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#author("2019-06-26T12:02:22+09:00","oda","oda")
#freeze
#author("2019-06-26T13:08:28+09:00","oda","oda")
- https://twiki.cern.ch/twiki/bin/viewauth/AtlasComputing/SoftwareTutorial
- https://atlassoftwaredocs.web.cern.ch/ABtutorial/
#contents
----
* Release Setup [#v35dbfba]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/release_setup/
$ ssh -Y username@lxplus.cern.ch
Replace "username" by your username.
You can check your shell by
$ echo $SHELL
If this command gives
/bin/bash
you use bash.
If you use bash, you need to add the following two lines to ~/.bashrc using emacs or vi or other editors.
export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'
If you use other login script or use other shell, you need to modify the corresponding script.
Then, you need to exit and log in lxplus.cern.ch again to activate the alias.
$ exit
$ ssh -Y username@lxplus.cern.ch
Now, you can run the setupATLAS command.
$ setupATLAS
You need to create some directories for this tutorial.
You may choose the directory locations. But here, I assume that you create directories under your home directory.
$ cd ~ # go to your home directory.
$ mkdir ROOTAnalysisTutorial
$ cd ROOTAnalysisTutorial
$ mkdir source
$ mkdir build
$ mkdir run
You are now at the ~/ROOTAnalysisTutorial/ directory.
Then, you need to create the ~/ROOTAnalysisTutorial/source/CMakeLists.txt using an editor.
$ emacs -nw source/CMakeLists.txt
#
# Project configuration for UserAnalysis.
#
# Set the minimum required CMake version:
cmake_minimum_required( VERSION 3.4 FATAL_ERROR )
# Try to figure out what project is our parent. Just using a hard-coded list
# of possible project names. Basically the names of all the other
# sub-directories inside the Projects/ directory in the repository.
set( _parentProjectNames Athena AthenaP1 AnalysisBase AthAnalysis
AthSimulation AthDerivation AnalysisTop )
set( _defaultParentProject AnalysisBase )
foreach( _pp ${_parentProjectNames} )
if( NOT "$ENV{${_pp}_DIR}" STREQUAL "" )
set( _defaultParentProject ${_pp} )
break()
endif()
endforeach()
# Set the parent project name based on the previous findings:
set( ATLAS_PROJECT ${_defaultParentProject}
CACHE STRING "The name of the parent project to build against" )
# Clean up:
unset( _parentProjectNames )
unset( _defaultParentProject )
# Find the AnalysisBase project. This is what, amongst other things, pulls
# in the definition of all of the "atlas_" prefixed functions/macros.
find_package( ${ATLAS_PROJECT} REQUIRED )
# Set up CTest. This makes sure that per-package build log files can be
# created if the user so chooses.
atlas_ctest_setup()
# Set up the GitAnalysisTutorial project. With this CMake will look for "packages"
# in the current repository and all of its submodules, respecting the
# "package_filters.txt" file, and set up the build of those packages.
atlas_project( UserAnalysis 1.0.0
USE ${ATLAS_PROJECT} ${${ATLAS_PROJECT}_VERSION} )
# Set up the runtime environment setup script. This makes sure that the
# project's "setup.sh" script can set up a fully functional runtime environment,
# including all the externals that the project uses.
lcg_generate_env( SH_FILE ${CMAKE_BINARY_DIR}/${ATLAS_PLATFORM}/env_setup.sh )
install( FILES ${CMAKE_BINARY_DIR}/${ATLAS_PLATFORM}/env_setup.sh
DESTINATION . )
# Set up CPack. This call makes sure that an RPM or TGZ file can be created
# from the built project. Used by Panda to send the project to the grid worker
# nodes.
atlas_cpack_setup()
Compile the file with AnalysisBase 21.2.75 at the build directory.
$ cd build/
$ asetup 21.2.75,AnalysisBase
$ cmake ../source/
$ make
$ source x86_64-*/setup.sh # This is necessary if you run some jobs.
----
* On Every Login [#z82fdace]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/on_every_login/
The next time you start a new session to start working, you’ll have to do the following.
$ ssh -Y username@lxplus.cern.ch
$ setupATLAS
$ cd ~/ROOTAnalysisTutorial
$ cd ./build
$ asetup --restore
$ source x86_64-*/setup.sh
----
* xAOD Samples [#o737d4bb]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/xaod_samples/
https://twiki.cern.ch/twiki/bin/viewauth/AtlasComputing/SoftwareTutorialSoftwareBasics#Define_ALRB_TutorialData
$ export ALRB_TutorialData=/afs/cern.ch/atlas/project/PAT/tutorial/cern-jan2018/
----
* Create Your Package [#fb8cc395]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/create_package/
You are now at the ~/ROOTAnalysisTutorial/build/ directory.
Let's create a new package.
