(r45) AnalysisOpenSpace < Main

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---+!! Analysis Open Space

%TOC%

---++ Introdução

Este é um espaço para que sejam discutidas questões relacionadas a análises desenvolvidas no grupo do SPRACE. Objetivos e condutas gerais são:

   * Colocar para o grupo problemas de caráter técnico (CMSSW, ROOT, condorg, crab, etc...) ou físico (questões teóricas)
   * Todos estão convidados a responder/opinar sobre os problemas colocados
   * Perguntas e respostas devem ser mantidas na página para referência futura
   * Coloque seu nome entre parêntesis ao fazer uma pergunta ou dar uma resposta
Crie uma nova questão com =---+++= dentro da seção correspondente (CMSSW, ROOT, grid, ...) para que ela apareça no sumário no topo da página (como no Exemplo 1 abaixo).

---+++ Exemplo 1: Como uso !LaTeX no ROOT?

(Fulano) Preciso fazer o título de um gráfico com símbolo !LaTeX, como faço?

(Cicrano) É só usar # antes do comando (ao invés de usar /)

(Beutrano) Por exemplo =-&gt;SetTitle("#theta (graus)")=

(Fulano) Ok, resolvido

---++ CMSSW

---+++ How to skip bad files in a CMSSW job

(Thiago) Sometimes, a CMSSW job is running over hundreds of input files, and it happens that one of then is bad/corrupted/cannot be opened. To avoid the job from crashing, you can do the following in your configuration:

=process.source.skipBadFiles = cms.untracked.bool( True )=

Remember to check which files are bad and take action afterwards!

---+++ How to setup debugging symbols in CMSSW

(Thiago) The best thing you can do when you encounter seg faults is add debugging symbols to your compiled code. To do this, edit the BuildFile for the package that is crashing with the following line:

<verbatim><flags CXXFLAGS="-O0 -g3 -fno-inline"/></verbatim>

Then, recompile your package and re-run. This time, the stack trace should tell you a line number in one of your files where the error is occurring.

---+++ How to setup random seeds in the Python config file.

(Thiago) Add the following lines to your _cfg.py file:

<verbatim>
import uuid
import random
x = uuid.uuid4()
random.seed(x)
</verbatim>

and them, after you load the !RandomNumberGeneratorService (usually wish something like =process.load('Configuration.StandardSequences.Services_cff') )=, add:

<verbatim>
randService = process.RandomNumberGeneratorService
for param in [x for x in randService.parameterNames_()
             if type(getattr(randService, x)) == cms.PSet]:
   getattr(randService, param).initialSeed = random.randint(1,100000)
</verbatim>

---+++ How to find the corresponding Monte Carlo of a dataset

(Caio) I need to find a MC corresponding to a specific dataset. This MC must simulates detector conditions during datataking, as well as the physics of the collision. How to find it? In the specific case the dataset is:

=/MinimumBias/Run2010A-Apr21ReReco-v1/RECO= com =CMSSW_4_2_1_patch1= e global tag =FT_R_42_V10A=.

[[https://twiki.cern.ch/twiki/bin/viewauth/CMS/Collisions2010Analysis#Reprocessed_Collision_Datasets][Esse link]] tem informações sobre os dados de 2010 e [[https://twiki.cern.ch/twiki/bin/view/CMS/GeneratorProduction2010][esse outro]] sobre os MC, mas como relacionar esses dados com esses MCs? Qual MC corresponde a qual dado? Tem a ver com a estação do ano?

---+++ Finding datasets

(Caio) In CMS, data are found in the [[https://cmsweb.cern.ch/das/][DAS]] website, which is a better version of [[https://cmsweb.cern.ch/dbs_discovery/][DBS]]. Example of DAS commands for dataset search:

   * =dataset = /Min*Bias*TuneZ2*7TeV*pythia6*Summer11*AODSIM= (The star is the wildcard character, e.g. all of these are similar: "heavy_ion" "h*y_ion" "heav*y_ion" "heavy_ion*"
   * =dataset = /MinimumBias/Run2010A*AOD=
   * =block = /MinimumBias/Run2010A-Apr21ReReco-v1/AOD#f9fe2e80-703d-11e0-9135-003048f1c5d0=
   * =release dataset = *7TeV*pythia*GEN-SIM-RECO= Shows all CMSSW releases which have this dataset
   * =dataset release = CMSSW_4_2_1_patch1= Shows all the datasets which have his CMSSW release
   * =dataset site = T2_BR_SPRACE= Shows all datasets which are available in SPRACE

---+++ How to create my own track collection?

