Introduction

This is a Twiki for the University of Geneva ATLAS "Analysis Discussion Group". It discusses data analysis issues that are common to all ATLAS physics analyses.

Where to Start?

A good place to start to understand the ATHENA framework is the ATLAS Workbook TWiki: https://twiki.cern.ch/twiki/bin/view/Atlas/WorkBook If you have trouble with anything in the WorkBook, please write it down in WorkBookTroubles - you might save someone else a lot of time!

Computing: The Geneva Cluster and Interactive Nodes

Description of the Geneva computing: GenevaATLASClusterDescription

As of Feb 07, we have interactive nodes on the Geneva cluster. There is currently one node operational atlas-ui01.unige.ch, to log in you need to have a CERN AFS account and ask Szymon to add you to the logins. What you've to give to Szymon is :

  • Your AFS login
  • Your certificate subject, which you can get typing : grid-cert-info

The node is afs mounted, so you have 4 different methods to run your jobs:

  • as an interactive job using the afs versions of ATHENA
  • using the local batch system (instructions to follow...)
  • using Nordugrid
  • using Gridpilot

For now, there is 1.6TB of disk space is available at grid00.unige.ch, mounted on the interactive node as /data/data1.
To copy a file to grid00, setup Nordugrid, then do:
globus-url-copy file:///full/path/to/file.pool.root gsiftp://grid00-cern.unige.ch/grid/users/ahamil/file.pool.root
You should then be able to see the file in /data/data1/users/ahamil/ (Obviously change to your username...) When you are copying a file from CERN, you need to change grid00.unige.ch to grid00-cern.unige.ch.
To read these data files you now need to copy them to the somewhere other than the /grid/users/ area:

  • [ahamil@atlas-ui01] > mkdir /data/data1/scratch/ahamil
  • =[ahamil@atlas-ui01] > globus-url-copy gsiftp://grid00.unige.ch/grid/users/ahamil/test.pool.root file:///data/data1/scratch/ahamil/test.pool.root =
  • now you should be able to read these files from your job options file

What release should I use?

Which release you should use depends slightly on what you want to do. Usually, it is recommended to use the most recent stable release (12.0.2 on 31/10/06). However, you will likely have trouble reading datasets made with older releases. So, if you are making your own dataset - use the most recent release, if you have a dataset that you need to analyse - use whatever release that dataset was produced with. (As of 2/11/06 the 12.0.2 Standard Model samples are expected to be ready for begining of December)

Grid Experience

First-exp-Grid.ppt: Till's experience with Nordugrid
Till has had success with LCG using Ganga
Andrew has submitted a test job to OSG using Panda - currently trying to get output with dq2_get...

Getting a Grid certificate
Starting page : https://ca.cern.ch/ca/
Click on : Request user certificate using xxxxxxxxxxxxx
Follow the steps (id etc..)
Then look at this page to know how to use your certificate : https://ca.cern.ch/ca/Help/?kbid=024010
Once you've got your userkey.pem in the .globus directory (previous step) you can then do:
  • source /afs/cern.ch/project/gd/LCG-share/sl3/etc/profile.d/grid_env.sh for LCG
  • then grid-proxy-init to get a grid token that will be valid for 24 hours
It should be fast (~1 hour) and easy if you follow all the steps.
When you get the certificate you should join the Atlas Virtual Organisation, to do so, follow the steps on : https://www.racf.bnl.gov/docs/howto/grid/voatlas

Renewing Grid Certificate
(Status: June 2008)

If your grid certificate is going to expire you will get a new one from the CERN certification authority: https://ca.cern.ch/ When you got your certificate (probably using your web browser) you can save the .p12 file. Then you need to convert it to .pem files using

  • openssl pkcs12 -in certificate.p12 -nocerts -out userkey.pem
  • openssl pkcs12 -in certificate.p12 -clcerts -nokeys -out usercert.pem
The .pem files you need to save to your .globus/ directory.

Your certificate comes with a Member DN and with a Member CA. The Member DN is something like

  • /DC=ch/DC=cern/OU=Organic Units/OU=Users/CN=username/CN=some_number/CN=Your Name
and the Member CA is probably
  • /DC=ch/DC=cern/CN=CERN Trusted Certification Authority

Now, if your "Member DN" and your "Member CA" did not change, you simply need to go to https://lcg-voms.cern.ch:8443/vo/atlas//vomrs and "Re-sign the Grid and VO AUPs". That's all!

dq2_get:

A dq2_get TWiki: WorkBookDQ2

Here is a 'quick list' of commands for Geneva UI machines (you don't need to set up ATHENA first):

> source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh

Then you need to get a valid proxy for your grid certificate. Please make sure that you get an ATLAS voms-enabled proxy and not a regular grid-proxy.