$ cd ../source/
$ mkdir MyAnalysis
$ mkdir MyAnalysis/MyAnalysis
$ mkdir MyAnalysis/Root
$ mkdir MyAnalysis/src
$ mkdir MyAnalysis/src/components
$ mkdir MyAnalysis/share
You are now at the ~/ROOTAnalysisTutorial/source/ directory.
Create a new file, ~/ROOTAnalysisTutorial/source/MyAnalysis/CMakeLists.txt.
$ emacs -nw MyAnalysis/CMakeLists.txt
# The name of the package:
atlas_subdir (MyAnalysis)
Compile the new package.
$ cd ../build/
$ cmake ../source/
$ make
You need to run the following commands as well.
$ cd ../build/
$ source x86_64-*/setup.sh
You are now at the ~/ROOTAnalysisTutorial/build/ directory.
----
* Create Algorithm [#p2e3a055]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/alg_basic_algorithm/
You need to move to the source directory.
$ cd ~/ROOTAnalysisTutorial/source/
You need to create a new file, MyAnalysis/MyAnalysis/MyxAODAnalysis.h.
$ emacs -nw MyAnalysis/MyAnalysis/MyxAODAnalysis.h
#ifndef MyAnalysis_MyxAODAnalysis_H
#define MyAnalysis_MyxAODAnalysis_H
#include <AnaAlgorithm/AnaAlgorithm.h>
class MyxAODAnalysis : public EL::AnaAlgorithm
{
public:
// this is a standard algorithm constructor
MyxAODAnalysis (const std::string& name, ISvcLocator* pSvcLocator);
// these are the functions inherited from Algorithm
virtual StatusCode initialize () override;
virtual StatusCode execute () override;
virtual StatusCode finalize () override;
private:
// Configuration, and any other types of variables go here.
//float m_cutValue;
//TTree *m_myTree;
//TH1 *m_myHist;
};
#endif
Create another file, MyAnalysis/Root/MyxAODAnalysis.cxx.
$ emacs -nw MyAnalysis/Root/MyxAODAnalysis.cxx
#include <AsgTools/MessageCheck.h>
#include <MyAnalysis/MyxAODAnalysis.h>
MyxAODAnalysis :: MyxAODAnalysis (const std::string& name,
ISvcLocator *pSvcLocator)
: EL::AnaAlgorithm (name, pSvcLocator)
{
// Here you put any code for the base initialization of variables,
// e.g. initialize all pointers to 0. This is also where you
// declare all properties for your algorithm. Note that things like
// resetting statistics variables or booking histograms should
// rather go into the initialize() function.
}
StatusCode MyxAODAnalysis :: initialize ()
{
// Here you do everything that needs to be done at the very
// beginning on each worker node, e.g. create histograms and output
// trees. This method gets called before any input files are
// connected.
return StatusCode::SUCCESS;
}
StatusCode MyxAODAnalysis :: execute ()
{
// Here you do everything that needs to be done on every single
// events, e.g. read input variables, apply cuts, and fill
// histograms and trees. This is where most of your actual analysis
// code will go.
return StatusCode::SUCCESS;
}
StatusCode MyxAODAnalysis :: finalize ()
{
// This method is the mirror image of initialize(), meaning it gets
// called after the last event has been processed on the worker node
// and allows you to finish up any objects you created in
// initialize() before they are written to disk. This is actually
// fairly rare, since this happens separately for each worker node.
// Most of the time you want to do your post-processing on the
// submission node after all your histogram outputs have been
// merged.
return StatusCode::SUCCESS;
}
Create the MyAnalysis/MyAnalysis/MyAnalysisDict.h
$ emacs -nw MyAnalysis/MyAnalysis/MyAnalysisDict.h
#ifndef MYANALYSIS_MYANALYSIS_DICT_H
#define MYANALYSIS_MYANALYSIS_DICT_H
// This file includes all the header files that you need to create
// dictionaries for.
#include <MyAnalysis/MyxAODAnalysis.h>
#endif
Create the MyAnalysis/MyAnalysis/selection.xml file
$ emacs -nw MyAnalysis/MyAnalysis/selection.xml
<lcgdict>
<!-- This file contains a list of all classes for which a dictionary
should be created. -->
<class name="MyxAODAnalysis" />
</lcgdict>
You need to update the CMakeLists.txt file for the package.
$ emacs -nw MyAnalysis/CMakeLists.txt
# The name of the package:
atlas_subdir (MyAnalysis)
# Add the shared library:
atlas_add_library (MyAnalysisLib
MyAnalysis/*.h Root/*.cxx
PUBLIC_HEADERS MyAnalysis
LINK_LIBRARIES AnaAlgorithmLib)
if (XAOD_STANDALONE)
# Add the dictionary (for AnalysisBase only):
atlas_add_dictionary (MyAnalysisDict
MyAnalysis/MyAnalysisDict.h
MyAnalysis/selection.xml
LINK_LIBRARIES MyAnalysisLib)
endif ()
if (NOT XAOD_STANDALONE)
# Add a component library for AthAnalysis only:
atlas_add_component (MyAnalysis
src/components/*.cxx
LINK_LIBRARIES MyAnalysisLib)
endif ()
# Install files from the package:
atlas_install_joboptions( share/*_jobOptions.py )
atlas_install_scripts( share/*_eljob.py )
Compile the updated package
$ cd ../build/
$ cmake ../source/
$ make
You are now at the ~/ROOTAnalysisTutorial/build/ directory.