(Caio) I have a RAW-RECO data file and I would like to create a track collection, like the "generalTracks" one, but something along the lines of a "myTracks" collection, where I put only tracks which pass a certain set of requirements. I would like to save that "myTracks" collection in other data file to be run over with cmsRun. How can I do that?

(Thiago) Use the following EDFilter, with the parameters you want:

<verbatim>
process.myTracks = cms.EDFilter("RecoTrackSelector",
    src = cms.InputTag("generalTracks"),
    maxChi2 = cms.double(10000.0),
    tip = cms.double(120.0),
    minRapidity = cms.double(-5.0),
    lip = cms.double(300.0),
    ptMin = cms.double(0.1),
    maxRapidity = cms.double(5.0),
    quality = cms.vstring('loose'),
    algorithm = cms.vstring(),
    minHit = cms.int32(3),
    min3DHit = cms.int32(0),
    beamSpot = cms.InputTag("offlineBeamSpot")
)
</verbatim>

and add an !OutputModule to save your new tracks into the output file.

<verbatim>
process.out = cms.OutputModule("PoolOutputModule",
    fileName = cms.untracked.string('patTuple.root'),
    outputCommands = cms.untracked.vstring(
        'keep *_myTracks_*_*',
    )
)
</verbatim>

---++ ROOT

---+++ Changing the individual colors of entries in a TLegend

(Thiago) If you want to change the individual colors of entries in a TLegend (for matching the colors of the objects they're related to), use the following recipe:

<verbatim>
// Say that you have a valid pointer for the TLegend
TLegend* leg = (TLegend*)0x0000000106bcfe20;
// Get the list of entries
TList* list->GetListOfPrimitives();
// Get each entry individually
TLegendEntry* l1 = (TLegendEntry*)list->At(0);
TLegendEntry* l2 = (TLegendEntry*)list->At(1);
// Now you can set text attributes
l1->SetTextColor(kBlue)
l2->SetTextColor(kRed)
</verbatim>

---+++ N-dimensional histograms with ROOT

(Caio) I know its possible to make an up-to-10 dimensions using ROOT. How to declare it and manipulate its content? (Caio) N-dimensional histograms are declared using =THnSparse= as following:

<verbatim>
    //                 {qT, qL, kT,  Nch}
    Int_t bins[4] =    {40, 40, 100, 150};
    Double_t xmin[4] = {0., 0., 0.,  0.};
    Double_t xmax[4] = {2., 2., 5.,  150.};
    THnSparse *FourDHistogram = new THnSparseF("4d-hist", "4d-hist", 4, bins, xmin, xmax);
    FourDHistogram->Sumw2();
</verbatim>

The call of =Sumw2()= right after histogram creation is to store statistics error. Although N-dimensional histogram is useful, is will use a lot of space in memory. If it space goes beyond 4 GB (that happened to me in a 5D histo) your program will crash. The best way to manipulate Ntuples of data is using =TTree=.

---+++ Dois Pads num Canvas sem o espaço em branco

(Angelo) Já vi no ROOT casos em que dois Pads (um em cima do outro) aparecem num único Canvas, mas sem a linha branca que aparece entre dois Pads quando se usa, por exemplo:
<verbatim>
canvas->Divide(1,2)
canvas->cd(1)
canvas->cd(2)
</verbatim>

Por exemplo: o Pad superior mostraria dois histogramas (data/MC), enquanto que o inferior mostraria algo como "(Data - MC)/sigma". Acredito que não se trata de usar canvas-&gt;Divide(1,2). Porém, deve haver alguma forma de dizer onde começa e onde termina cada Pad. Alguma idéia?

(Caio) Estava fazendo uns testes e encontrei essa opção:

<verbatim>
//faz o seu Canvas
TCanvas *canvas = new TCanvas();
//depois cria dois Pads
TPad *pad1 = new TPad();
TPad *pad2 = new TPad();
//e desenha seus pads dentro do canvas
canvas->cd();
pad1->Draw();
pad2->Draw();
//os pads vao cobrir todo o canvas, precisa ir com o mouse e redimensionar eles
//note que o pad2 vai ficar por cima do pad1
//aí vc desenha seu gráfico principal no pad1
pad1->cd();
grafico->Draw("ap");
//e o de residuos no pad 2
pad2->cd();
residuos->Draw();
//ai tem que ajustar com o mouse pro pad2 ficar por cima do eixo-X do pad 1
</verbatim>

[[/twiki/bin/viewfile/Main/AnalysisOpenSpace?rev=1;filename=dois-pads-num-canvas.png][Esse gráfico]] é um exemplo de como as coisas podem ficar, e [[/twiki/bin/viewfile/Main/AnalysisOpenSpace?rev=1;filename=dois-pads-num-canvas.root][esse]] é o arquivo root correspondente. É uma solução meio grosseira, mas funcional. Alguma idéia melhor?

