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ATLAS Software

Muon Cosmic Data Reconstruction Tutorial

Authors: Tiesheng Dai and Steven Goldfarb | BU Workshop : Home | Agenda | Slides for Details


This tutorial provides recipes for running the ATLAS Muon Standalone Reconstruction on Raw Cosmic Data sets to create Standard Athena-Aware N-Tuples and Muon Calibration N-Tuples. It is was written for the U.S. ATLAS Muon Software Workshop held at Boston University on Dec 18-19, 2008. The instructions will work equally at CERN, at BNL, and on the University of Michigan Tier 3 Cluster. For simplicity, we will run on the UM Cluster.

Goals of the Tutorial

This is a very short tutorial, primarily designed to get new users started analysing real data in the ATLAS Muon Spectrometer. By the end of the tutorial, you should know how to:
  1. Set up the environment for running reconstruction using a recent version of Athena;
  2. Install and build the necessary packages;
  3. Find Cosmic Muon data sets;
  4. Run Muon Standalone Reconstruction on those data sets;
  5. Learn to add data to the N-tuples by making changes in Athena;
  6. Produce AANT and Calibration N-tuples for analysis;
  7. Fill histograms with data from those N-tuples.

There are many topics we will not cover, including:
  1. Running jobs on the grid;
  2. Combined reconstruction;
  3. Physics analysis;
  4. Running simulation;
  5. Usage of Visualization and other Physics Analysis Tools

Please sign up for the next Jamboree, if you are interested in these topics.


Here are the basic requirements for running this tutorial:
  1. User has laptop and can run ssh or PuTTY to connect to one of the facilities.
  2. User has registered for the workshop and received an account on the UM Tier 3 Facility (or ask Steve for a guest account).
    • username/password
    • interactive machine name
  3. User has an afs account at CERN (necessary for checking out software packages).

Site-Dependent Running Instructions

UM Tier 3 Facility

Registered participants have been given accounts on the University of Michigan Tier 3 Facility. Usernames and passwords have been sent out to the participants. If you did not register or have not received the information, please let me know.

  1. Login to your assigned interactive machine (see your e-mail from Bob Ball):
    ssh -Y
  2. If you do not have an assigned machine, login to one of the interactive nodes:
    ssh -Y
  3. Change your password, if you have not yet done so:

BNL Tier 1 Facility

This assumes the users have already obtained accounts at BNL and passed all of the cybersecurity tests. If you have not used your account recently, you might need to upload your public key. More information can be found at:

  1. Login to the BNL Gateway and run kinit to obtain Kerberos and AFS tokens
    ssh -Y
    kinit -5 -4 -l 7d 
  2. Login to one of the interactive nodes:
    rterm -i


The user must have an account on lxplus or any SLC4 linux box with afs supported. Specifying the full path might be needed for latter (e.g. /afs/

  • Login to one of the interactive nodes:
    ssh -Y

BU Tier2 Facility

The user must have an account on BU Tier2.

  • Login to the login node:
    ssh -Y

Finding the 2008 Cosmic and Beam Raw Data

To obtain more information about data, visit Most data are saved on CASTOR and DCACHE.

  • CERN online: /castor/, /castor/ for May, June and early July 2008 data
  • CERN offline: /castor/ (X = 1beammag, calib, cos, cosmag, cvalid and idcomm, Y = RAW for raw data, AOD, ESD, CBNT, TAG \x85 for reco.)
  • *AGLT2 (Only Muon Data = MDT+CSC+TGC+RPC+TRIG) kiss /pnfs/
  • *BNL (Only run 91060 Muon Data) kiss /pnfs/
  • *BU Tier2 (Only run 91060 Muon Data) kiss /data4/bu/daits/mdaq/

It is possible to retrieve raw data using DQ2, which needs a lot of space and time and is not recommended.

Line-By-Line Instructions to Install & Run the Reconstruction

Once logged in to your favorite machine, here are the line-by-line instructions for installing and running the software.