----
* Configuration (EventLoop) [#dbbb2075]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/alg_basic_macro/
Create a Python macro.
$ cd ../
$ emacs -nw source/MyAnalysis/share/ATestRun_eljob.py
#!/usr/bin/env python
# Read the submission directory as a command line argument. You can
# extend the list of arguments with your private ones later on.
import optparse
parser = optparse.OptionParser()
parser.add_option( '-s', '--submission-dir', dest = 'submission_dir',
action = 'store', type = 'string', default = 'submitDir',
help = 'Submission directory for EventLoop' )
( options, args ) = parser.parse_args()
# Set up (Py)ROOT.
import ROOT
ROOT.xAOD.Init().ignore()
# Set up the sample handler object. See comments from the C++ macro
# for the details about these lines.
import os
sh = ROOT.SH.SampleHandler()
sh.setMetaString( 'nc_tree', 'CollectionTree' )
inputFilePath = os.getenv( 'ALRB_TutorialData' ) + '/r9315/'
ROOT.SH.ScanDir().filePattern( 'AOD.11182705._000001.pool.root.1' ).scan( sh, inputFilePath )
sh.printContent()
# Create an EventLoop job.
job = ROOT.EL.Job()
job.sampleHandler( sh )
job.options().setDouble( ROOT.EL.Job.optMaxEvents, 500 )
# Create the algorithm's configuration.
from AnaAlgorithm.DualUseConfig import createAlgorithm
alg = createAlgorithm ( 'MyxAODAnalysis', 'AnalysisAlg' )
# later on we'll add some configuration options for our algorithm that go here
# Add our algorithm to the job
job.algsAdd( alg )
# Run the job using the direct driver.
driver = ROOT.EL.DirectDriver()
driver.submit( job, options.submission_dir )
Make it executable.
$ chmod +x source/MyAnalysis/share/ATestRun_eljob.py
Compile the package again.
$ cd ./build/
$ cmake ../source/
$ make
Run the macron in the run directory.
$ cd ../run/
$ ATestRun_eljob.py --submission-dir=submitDir
----
* Add some printouts [#a87633a9]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/alg_basic_printout/
Move to the source directory.
$ cd ../source/
Update the MyxAODAnalysis.cxx file.
$ emacs -nw MyAnalysis/Root/MyxAODAnalysis.cxx
Add the following line in the execute method.
ANA_MSG_INFO ("in execute");
Add the following line in the initialize method.
ANA_MSG_INFO ("in initialize");
Compile the package again.
$ cd ../build/
$ make
Run the macro.
$ cd ../run
$ rm -rf submitDir
$ ATestRun_eljob.py --submission-dir=submitDir
----
* xAOD access [#w879ae9d]
https://atlassoftwaredocs.web.cern.ch/ABtutorial/alg_basic_xaod/
$ cd ../source/
Update MyAnalysis/CMakeLists.txt to be able to use xAODEventInfo class.
$ emacs -nw MyAnalysis/CMakeLists.txt
Change
# Add the shared library:
atlas_add_library (MyAnalysisLib
MyAnalysis/*.h Root/*.cxx
PUBLIC_HEADERS MyAnalysis
LINK_LIBRARIES AnaAlgorithmLib)
to
atlas_add_library (MyAnalysisLib
MyAnalysis/*.h Root/*.cxx
PUBLIC_HEADERS MyAnalysis
LINK_LIBRARIES AnaAlgorithmLib xAODEventInfo)
Update MyAnalysis/Root/MyxAODAnalysis.cxx.
$ emacs -nw MyAnalysis/Root/MyxAODAnalysis.cxx
Add the following line to the beginning of the file.
#include <xAODEventInfo/EventInfo.h>
Change the execute method as follows.
StatusCode MyxAODAnalysis :: execute ()
{
// Here you do everything that needs to be done on every single
// events, e.g. read input variables, apply cuts, and fill
// histograms and trees. This is where most of your actual analysis
// code will go.
ANA_MSG_INFO ("in execute");
// retrieve the eventInfo object from the event store
const xAOD::EventInfo *eventInfo = nullptr;
ANA_CHECK (evtStore()->retrieve (eventInfo, "EventInfo"));
// print out run and event number from retrieved object
ANA_MSG_INFO ("in execute, runNumber = " << eventInfo->runNumber() << ", eventNumber = " << eventInfo->eventNumber());
return StatusCode::SUCCESS;
}
Compile the package.
$ cd ../build/
$ make
Run the macro.
$ cd ../run
$ rm -rf submitDir
$ ATestRun_eljob.py --submission-dir=submitDir
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