRootCore-2012/TopD3PDBoosted/FilesToReplace/2012/packages.txt .
~> ./build-all.sh
~> exit

We need to create two new files (mc_ch_file.txt and Data_file_list.txt) with the full path of the files you want to run over, inside the run/ folder. Go at folder where are stored these files and do:

~> cd $HOME/samples
~> FILE=NTUP_TOP.00993413._000001.root.1
~> DATASET=mc12_8TeV.105200.McAtNloJimmy_CT10_ttbar_LeptonFilter.merge.NTUP_TOP.e1193_s1469_s1470_r3542_r3549_p1230_tid00993413_00
~> dq2-get -f $FILE $DATASET   ### or ### dq2-get -n1 $DATASET
~> 
~> DATASETmc=XXXXXXXXX
~> cd $DATASETmc
~> echo $PWD > mc_ch_file.txt
~> emacs mc_ch_file.txt &   ### add the NTUP*.root name and NEW LINE!!!
~> cp mc_ch_file.txt $HOME/TopRootCore-2012/run/
~> 
~> DATASETdata=XXXXXXXXX
~> cd $DATASETdata
~> echo $PWD > Data_file_list.txt
~> emacs Data_file_list.txt &   ### add the NTUP*.root name
~> cp Data_file_list.txt $HOME/TopRootCore-2012/run/

To run locally an example, you can get a file and save it at your lxplus' /tmp/:

~> ssh -Y vsanchez@lxplus303.cern.ch
~> cd /tmp/vsancehz/samples/MC
~> FILE=NTUP_TOP.00993413._000001.root.1
~> DATASET=mc12_8TeV.105200.McAtNloJimmy_CT10_ttbar_LeptonFilter.merge.NTUP_TOP.e1193_s1469_s1470_r3542_r3549_p1230_tid00993413_00
~> dq2-get -f $FILE $DATASET   ### or ### dq2-get -n1 $DATASET
           ### ~> FILE=NTUP_TOPBOOST.706226._000961.root.1
           ### ~> DATASET=mc11_7TeV.105200.T1_McAtNlo_Jimmy.merge.NTUP_TOPBOOST.e835_s1272_s1274_r3043_r2993_p841_tid706226_00
           ### ~> CONTAINER=mc11_7TeV.105200.T1_McAtNlo_Jimmy.merge.NTUP_TOPBOOST.e835_s1272_s1274_r3043_r2993_p841/

Every time you do some change in the files, you should compile the package: [@lxplus403]~>

~> cd TopRootCore-2012/
~> ./RootCore/scripts/compile.sh   ###to compile all the packages
~> 
~> cd TopRootCore-2012/FOLDERtoCOMPILE/cmt/
~> make -f Makefile.RootCore

Running BoostedCutFlow

Be sure you are at run/ folder and you've done the TRC and ROOT set up:

~> ssh -Y vsanchez@lxplus303.cern.ch
~> source startRoot5-32.sh
~> cd TopRootCore-2012
~> source RootCore/scripts/setup.sh
~> cd run/

Running MC (NO correction):

~> BoostedCutFlow -f mc_ch_file.txt -boost -mcType mc12 -rndmType debug > OUTscreen.txt
### BoostedCutFlow -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger > OUTscreen.txt

• Debug will operate with SeedTool, due to the replace of files. (no correction)
• When jetTrigger is not specify then lepTrigger is the default one.

Running Data (NO correction):

~> BoostedCutFlow -f mc_ch_file.txt -boost   ### you can add -dataStream Egamma (or whatever you need)

Running D3PD2MiniSLBoost

~> D3PD2MiniSLBoost --help
---- Starting D3PD2MiniSL
 Usage: D3PD2MiniSLBoost [OPTION]
  The list of options are:
  -f <value>             input file list file (default: "control/file_list.txt")
  -h                print this message
  -mcType <value>      set the MC type (mc11b, mc11c, mc12, atlfast2) (default: use directory name.)
  -nf <value>               number of input files to consider (default: 1)
  -n <value>                maximum number of events to process (default: all events)
  -nocache                   turn off the TTreeCache, reduce read failures with DPM RFIO
  -o <value>                output ROOT file (default "OutputHistos.root")
  -i <value>                 index of the output file name (default nothing)
  -p <value>                parameters file (default: "control/settings.txt")
  -rndmType <value>   reseeding strategy (once, file, debug) (default: once)
  -skn <value>             number of events to skip (default: 0)
  -sknf <value>            number of files to skip (default: 0)
  -vin                            validate input files (default: false)
  -dataStream               data stream name: Egamma,Muons.   
  -useLooseElectrons    use loose lepton definition.   
  -useLooseMuonss      use loose lepton definition.   
  -boost                        use boosted branches (default: false)
  -JetTrigger                 use Jet Trigger      (default: false)
  -useTruthParticles      use TruthInfo or not (default: false)
  -useClusteris              use (default: false)
  -findEvent <value>    use this to run on one event number, this is good for debuging