> voms-proxy-init -voms atlas

You are now ready to use the DQ2 clients. For an easy start, try tab-completion on 'dq2-' to see which commands are available.

Useful Links

Athena Cross Reference: http://alxr.usatlas.bnl.gov/lxr/source
Athena Releases: http://atlas.web.cern.ch/Atlas/GROUPS/SOFTWARE/OO/dist/
DC3 Job Option Files: http://alxr.usatlas.bnl.gov/lxr/source/atlas/Generators/DC3_joboptions/share/
CMT: http://www.cmtsite.org/
C++: http://www.dinkumware.com/manuals/
STL: http://www.sgi.com/tech/stl/index.html
ROOT: http://root.cern.ch/
NorduGrid: http://www.nordugrid.org/
LCG user guide : http://egee.itep.ru/User_Guide.html
OSG and Panda: https://twiki.cern.ch/twiki/bin/view/Atlas/DAonPanda
Histogram Manager: HistogramManagerTool
Geneva Meeting Minutes: http://dpnc.unige.ch/ATLAS_GENEVA_MEETINGS/index.html

Monte Carlo Documentation

AcerMC_3_4.pdf: Acer MC documentation
Alpgen_0206293.ps: Alpgen documentation
Herwig6_0011363.ps: Herwig documentation
Herwig6_5_0210213.ps: Herwig 6.5 release notes
Jimmy_draft20051116.ps: Jimmy documentation
MCatNLO.ps: MC@NLO documentation
Pythia_lutp0613man2.pdf: Pythia documentation
Sherpa_0311263.pdf: Sherpa documentation

MC numbering/PDG: http://pdg.lbl.gov/pdg.html
MC usage in Athena: http://www-theory.lbl.gov/~ianh/monte/Generators/

ATLAS Detector Paper Talks

ATLAS detector paper can be found at: AtlasTechnicalPaper

Meeting: Friday Dec 14 9h00-12h00 in 13-1-017 Purpose: review the ATLAS detector paper with the entire Geneva group to familiarize ourselves with the detector (this is for our good, not for comments or feedback to the editors of the paper) - we will just cover detector performance section

Talk List

section speaker time outline
10.2 Andree 20+5 Tracking performance and ID introduction
10.3 Arno 20+5 Muon performance and muon detector introduction
10.4 Gauthier 20+5 Egamma performance and LAr introduction
10.5/.6 Andrew 20+5 Jets+Met Jet+met performace and Tile Cal introduction
10.7 Ahmed 10+5 Hadronic Taus Hadronic Tau performance (I think all relevant detectors will have been covered)
10.8 Szymon 20+5 Flavour tagging (may need to introduce some of the pixel detector)
10.9 Till 20+5 Trigger performance (basic introduction of trigger hardware)

Topic attachments
I Attachment History Action Size Date Who Comment
PDFpdf AcerMC_3_4.pdf r1 manage 2392.4 K 2006-10-24 - 19:02 UnknownUser AcerMC documentation
Postscriptps Alpgen_0206293.ps r1 manage 319.2 K 2006-10-24 - 19:04 UnknownUser Alpgen documentation
PowerPointppt First-exp-Grid.ppt r1 manage 106.0 K 2006-11-11 - 18:53 TillEifert slides: First experience with the grid
Postscriptps Herwig6_0011363.ps r1 manage 673.9 K 2006-10-24 - 19:13 UnknownUser Herwig documentation
Postscriptps Herwig6_5_0210213.ps r1 manage 129.4 K 2006-10-24 - 19:14 UnknownUser Herwig 6.5 release notes
Postscriptps Jimmy_draft20051116.ps r1 manage 269.1 K 2006-10-24 - 19:04 UnknownUser Jimmy documentation
Postscriptps MCatNLO.ps r1 manage 1156.0 K 2006-10-24 - 19:01 UnknownUser MC@NLO documentation
PDFpdf Pythia_lutp0613man2.pdf r1 manage 2834.0 K 2006-10-24 - 19:06 UnknownUser Pythia documentation
PDFpdf Sherpa_0311263.pdf r1 manage 509.7 K 2006-10-24 - 19:06 UnknownUser Sherpa documentation
Unknown file formatext workbook_output_file r1 manage 2.5 K 2006-10-25 - 16:31 AndreeRobichaudVeronneau Output file from workbook example
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Topic revision: r48 - 2008-09-29 - AndrewHamilton
 
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