  1. Move to the directory where you want to install the software. (Note: software cannot be moved afterward without a re-installation):
    mkdir work
    cd work
  2. Run Tiesheng's installation script to create the requirements file, install packages, and set up the environment (copy script locally, if you want to make changes):
    ~daits/public/scripts/installProdMuonRec -checkout MuonSpectrometer/MuonCalib/MuonCalibNtuple
    where package MuonCalibNtuple will be used later as an example to add user software. Note: When running on the UM facility, you will be prompted for your CERN AFS password. This is to allow access to the software repository to check out any packages that might be modified. Details of script installProdMuonRec are given in the Slides for Details, including examples and instructions for adding user codes.
  3. After installation go to the p14.5.0.1 directory and take a look:
    cd p14.5.0.1; ls -l
    Here is what you ought to see:
    drwxr-xr-x  2 docsteve umatlas 2048 Dec 12 04:15 cmthome/
    lrwxr-xr-x  1 docsteve umatlas   50 Dec 12 04:16 data08list -> /atlas/data18c/data01/home/daits/public/data08list/
    drwxr-xr-x  6 docsteve umatlas 2048 Dec 12 04:16 InstallArea/
    drwxr-xr-x  2 docsteve umatlas 2048 Dec 12 05:07 job/
    drwxr-xr-x  3 docsteve umatlas 2048 Dec 12 04:15 MuonSpectrometer/
    drwxr-xr-x  2 docsteve umatlas 2048 Dec 12 04:16 runCtrl/
    where 2008 RAW data are listed run by run under data08list.
  4. Make test directory and run Athena interactively:
    mkdir test; cd test
    ../job/run_using_default | tee my.log
    tail -100 my.log | more
    Here is what you ought to see for the timing at the end. Calls to recomu should be 100:
               |             |   #   |   time of   | time / call |             |             |
       name    |  total time | calls |  first call | w.o. 1st c. | time / call | time / event|
       initiali|         3.07|      1|         3.07|         0.00|         3.07|         3.07|
       finicoco|         0.02|    100|         0.00|         0.00|         0.00|         0.02|
       t0fitter|       142.60|    100|         0.35|         1.44|         1.43|       142.60|
       recomu  |        99.46|    100|         0.25|         1.00|         0.99|        99.46|
       s values|         0.09|    100|         0.00|         0.00|         0.00|         0.09|
       inne seg|         0.00|    100|         0.00|         0.00|         0.00|         0.00|
       stri seg|        26.72|    100|         0.03|         0.27|         0.27|        26.72|
       Rec. T,P|         0.00|    100|         0.00|         0.00|         0.00|         0.00|
       loos seg|        40.77|    100|         0.05|         0.41|         0.41|        40.77|
       scan    |         1.02|   6866|         0.00|         0.00|         0.00|         1.02|
       fit i 2 |         0.61|    365|         0.00|         0.00|         0.00|         0.61|
    The muon calibration n-tuple CalibrationNtuple.root and the muon AANT ntuple.root should be produced.
  5. Make the anal directory and generate calibration NTUPLE analysis software:
    mkdir ../anal/; cd ../anal
    ~daits/public/scripts/generate_cppfile_for_calibNtuple ../test/CalibrationNtuple.root mytest
    The files mytest.C and mytest.h are generated. The Slides for Details shows a way to modify this software. Here is how you can get a previously modified example:
  6. Copy pre-prepared calibration n-tuple analysis software and process calibration n-tuples:
    /bin/cp -f ~daits/public/muon_calib_ntup_demo/mytest.h .
    /bin/cp -f ~daits/public/muon_calib_ntup_demo/mytest.C .
  7. Process the the new calibration n-tuples:
    ~daits/public/scripts/run_cppfile mytest 
    This will produce the files mytest.root and All_plots.pdf.
  8. There is a similar procedure for the muon AANT analysis:
    mkdir ../aa_anal/; cd ../aa_anal
    ~daits/public/scripts/generate_cppfile_for_muonNtuple ../test/ntuple.root mytest
    /bin/cp -f ~daits/public/muon_AA_ntup_demo/mytest.h .
    /bin/cp -f ~daits/public/muon_AA_ntup_demo/mytest.C .
    ~daits/public/scripts/run_cppfile mytest 
    Again, this will produce: mytest.root and All_plots.pdf.

-- SteveGoldfarb - 12 Dec 2008 (creation) -- SteveGoldfarb - 16 Dec 2008 (updates before flying) -- SteveGoldfarb - 18 Dec 2008 (updates while and after flying)
Topic attachments
I Attachment Action Size Date Who Comment
MS_Naming.pptppt MS_Naming.ppt manage 1 MB 16 Dec 2008 - 16:53 UnknownUser Muon Spectrometer Nomenclature
MuonCosmicRecoTutorial.pptppt MuonCosmicRecoTutorial.ppt manage 1 MB 19 Dec 2008 - 19:10 UnknownUser Complementary Presentation of the Tutorial
Muon_Reconstruction_Tutorial_12182008.pptppt Muon_Reconstruction_Tutorial_12182008.ppt manage 753 K 18 Dec 2008 - 15:36 UnknownUser Muon Reconstruction Tutorial
muonfixedid.hh muonfixedid.h manage 22 K 18 Dec 2008 - 17:47 UnknownUser MuonFixedid Class for ROOT ntuple analysis
Topic revision: r12 - 19 Dec 2008, SteveGoldfarb
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