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---+!! Steve's Notes
---+!! _Installing & Running Athena (Release 14.5.1)_
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---
[[StevenGoldfarbAthena][Athena]] | [[StevenGoldfarbVP1][VP1]] | [[StevenGoldfarbDQ2][DQ2]]
---

%TOC%

---++ Introduction

This is an informal summary of notes on installing and running Athena.  It currently works for CERN (lxplus) and UMT3 (University of Michigan Tier 3 Cluster).  It is complementary to the existing documentation found on the Atlas.WorkBook with a focus on providing a set of cut & paste examples.  Please send comments and corrections to [[mailto:Steven.Goldfarb@cern.ch][Steven.Goldfarb@cern.ch]].

---++ Set Up the CMT Environment

Here we define and export variables for CMT.  The correct version of CMT to use for any particular release is found on the [[http://cern.ch/atlas-computing/projects/releases/status/][Offline Release Status Page]].  In this example, we will use [[http://cern.ch/atlas-computing/projects/releases/status/14.5.1][Release 14.5.1]].  The corresponding version of CMT is *v1r20p20080222*.

   1. Login to the appropriate machine _(the "-Y" option passes the necessary X-Window information)_
   <verbatim>
CERN> ssh -Y myusername@lxplus.cern.ch
UMT3> ssh -Y myusername@umt3int03.physics.lsa.umich.edu (can also use umt3int01 or umt3int02)
   </verbatim>
   1. Setup the cmt environment corresponding to the release _(do whenever there is a new version of CMT)_
   <verbatim>
CERN> source /afs/cern.ch/sw/contrib/CMT/v1r20p20080222/mgr/setup.sh
UMT3> source /atlas/data08/OSG/APP/atlas_app/atlas_rel/14.5.1/CMT/v1r20p20080222/mgr/setup.sh
   </verbatim>

---++ Set Up the Athena Environment

This sets up the Athena working environment.  More details at Atlas.WorkBookSetAccount .

   1. Create a directory structure  _(do this once for the release)_
   <verbatim>
mkdir -p ~/TestArea/14.5.1/cmthome
cd ~/TestArea/14.5.1/cmthome
   </verbatim>
   1. Download the appropriate requirements file:
      * =[[%ATTACHURL%/requirements-cern][requirements-cern]]= (save as =requirements=)
      * =[[%ATTACHURL%/requirements-umt3][requirements-umt3]]= (save as =requirements=)
   1. Configure cmt (creates the scripts for setting up the environment):
   <verbatim>
cmt config
   </verbatim>
   1. Setup the Athena environmental variables: _(every time you login)_
   <verbatim>
source ~/TestArea/14.5.1/cmthome/setup.sh
   </verbatim>
   1. Check the CMT variables:
   <verbatim>
echo $CMTCONFIG
CERN> i686-slc4-gcc34-opt
UMT3> i686-slc4-gcc34-opt
echo $CMTPATH
CERN> ~/TestArea/14.5.1:/afs/cern.ch/atlas/software/releases/14.5.1/AtlasOffline/14.5.1
UMT3> ~/TestArea/14.5.1:/atlas/data08/OSG/APP/atlas_app/atlas_rel/14.5.1/AtlasOffline/14.5.1
   </verbatim>

---++ Check Out the !UserAnalysis Package

Analysis is typically run from within this package.  Here we do a quick test with Hello World.

   1. If not done already, set up the environmental variables.
   <verbatim>
cd ~/TestArea/14.5.1
source cmthome/setup.sh
   </verbatim>
   1. Find out which version of !UserAnalysis to checkout (in this case !UserAnalysis-00-13-09):
   <verbatim>
cmt show versions PhysicsAnalysis/AnalysisCommon/UserAnalysis
   </verbatim>
   1. On UMT3, get kerberos permission (using CERN afs password):
   <verbatim>
UMT3> /usr/kerberos/bin/kinit myusername@CERN.CH
   </verbatim>
   1. Checkout, configure and build the package.
   <verbatim>
cmt co -r UserAnalysis-00-13-09 PhysicsAnalysis/AnalysisCommon/UserAnalysis
cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/cmt
source setup.sh
gmake
   </verbatim>

---++ Test the !UserAnalysis Package

See more detailed instructions at Atlas.WorkBookReconstruction .  This example will create ESD and AOD files from a simulated RDO file.