Running boosted regime for MC and data:

~> D3PD2MiniSLBoost -f mc_file_list.txt -boost -mcType mc12 -rndmType debug  > OUTscreen2.txt
###~> D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -addGenerator > OUTscreen3.txt
###~> D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -useTruthParticles > OUTscreen4.txt

~> D3PD2MiniSLBoost -f data_file_list.txt -boost -dataStream "VAL" 

Running resolved regime for MC and data:

~> D3PD2MiniSLBoost -f MC_file_list.txt -mcType mc12 -rndmType debug 

~> D3PD2MiniSLBoost -f data_file_list.txt -dataStream "VAL" ###(same as above)

Running OLD:

~> D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger > OUTscreen2.txt
###~> D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger -addGenerator > OUTscreen3.txt
###~> D3PD2MiniSLBoost -f mc_ch_file.txt -rndmType debug -mcType mc12 -boost -jetTrigger -useTruParticles > OUTscreen4.txt

• Debug will operate with SeedTool, due to the replace of files. (no correction)
• When jetTrigger is not specify then lepTrigger is the default one.

~> ./D3PD2MiniSLBoost -f Data_file_list.txt -boost -jetTrigger

• This will produce a mini NTUP
• Same as running on the grid.
• Too add new variables go you, do it al a Root/MiniSLBoosted.cxx

Skimmed samples

My analysis with TopD3PDBoosted & TopRootCore

.git Repository (IFIC-IFAE)

Input files

~> ssh -Y vsanchez@lxplus403.cern.ch
~> asetup 16.7.0   ### if this doesn't work, try with "asetup 17.0.0"
~> cd /tmp/vsanchez/IFAE
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/asymmetry_ntuples
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/asymmetry_ntuples/Histogrammer-01-15-02.tgz .
~> tar -xvf Histogrammer-01-15-02.tgz
~> cd Histogrammer-01-15-02
~> cd nominal
~> ls MUON/Dibosons_MUON_OutputHisto.root   ### for instance

If this doesn't work, I have saved a copy in my laptop:

MAC~> cd $HOME/Analysis/IFIC_IFAE/git_repositories
MAC~> scp Histogrammer-01-15-02.tgz vsanchez@lxplus403.cern.ch:/tmp/vsanchez/IFAE 

The code

~> ssh -Y vsanchez@lxplus403.cern.ch
~> asetup 16.7.0   ### if this doesn't work, try with "asetup 17.0.0"
~> cd IFIC_IFAE/asymmetry.git/asymmetryAtlas
~> 
~> git checkout -b branchVIKI   ### VERY IMPORTANT
~> emacs python/setup.py &   ### add Location en L10
~> emacs python/Histogrammer.py &   ### add hetaleptoncharge
~> emacs python/analyzer.py &   ### add hetaleptoncharge
~> git commit -m 'change A,B' python/setup.py
~> git commit -m 'change A,B' python/ Histogrammer.py
~> git commit -m 'change A,B' python/ analyzer.py
~> 
~> python python/analyzer.py nominal

Output files

~> ssh -Y vsanchez@lxplus403.cern.ch
~> asetup 16.7.0   ### if this doesn't work, try with "asetup 17.0.0"
~> cd IFIC_IFAE/asymmetry.git/asymmetryAtlas
~> cd plots/nominal
~> ls muon/*.root
~> ls muon/*.png

To copy the output files in my laptop:

MAC~> cd $HOME/Analysis/IFIC_IFAE/git_repositories/out_asymmetryAtlas/
MAC~> scp vsanchez@lxplus403.cern.ch:/afs/cern.ch/user/v/vsanchez/IFIC_IFAE/asymmetry.git/asymmetryAtlas/plots/nominal/muon/*.png .
MAC~> open *.png

Useful macros

If you want to create a file.root (like a ntuple) from a file.lhe (MadGraph's output), you must use this package (createFileRoot) and run:

~> cd createFileRoot/
~> make
~> ./plot_top_marcel
         

If you have several samples with similar name (for instance, testName.generator.X.Y.lhe, with X=1,2,3....10 and Y=10,20,30,40,50), you can change file's names (for example, NewTestName.user.X.Y.lhe) with this program. Whether if these samples has been generated with MadGraph or Pythia, you can also change the particle's code. Also, if you want to merge all these samples, you can use this script.