(Angelo) Após testar o seu método, achei uma novo caminho que permite fazer tudo automático sem a necessidade de usar o mouse. Basta colocar as dimensões correspondentes do pad usando Pad(), além de funcões como !SetTopMargin() e !SetBottomMargin():
<verbatim>
TCanvas *canvas = new TCanvas();
canvas->cd();
// Aqui você declara as dimensões do pad superior, por exemplo.
// A ordem correta é TPad("", "", xMin, yMin, xMax, yMax)
TPad *pad1 = new TPad("pad1","",0.,0.3,1.,1.);
pad1->Draw();
pad1->cd();
// Desapareça com que o espaço em branco na parte de baixo do pad superior.
pad1->SetBottomMargin(0.);
// Se preferir, apague o label e o título do eixo "x" do gráfico superior.
grafico1->GetXaxis()->SetLabelSize(0.);
grafico1->GetXaxis()->SetTitleSize(0.);
grafico1->Draw();
canvas->cd();
// Aqui o pad inferior é declarado.
// Veja que o eixo vertical ("y") do pad2 termina onde o pad1 começa.
TPad *pad2 = new TPad("pad2","",0.,0.,1.,0.3);
pad2->Draw();
pad2->cd();
// Desapareça com que o espaço em branco no top do pad inferior
pad2->SetTopMargin(0.0);
// Diga ao ROOT onde que o gráfico do pad inferior vai ser iniciado.
// Isto é importante para permitir que o label do eixo "x" apareça e não seja cortado.
pad2->SetBottomMargin(0.2);
// É provável que não seja possível ver o label do gráfico do pad2, pois pode
// estar automaticamente com tamanho "0".
// Caso isso acontença, forneça o tamanho do label e do título. Por exemplo:
grafico2->GetXaxis()->SetLabelSize(0.07);
grafico2->GetXaxis()->SetTitleSize(0.07);
grafico2->Draw();
</verbatim>

---+++ Como construir histogramas com bins não homogêneos?

(Angelo) Esse é um exemplo de como plotar histogramas com bins variáveis (Franciole's example):

<verbatim>
void variable_bin(){

  //histo with variable size bins

  //# of bins = 3 
  int nbins = 3;

  //# of edges. Includes the lowest and highest
  const int nedges = nbins+1;

  //Defines edges
  float xbins[nedges] = {0.0,1.0,3.0,6.0};

  //creates histo
  TH1F *hvar = new TH1F("hvar","hvar title",nbins,xbins);

  //Writes width of all bins
  //Note bin zero is reserved for other purposes (see ROOT documentation)
  //size will be equals to 1
  std::cout << "first bin size:  " << hvar->GetBinWidth(1) << std::endl;
  std::cout << "second bin size: " << hvar->GetBinWidth(2) << std::endl;
  std::cout << "third bin size:  " << hvar->GetBinWidth(3) << std::endl;
}
</verbatim>

---++ Grid

---+++ First login to =access= machine

To log on, use =ssh=

<verbatim> ssh <username>@access.sprace.org.br </verbatim>

Set up the CMS VO certificate according to instructions [[https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookStartingGrid#ObtainingCert][here]]. Verify it all works by executing

=voms-proxy-init --voms cms=

To navigate through the =T2_BR_SPRACE= storage use =srmls= command

<verbatim>srmls srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/<username></verbatim>

More useful =srm= commands [[https://www.sprace.org.br/twiki/bin/view/Main/AnalysisOpenSpace#Useful_srmcp_commands][here]].

---+++ Using =condorg=

(Franciole) Temos utilizado o cluster com o condorg para fazer parte de nossas analises. Os jobs variam desde producao de ntuplas, pequenas producoes de MC, codigos privados do ROOT e por ai vai. No entanto, temos cada um uma solucao particular para seu problema. Sera que poderiamos partilhar essas solucoes? Sera que isso ajudaria num futuro proximo?

(Caio) I create a TTree with cmsRun and then run ROOT over it using =condor=. This is the way how to do that:

tar-compact the area where your ROOT macro are. The TTree might be in this directory or it can be in the storage element.

