You are here: Foswiki>Main Web>DbxaTr (03 Aug 2016, SerayBeser)EditAttach
-- SaimeG - 22 Jan 2016

--Edited by Aytul -03 Feb 2016

--Edited by Seray - 12 Jul 2016 , 26 Jul 2016 , 03 Aug 2016

Welcome to the dbxa wiki pages.

Setting Up Accounts

1. Have an user account at CERN.

2. Get Grid certificate: https://www.racf.bnl.gov/docs/howto/grid/installcert/

3. Check your VO membership. If you dont have, you should request to be a member of VO atlas : https://www.racf.bnl.gov/docs/howto/grid/voatlas

About dbxa

Attached a presentation about dbxa (look end of the page).

E6-GUT Models

Attached a presentation about E6-GUT models (look end of the page).

Downloading dbxa to local

https://www.dropbox.com/home/dbxa.git

Installing dbxa to local

If you work dbxa locally, first you should install 'git' and 'root'. Then create a working directory in your local area.

Copy dbxa.git to your working directory then use following command line.
git clone dbxa.git

Getting dbxa packages without using password

from Gokhan

If you repeatedly get asked for a password, then you need to make sure you have svn authentication working. There are several ways to achieve this, but the CERN recommended method is to use Kerberos. Firstly, make sure you have it set up correctly, make sure you have a valid token, and also make sure you have the following in your .ssh/config file:

Host svn.cern.ch svn
Protocol 2
GSSAPITrustDns yes
PubkeyAuthentication no
GSSAPIAuthentication yes
GSSAPIDelegateCredentials yes

from: https://twiki.cern.ch/twiki/bin/view/AtlasComputing/SoftwareTutorialxAODEDM#On_your_local_machine_optional

From Aytul

Setup:

1.Create a key and do not enter a passphrase.

ssh-keygen -t dsa

Note that the default key file will be id_dsa and id_dsa.pub but you can create it with a different name (in case you need different keys for different remote hosts but try not to do that unless you have good reason !) by adding the option -f ~/.ssh/<filename>.

2. Create . ssh directory under it, using following command (The directory may already exist, which is fine).

ssh username@lxplus.cern.ch mkdir -p .ssh

3. Copy the public key to your remote machine; replace <username> and <remote machine name> below.

cat ~/.ssh/id_dsa.pub | ssh <username>@<remote machine name> 'cat >> .ssh/authorized_keys'

4. After copying the above public key to lxplus, login to lxplus and type /afs/cern.ch/project/svn/dist/bin/set_ssh. This will fix the acl permissions of the file on lxplus.

5. Create a file ~/.ssh/config with the following information.
Host lxplus*.cern.ch lxplus 
User username 
PubkeyAuthentication no 
PasswordAuthentication yes
ForwardX11 yes

Host svn.cern.ch svn 
GSSAPIAuthentication yes 
GSSAPIDelegateCredentials yes 
User username 
ForwardX11 no

Host *
Protocol 2
IdentityFile ~/.ssh/id_dsa

6. Make sure the permissions of the ~/.ssh directory and its contents have permissions set correctly; an example is

chmod 700 ~/.ssh
chmod 600 ~/.ssh/id_dsa
chmod 644 ~/.ssh/config ~/.ssh/id_dsa.pub

How to run dbxa

Attached README file for this (look end of the page).

xAOD


xAOD (Analysis Object Data) a new format for Run 2 which is a summary of the reconstructed event, and contains sufficient information for common analyses (tracks, jets, taus, etc.), accessible in using Athena or Standalone ROOT.

xAOD: Prerequisites


Computing facilities

  • AFS Workspaces
The AFS (Andrew File System) Service provides networked file storage for CERN users, in particular home directories, work spaces and project spaces. The AFS Service is based on OpenAFS, an open-source distributed filesystem which provides a client-server architecture for location-independent, scalable, and secure file sharing.

You can increase your disk quota on your lxplus home (maximum 10 GB) and workspace (maximum 100 GB) areas:

https://resources.web.cern.ch/resources/Manage/AFS/Settings.aspx

Setting up the ATLAS computing environment

There is an environment variable you can call that will give you access to most/all of the software used in a typical ATLAS analysis. From lxplus type:
setupATLAS

We usually recommend you add these lines to your login shell script so you don't need to type it every time you log in.To determine the type of shell you are using (bash or zsh) type ps -p $$. Depending on the shell you will need to edit (or create) your login script file .login, .zlogin or .bash_login in your home directory. If you are using the zsh shell, try .zlogin . If using bash , try .bash_profile (or .bash_login).

Grid certificate

You will need a valid grid certificate and membership of the Atlas Virtual Organisation for some aspects of the tutorial. Instructions can be found here:

https://twiki.cern.ch/twiki/bin/view/AtlasComputing/XAODMiniTutorialPrerequisites#Grid_certificate

Setting up the Analysis Release

We will work on lxplus, so let's log in there:
ssh -X lxplus.cern.ch
  • Using the Analysis Release
We will use the ATLAS Analysis Release to setup our ROOT environment and other RootCore packages.
  • Downloading source code of a release
To download Base-2.0.14 (we use release 20), just run
rcSetup -d Base,2.0.14

which would download all the required packages for Base-2.0.14, at the end print out a list of package tags downloaded, and a list of packages not downloaded because they already exist under the working directory.