   1. Set up Athena and !UserAnalysis environments: _(once per login)_
   <verbatim>
cd ~/TestArea/14.5.1
source cmthome/setup.sh
cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/run
source ../cmt/setup.sh
   </verbatim>
   1. See what options you can run with:
   <verbatim>
athena -h
   </verbatim>
   1. Try running Hello World: _(See Atlas.WorkBookRunAthenaHelloWorld for explanation of output)_
   <verbatim>
get_files -jo HelloWorldOptions.py
athena HelloWorldOptions.py
   </verbatim>
   1. Copy some example files to the run area:
   <verbatim>
RecExCommon_links.sh
   </verbatim>
   1. Run the default !jobOptions: _(the -s option gives output from all included !jobOptions)_
   <verbatim>
athena -s | tee athena.log
   </verbatim>

---++ Run Reconstruction on a Stripped Cosmic Bytestream Data File (only Muon data)

   1. Set up Athena and !UserAnalysis environments: _(once per login)_
   <verbatim>
cd ~/TestArea/14.5.1
source cmthome/setup.sh
cd PhysicsAnalysis/AnalysisCommon/UserAnalysis/run
source ../cmt/setup.sh
   </verbatim>
   1. Download a small stripped bytestream data file and some example !jobOption files from this wiki page:
      * =[[%ATTACHURL%/mdaq.ATLAS.0091060.physics.CosmicMuons.LB0001.SFO-1._0001.data][mdaq.ATLAS.0091060.physics.CosmicMuons.LB0001.SFO-1._0001.data]]= (save with same name)
      * =[[%ATTACHURL%/makeESD_align.py.txt][makeESD_align.py.txt]]= (save as =makeESD_align.py=)
      * =[[%ATTACHURL%/makeESD_noalign.py.txt][makeESD_noalign.py.txt]]= (save as =makeESD_noalign.py=)
   1. Create an ESD (with alignment correction on) from the bytestream file:
   <verbatim>
athena -s makeESD_align.py | tee makeESD_align.log
   </verbatim>
   1. Create an ESD (w/o alignment correction on) from the bytestream file:
   <verbatim>
athena -s makeESD_noalign.py | tee makeESD_noalign.log
   </verbatim>
   *Note:* Output is visible on the screen and is written to the log file.

---++ Find data sets with DQ2 at CERN

See my notes at StevenGoldfarbDQ2 for details.

---++ Install and View Data with VP1

See my notes at StevenGoldfarbVP1 for details.

---++ References

   * Atlas.WorkBook - ATLAS Workbook for Computing
   * Atlas.WorkBookReconstruction - ATLAS Workbook Reconstruction Recipe
   * [[https://hep.pa.msu.edu/twiki/bin/view/AGLT2/MuonReco][AGLT2.MuonReco]] - Muon Cosmic Reconstruction Tutorial (Dec 2008)
   * Atlas.RecExCommonFlags - Flags to be set for Reconstruction
   * [[http://cern.ch/atlas-computing/links/nightlyDevDirectory/AtlasOffline/latest_doxygen/InstallArea/doc/MuonRecExample/html/MuonDataRec__myTopOptions_8py-source.html][MuonDataRec_myTopOptions.py]] - Latest Top !jobOptions for Muon Reconstruction

---
*Major updates*:%BR%
Main.StevenGoldfarb - 29 Jan 2009 (creation)
-- Main.StevenGoldfarb - 02 Feb 2009 (updated for demo)
-- Main.StevenGoldfarb - 04 Feb 2009 (updated to 14.5.1)

Attachments

Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
txt	makeESD_align.py.txt	r1	manage	6.6 K	2009-02-02 - 10:52	StevenGoldfarb	top jobOption to create ESD from bytestream w/alignment corrections
txt	makeESD_noalign.py.txt	r1	manage	6.6 K	2009-02-02 - 10:53	StevenGoldfarb	top jobOption to create ESD from bytestream w/o alignment corrections
data	mdaq.ATLAS.0091060.physics.CosmicMuons.LB0001.SFO-1._0001.data	r1	manage	707.1 K	2009-02-02 - 11:02	StevenGoldfarb	Stripped Cosmic Bytestream Data File (only Muon data)
txt	myRecOptions.py.txt	r1	manage	0.4 K	2009-02-04 - 12:37	StevenGoldfarb	top jobOption to run reconstruction
ext	requirements-cern	r1	manage	0.5 K	2009-02-04 - 11:53	StevenGoldfarb	requirements file for CERN 14.5.1
ext	requirements-umt3	r1	manage	0.5 K	2009-02-04 - 11:53	StevenGoldfarb	requirements file for UMT3 14.5.1

Topic revision: r16 - 2009-02-06 - StevenGoldfarb

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