=tar -czvf CMSSW_3_6_2.tgz CMSSW_3_6_2/=

then gets proxy

=grid-proxy-init -debug -verify=

=voms-proxy-init -voms cms=

and submit the job with

=condor_submit condor_run=

The script I pass to =condor= to run ROOT is [[/twiki/bin/viewfile/Main/AnalysisOpenSpace?rev=2;filename=condor_ROOT][this]]. (see [[http://aurelio.net/shell/canivete/][this link]] for useful information about bash programming). [[/twiki/bin/viewfile/Main/AnalysisOpenSpace?rev=1;filename=condor_run_root][This]] is the condor configuration file (might be obsolete, not sure).

(Cesar) Eu utilizo um script similar a esse do Caio para executar o cmsRun com o condor_g ([[/twiki/bin/viewfile/Main/AnalysisOpenSpace?rev=1;filename=condor_test][condor_test]]). Testei uns dois dias atrás e funcionou na versão CMSSW_4_2_5. O arquivo de configuração no caso lê um arquivo .root do dCache. Não consegui fazer funcionar quando o aquivo .root está na tarball, ou seja, em um dos subdiretórios do CMSSW (Alguém tem alguma idéia? Já tentei usar =$WORKING_DIR/CMSSW_4_2_5/src/flatTuple/patTuple_PATandPF2PAT.root= e =$IWD/CMSSW_4_2_5/src/flatTuple/patTuple_PATandPF2PAT.root=, uma vez que o caminho na access, por exemplo, seria =/home/bernardes/CMSSW_4_2_5/src/flatTuple/patTuple_PATandPF2PAT.root=). A solução encontrada no momento foi copiar o arquivo para meu diretório no dCache, usando:

=srmcp -2= file:///CMSSW_4_2_5/src/flatTuple/patTuple_PATandPF2PAT.root srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/caber/te st/patTuple_PATandPF2PAT.root

---+++ Opening files in =dcap=

(Caio) It is possible to open ROOT with a file in =dcap= as paremeter. The syntax (thanks to Marco) is given in the following example, where the file =7TeV_Jul16th_Tree_All+-Tracks_2Nch150_noSplitTracks-beamSpot_Rxy.root= is opened

<verbatim>
root dcap://osg-se.sprace.org.br:/pnfs/sprace.org.br/data/cms/store/user/lagana/7TeV_Jul16th_Tree_All+-Tracks_2Nch150_noSplitTracks-beamSpot_Rxy.root
root [0] 
Attaching file dcap://osg-se.sprace.org.br:/pnfs/sprace.org.br/data/cms/store/user/lagana/7TeV_Jul16th_Tree_All+-Tracks_2Nch150_noSplitTracks-beamSpot_Rxy.root as _file0...
root [2] _file0->ls()
TDCacheFile**           dcap://osg-se.sprace.org.br/pnfs/sprace.org.br/data/cms/store/user/lagana/7TeV_Jul16th_Tree_All+-Tracks_2Nch150_noSplitTracks-beamSpot_Rxy.root
 TDCacheFile*           dcap://osg-se.sprace.org.br/pnfs/sprace.org.br/data/cms/store/user/lagana/7TeV_Jul16th_Tree_All+-Tracks_2Nch150_noSplitTracks-beamSpot_Rxy.root
  KEY: TTree    track_tree;2    track_tree
  KEY: TTree    track_tree;1    track_tree
  KEY: TH1F     Rxy;1   Rxy
  KEY: TTree    ev_tree;1       ev_tree
</verbatim>

---+++ Useful =srmcp= commands

These are some useful =srm= commands

<verbatim>
voms-proxy-init --voms cms
</verbatim>

   * Listing files at T2_SPRACE
<verbatim>
 srmls srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3
</verbatim>

   * Making a new directory at T2_SPRACE
<verbatim>
srmmkdir srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3
</verbatim>

   * Copying from T2_SPRACE to directory at access
<verbatim>
srmcp srm://osg-se.sprace.org.br:8443/pnfs/sprace.org.br/data/cms/store/himc/Fall10/Hydjet_Quenched_MinBias_2760GeV/GEN-SIM-RECO/Pyquen_GammaJet_pt15_MC_38Y_V12-v2/0001//2439BAA1-FDDF-DF11-ACC0-001D096760DE.root file:////home/lagana/2439BAA1-FDDF-DF11-ACC0-001D096760DE.root
</verbatim>

   * Copying from directory at access to T2_SPRACE
<verbatim>
srmcp -2 file:///rootlogon.C srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/rootlogon.C
</verbatim>

   * Copying from castor to SPRACE:
<verbatim>
srmcp --debug=true  -srm_protocol_version=2 srm://srm-cms.cern.ch:8443/srm/managerv2?SFN=/castor/cern.ch/user/m/mohammed/MC_PYTHIA8/edmfile_9900.root file:////home/lagana/edmfile_9900.root
</verbatim>