When you want to compare a DATA sample with the equivalent MC samples, you must take into account the integrated luminosity, the cross section and the total number of events produced in MC to compute a "scale factor". This factor is necessary to compare DATA with MC. Here there is a small program which allow you to do so.

If you have several ntuples with different extension to .root, for instance .root1 or .root__DQ2_748574, you can change all these extensions to be equal to .root with this executable file (you have to remove the extension .txt), and then merge all ntuples. The following steps should be performed:

~> ssh -X vicsanma@ui06.ific.uv.es
~> cd $DIRECTORY      #it may be /tmp/ or /T3/, and it should contain extension.py
~> cp /way/ALLfiles.root* .
~> python extension.py      #here you are running the executable file downloaded
         

To draw a concrete branches from differents ntuples, it means, with data, with background, with your signal... you can use this macro, or if you only need to compare two branches with a given cut, use this one. Be careful to change all file names, its path...

To create a dataset registered in DQ2 with D4PD which are stored in T3 space (script).

To reduce the number of branches in a D3PD and add new ones, use this package, it contains a MakeFile.

To compile a MakeClass files (.C and .h) with a Makefile, you can use one of these packages: packageLOCAL or packageGRID. With local-package, only run source cppmake.sh; ./skimD3PD_addTRUTHbranch. With grid-package, only run source runPRUN.sh.

If....

fbu 0.0.1

• FBU package - actual FBU python module
• histo2json.py - code to build the json inputs

• quickstart - quick start instructions -->
• tutorial - Simple tutorial -->
• source - to download fbu-0.0.1.tar.gz (md5) -->

To do the first time:

cd /afs/cern.ch/work/v/vsanchez/
virtualenv fbu
cd fbu
source bin/activate
pip install numpy==1.7.0
pip install fbu
### git clone https://github.com/gerbaudo/fbu.git (Alternatively one can check out the development version of the code from the GitHub repository)
### cat requirements.txt | xargs pip install
### python tests/pymc_test/unfold.py

To do from then on:

cd /afs/cern.ch/work/v/vsanchez/fbu
source bin/activate
...
...
... 
bin/deactivate

eos

~> ssh -Y vsanchez@lxplus403.cern.ch  
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/TRC
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/VALIDATION
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/asymmetry_ntuples
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/MatchingSTUDY
~> 
~> 
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/validationWITHjets.tar .
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/7TeV/validation_vsm_MatchingStudy.tar .
~> 
~> FILE=Plots_test1.tar
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/MatchingSTUDY/7TeV
~> xrdcp $FILE root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/7TeV/$FILE
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/7TeV/$FILE .
~> 
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV
~> xrdcp $FILE root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV/$FILE
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV/$FILE .
~> 
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV/mass500
~> xrdcp $FILE root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV/mass500/$FILE
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/MatchingSTUDY/8TeV/mass500/$FILE .
~> 
~> 
~> xrdcp FILE.tar root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/FOLDER/FILE.tar
~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/FOLDER/FILE.tar .
~> 
~> eos rm eos/atlas/user/v/vsanchez/FOLDER/FILEtoREMOVE.tar
~> eos rm -r eos/atlas/user/v/vsanchez/FOLDERtoREMOVE


~> xrdcp root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/TRC_testSamples_February2014/MC/117050/el.root .
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/TRC_testSamples_February2014/

~> eos mkdir /eos/atlas/user/v/vsanchez/Samples_AnalysisTop-1.5.0_June2014/Data/HadDelayed_Dominik
~> xrdcp $FILE root://eosatlas.cern.ch//eos/atlas/user/v/vsanchez/Samples_AnalysisTop-1.5.0_June2014/Data/HadDelayed_Dominik/$FILE
~> xrd eosatlas dirlist /eos/atlas/user/v/vsanchez/Samples_AnalysisTop-1.5.0_June2014/Data/HadDelayed_Dominik

Work space at CERN:

~>cd /afs/cern.ch/work/v/vsanchez
~>cd /afs/cern.ch/work/v/vsanchez/private
~>cd /afs/cern.ch/work/v/vsanchez/public

My Links

KK-gluon

• KKGluonTopAntiTop - Atlas Protected Web: twiki KKGluon Top-AntiTop
• PreparingLesHouchesEven - How to prepare external LesHouches compliant files for central grid production
• ExoticsMCRequestsHowTo - Guide for official Monte carlo production requests
• AMI - Dataset search

Athena

• AthenaMCExamples - Athena MonteCarlo examples
• WorkBook - The ATLAS Computing Workbook
• AtlasPythonTrf - Atlas Python JobTransforms
• MonteCarloProduction - Monte Carlo production
• AtlasProductionGroupMC10 - MC10 Production Campaign details
• SimuJobTransforms - Simulation Job Transforms
• Generation1530 - Generating Events with Athena Release 15.3.0
• AthenaFramework - Athena Framework
• DAGangaFAQ - Frequently Asked Question for Distributed Analysis using GANGA
• CoolProdTags - Cool Production Tags
• PandaAthena - How to submit Athena jobs to Panda
• RunningOnData - Running on REAL DATA

DQ2

• DQ2ClientsHowTo - DQ2 Clients How To
• InfoDq2 - Information dq2
• DDM - Distributed Data Management (DDM)
• DQ2ClientsTroubleshooting - DQ2 Clients Troubleshooting
• DQ2ClientsForAdvancedUsers - DQ2 Clients For Advanced Users

TopRootCore

• RootCore - RootCore twiki
• 2011PLHC - TopCommonObjects2011PLHC twiki
• TopRootCore - TopRootCore twiki
• TopMiniNtuple - TopMiniNtuple twiki
• TopD3PDSelection - TopD3PDSelection twiki
• TopD3PDCorrections - TopD3PDCorrections twiki
• Summer2011BoostedTopResonances - Summer2011BoostedTopResonances twiki
• ATLAStopCross-Section - Updated L+jets (AtlasPhysics-16.6.5.5.1)
• ATLAStopCross-Section - L+jets (TopPhys-16.6.3.5.1, PLHC)
• Setting_up_RootCore - Setting up RootCore

BoostedTopRootCore

• TopD3PDBoosted - TopD3PDBoosted twiki
• TopRootCoreRelease - TopRootCoreRelease twiki
• atlasoff - some new packages to add inside TopRootCore
• CLICK - description

ATLAS offline software tutorial

• COMPLETE - Complete tutorials.
• SoftwareTutorialSoftwareBasics - Software Basics Tutorial
• SoftwareTutorialPythonTutorial - Software Python Tutorial
• AMI_pyAMI - Using AMI and pyAMI
• DATA_MC - Getting DATA and MC with DQ2
• SetUpARA - Setting up an ARA session
• UsingARA - Using ARA to plot dat
• AnalyzingD3PDsRoot - Stand-alone D3PD Analysis
• MakingD3PDs - Making your own D3PDs
• AnalyzingD3PDsAthena - Athena for D3PD Analysis
• UsingGRID - The Grid
• MakingDAOD - Derived AOD
• AnalysisInAthena - Luminosity calculation and Athena-based analysis
• wsvn - (root)/PhysicsAnalysis/TopPhys/ - Rev 509493

Twiki rules

• DocumentationManagementTWikiRules - Twiki Rules
• TextFormattingRules - TWiki Text Formatting
• GoodStyle - Good Style Collaboration Tips
• TWikiPreferences - Level Preferences (colors)
• TWikiDocGraphics - TWiki Documentation Graphics and Filetype icons
• TWikiVariables - TWiki Variables
• SymbolsTable - Symbol table

By default

• ATasteOfTWiki - view a short introductory presentation on TWiki for beginners
• WelcomeGuest - starting points on TWiki
• TWikiUsersGuide - complete TWiki documentation, Quick Start to Reference
• Sandbox - try out TWiki on your own
• VictoriaSanchezMartinezSandbox^? - just for me
• ChangePassword for changing your password
• ChangeEmailAddress for changing your email address
• TWikiUsers has a list of other TWiki users
• CLICK^? - Description

.............................

Victoria Sánchez Martínez
--- IFIC ---
Edificio Institutos de Investigación
Paterna, apartado 22085
E-46071 Valencia (Spain)

.............................