Then you can compile all the packages via command

rc compile
  • Building a release locally
If you like to use your local release in the future, you can build the release via command "rcSetup -b". For example, to build ASG release of Base-2.0.14, just run

rcSetup -b Base,2.0.14

which will
  1. create directory $PWD/AnalysisBase/2.0.14/,

  2. download the packages (if not downloaded yet) in ASG release Base-2.0.14,

  3. compile the release,

  4. write a private configuration file $HOME/.rcSetup.conf if the above compilation is successful.

Later you can just run "rcSetup Base,2.0.14" to use this local ASG release.

Note: this feature is still under development stage.

After you have setup the Analysis Release you can check what versions of each package are in the release by typing:
rc version
  • On your local machine (RECOMMENDED)
setupATLAS 
rcSetup -d Base,2.0.14
lsetup 'rcsetup -r'
lsetup 'rcsetup Base,2.0.14'
rc find_packages
rc compile

You need to type

lsetup rcsetup

every time you log in, after setupATLAS.
How to update to a newer Analysis Release (advanced/optional)
 lsetup 'rcsetup -u'
lsetup 'rcsetup Base,9.9.99'
rc find_packages
rc clean
rc compile
Useful Commands

rcSetup -r -> List available releases

rcSetup <project>,<release> -> Setup a release

rc version -> Show package version

rc find_packages -> Prepare to compile all packages

rc compile -> Compile all packages

rcSetup -u -> Unsetup previous version

rcSetup -d -> Download packages from SVN instead of creating links
Usage of rcSetup

The script rcSetup is available on both CERN AFS and CVMFS, and is accessible by doing one of the following:
  1. rcSetup after running setupATLAS (using CVMFS)
  2. alias rcSetup="source /afs/cern.ch/atlas/software/ASG/scripts/rcSetup.sh" (using AFS)
  3. alias rcSetup="source /afs/cern.ch/atlas/software/ASG/scripts/cvmfs/rcSetup.sh" (using CVMFS)

Looking at xAOD

  • Method 1. If you are at ANL, copy it :
cp /data/nfs/chakanau/tutorial_xAOD_long/valid2.117050.PowhegPythia_P2011C_ttbar.digit.AOD.e2657_s1933_s1964_r5534_tid01482225_00/AOD.01482225._000140.pool.root.1 AOD.01482225._000140.pool.root
  • Method 2. Use xrdcp:(recommended)
localSetupFAX --rootVersion=current-SL6 
voms-proxy-init -voms atlas
xrdcp $STORAGEPREFIX/atlas/rucio/valid2:AOD.01482225._000140.pool.root.1 AOD.01482225._000140.pool.root
  • Method 3: If you work at CERN, use this file:(recommended)
/afs/cern.ch/atlas/project/PAT/xAODs/r5597/data12_8TeV.00204158.physics_JetTauEtmiss.recon.AOD.r5597/AOD.01495682._003054.pool.root.1
/afs/cern.ch/atlas/project/PAT/xAODs/r5591/mc14_8TeV.117050.PowhegPythia_P2011C_ttbar.recon.AOD.e1727_s1933_s1911_r5591/AOD.01494882._111853.pool.root.1
  • Method 4: If you work at your Tier3
setupATLAS
diagnostics
setMeUpData anl-oct2014

Once your environment is setup and you have an xAOD, you can run this script by doing:

checkxAOD.py xAODFile.root

where xAODFile.root is the full path and name of your xAOD.

xAOD: Interactive ROOT with the xAOD

Let's use interactive ROOT to look at the xAOD and make a simple plot:

setupATLAS 
rcSetup Base,2.0.14
root.exe
root[0]gROOT->Macro("$ROOTCOREDIR/scripts/load_packages.C");
root[1]xAOD::Init();
root[2]f=TFile::Open("~/AOD.01495682._003054.pool.root.1");
root[3]t=xAOD::MakeTransientTree(f);
root[4]t->Draw("EventInfo.eventNumber()");

-Useful Links

xAOD mini-tutorial: https://indico.cern.ch/event/328458/

The main xAOD mini-tutorial wiki page can be found here: https://twiki.cern.ch/twiki/bin/view/AtlasComputing/XAODMiniTutorial x

AOD prerequisites: https://twiki.cern.ch/twiki/bin/view/AtlasComputing/XAODMiniTutorialPrerequisites

xAOD: https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsAnalysisWorkBookRel20xAODContent

CompHEP Errors on Mac

1. When you compile ComHEP on Mac, you can face following error:

gcc -fsigned-char -Wall -DNUM_LONG -m64 -DCOMPHEP -o bin/s_comphep.exe src/symb/s_comphep.o -lsymb -lserv -lmssm -lexternal -Llib -L/usr/X11R6/lib -lX11 -lm -lgfortran -lgcc
Undefined symbols for architecture x86_64:
"__gfortran_transfer_character_write", referenced from:
_feynhiggsfast_ in libexternal.a(FeynHiggsFast.o)
_b0ss_ in libexternal.a(FeynHiggsFastCodes.o)
_gentadh_ in libexternal.a(FeynHiggsFastCodes.o)
_genhquad_ in libexternal.a(FeynHiggsFastCodes.o)
_genzquad_ in libexternal.a(FeynHiggsFastCodes.o)
_gengquad_ in libexternal.a(FeynHiggsFastCodes.o)
_genwquad_ in libexternal.a(FeynHiggsFastCodes.o)
...
"__gfortran_transfer_real_write", referenced from:
_feynhiggsfast_ in libexternal.a(FeynHiggsFast.o)
_sigmaz_ in libexternal.a(FeynHiggsFastCodes.o)
_sigmaa_ in libexternal.a(FeynHiggsFastCodes.o)
_dsigmaa_ in libexternal.a(FeynHiggsFastCodes.o)
_sigmaaz_ in libexternal.a(FeynHiggsFastCodes.o)
_sigmaw_ in libexternal.a(FeynHiggsFastCodes.o)
_dsigmag_ in libexternal.a(FeynHiggsFastCodes.o)
...
"__gfortran_transfer_integer_write", referenced from:
_wgplg_ in libexternal.a(FeynHiggsFastCodes.o)
_dsigmalh_ in libexternal.a(FeynHiggsFastCodes.o)
_msbartoonshellpptopbot_ in libexternal.a(FeynHiggsFastSub.o)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make: *** [link] Error 1

Then you need to check where gfortran and gcc are located and which version you use. May be they clash if they are in more than one location and CompHEP can call another version.

So you need to change version name in CC and F77 file. Change gcc -> gcc-4.9 in CC and gfortran -> gfortran-4.9 then do make. Hope it works :)

2. Another error about CXX. If you use different compiler (c++), ComHEP may not set it. So open Makefile and set CXX as c++ (CXX=c++-4.9).

ifneq (${ROOTSYS},)
$(CXX) $(CFLAGS) -o bin/rtupler.exe src/num/rtuple.o -ltranls -lnum -levents -lpdf -lserv $(CLIBS) $(F77LIBS) $(ROOTLIBS)

Thesis done using dbxa

Ismet Siral https://www.dropbox.com/s/mzfgazpk8enx458/ATL-COM-PHYS-2014-1277-2.pdf?dl=0

Topic attachments
I Attachment Action Size Date Who Comment
ATLAS_Event_Data_Model.pdfpdf ATLAS_Event_Data_Model.pdf manage 3943.3 K 12 Jul 2016 - 21:06 SerayBeser An Introduction to the ATLAS Event Data Model, The new EDM: xAOD
AnalysisModel.pdfpdf AnalysisModel.pdf manage 330.0 K 12 Jul 2016 - 21:07 SerayBeser RunII analysis model, The xAOD data format
CERN-THESIS-2015-071.pdfpdf CERN-THESIS-2015-071.pdf manage 3059.0 K 12 Feb 2016 - 13:21 AhmetCoskuner Merve Şahinsoy'un Tezi
DBXAEss.pdfpdf DBXAEss.pdf manage 2916.9 K 27 Jul 2016 - 11:14 SerayBeser DBX_A CODE ESSENTIALS
DownTypeIsoSinglet_0711.1116.pdfpdf DownTypeIsoSinglet_0711.1116.pdf manage 233.7 K 11 Feb 2016 - 08:30 AytulA E6 Model
E6-GUT-MODELS.pdfpdf E6-GUT-MODELS.pdf manage 3346.7 K 04 Feb 2016 - 10:21 AytulA E6-GUT Models
E6Isosinglet.pdfpdf E6Isosinglet.pdf manage 765.2 K 11 Feb 2016 - 08:31 AytulA E6 Model
README.pdfpdf README.pdf manage 35.8 K 04 Feb 2016 - 11:12 AytulA How to run dbxa
dBXA.pdfpdf dBXA.pdf manage 2019.8 K 04 Feb 2016 - 10:22 AytulA Presentation about dbxa
e6-model.rarrar e6-model.rar manage 2.9 K 10 Feb 2016 - 16:10 AhmetCoskuner E6 model files, add them to the "models" folder in CompHEP
tutorial_xAODEDM.pdfpdf tutorial_xAODEDM.pdf manage 195.3 K 12 Jul 2016 - 21:01 SerayBeser xAOD: The essentials
xAODs_and_ROOT_2014.07.08..pdfpdf xAODs_and_ROOT_2014.07.08..pdf manage 5040.6 K 27 Jul 2016 - 11:09 SerayBeser Analysing/Using xAODs in ROOT
xrootd-SanDegio-talk.combined.pdfpdf xrootd-SanDegio-talk.combined.pdf manage 1880.3 K 27 Jul 2016 - 11:16 SerayBeser ATLAS Data Formats and Impact on Federated Access
Topic revision: r14 - 03 Aug 2016, SerayBeser
 

This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Foswiki? Send feedback