   * Listing files at T2_MIT
<verbatim>
srmls -2 srm://se01.cmsaf.mit.edu:8443/srm/v2/server?SFN=/mnt/hadoop/cms/store/user/davidlw/MinimumBias/
</verbatim>

   * Copying 1 file from T2_MIT to T2_SPRACE
<verbatim>
srmcp -2 srm://se01.cmsaf.mit.edu:8443/srm/v2/server?SFN=/mnt/hadoop/cms/store/user/davidlw/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3/b6b6bdfea548f61b58c6395522e54da5/nohup.out srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/nohup.out
</verbatim>

   * Copying many files from T2_MIT to T2_SPRACE
<verbatim>
for i in $(srmls -2 srm://se01.cmsaf.mit.edu:8443/srm/v2/server?SFN=/mnt/hadoop/cms/store/user/davidlw/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3/b6b6bdfea548f61b58c6395522e54da5/ | cut -d " " -f 8 | cut -c115-); do echo "srmcp -2 srm://se01.cmsaf.mit.edu:8443/srm/v2/server?SFN=/mnt/hadoop/cms/store/user/davidlw/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3/b6b6bdfea548f61b58c6395522e54da5/$i srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3/$i";done
</verbatim>

   * Saving =srmls= output in a format ready to be read by =_cfg.py= file
<verbatim>
for i in $(srmls srm://osg-se.sprace.org.br:8443/srm/managerv2?SFN=/pnfs/sprace.org.br/data/cms/store/user/lagana/MinimumBias/MB-C10-398p2-MINBIASTRKANASKIM-v3 | cut -d " " -f 8 | cut -c29-); do echo "'$i',";done > to_cfg_file.out
</verbatim>

---+++ Using =CRAB= to publish =FullSim= dataset in 2012

(César) We have some instructions to do =FullSim= using =CRAB= in FullSim2012

---++ Analysis in 2012

(Thiago) I am going to prepare a Twiki about the analyses we will be setting up in 2012. It will reside in AnalysisSprace

---++ Analysis in 2013

(Cesar) Detailed recipe for !DoubleMuon HLT triggers in EXOTICA [[https://twiki.cern.ch/twiki/bin/view/CMS/MuonHLTEfficiencyWithReferenceMethod#Recipe_for_HLT_Mu22_TkMu8_and_HL][here]] .

(Jose) Pixel Detector Simulation. Instructions [[https://www.sprace.org.br/twiki/bin/view/Main/PixelEcal][here]].

---++ Subscription

Para receber um email de notificação toda vez que alguém faz alguma modificação no Analysis Open Space, coloque seu nome [[/twiki/bin/view/Main/WebNotify][nessa área do WebNotify]].

-- Main.CaioLagana - 18 Jul 2011 -- Main.ThiagoTomei - 09 May 2012
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
txt	Zprime_M1500GeV_to_WW_8TeV_pythia8_cff_py_GEN_SIM.py.txt	r1	manage	4.0 K	2012-09-03 - 19:14	CesarBernardes
txt	Zprime_M1500GeV_to_WW_8TeV_pythia8_cff_py_GEN_SIM_REDIGI_DIGI_L1_DIGI2RAW_HLT_PU.py.txt	r1	manage	3.5 K	2012-09-03 - 19:54	CesarBernardes
EXT	condor_ROOT	r2 r1	manage	0.6 K	2011-10-21 - 18:38	CaioLagana	script para rodar ROOT via condor
EXT	condor_run	r1	manage	0.5 K	2011-09-20 - 02:50	CaioLagana	condor default script
EXT	condor_run_root	r1	manage	0.5 K	2011-10-21 - 18:39	CaioLagana	script para rodar ROOT via condor
EXT	condor_test	r1	manage	0.9 K	2011-09-20 - 10:01	CesarBernardes	condor_test
cfg	crab02.cfg	r1	manage	1.1 K	2012-09-03 - 18:47	CesarBernardes
cfg	crab03.cfg	r1	manage	1.5 K	2012-09-03 - 20:11	CesarBernardes
png	dois-pads-num-canvas.png	r1	manage	10.0 K	2011-07-23 - 17:26	CaioLagana	Teste para desenhar dois graficos sem espaço entre eles
root	dois-pads-num-canvas.root	r1	manage	19.0 K	2011-07-23 - 19:18	CaioLagana
Topic revision: r45 - 2013-09-06 - bernardes
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