Athena related notes and observations

TABLE OF CONTENTS

Notation Throughout the TWiki

Text type	Example	Meaning
Brown verbatim text	> source script.sh	Type the command into the shell prompt
Purple verbatim text	> TBrowser t	Type the command into the Athena/Python/ROOT prompt
Standard verbatim text	script.sh	Code snippets and file names
Green verbatim text	Output="Hello"	Run/job/script output
Blue verbatim text	Package-01-02-03	Package names
Italics	Terminus Technicus	Any technical term
Bold	important	Anything important within the text
Red bold text	VERY IMPORTANT	Anything deadly important
< Text within tags >	<Example>	Substitute for your concrete instance

1 Athena

1.1 Athena 32-bit vs. 64-bit

Please note that 64-bit Athena is not officially supported and you are discouraged from using it. 32-bit and 64-bit give different results.

To ensure you use only 32-bit, always use the following tag in your requirements files:

apply_tag 32

1.2 Using modified packages

Your $InstallArea gets detected automatically. To run with modified packages:

cd ${HOME}/${TestArea}/<MODIFIED PACKAGE>/cmt
source setup.sh
cmt config

1.3 ATLAS Geometries

Description of different ATLAS geometry tags here:

https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasGeomDBTags

https://twiki.cern.ch/twiki/bin/view/Atlas/InDetGeometryTags

1.4 Job Transformations hack for modified packages

If you want Job Transformations for running Athena to use your modified packages in your $TestArea, use the following lines to prepend the Athena environment variables:

export PATH=${TestArea}/InstallArea/share/bin:${TestArea}/InstallArea/i686-slc3-gcc323-opt/bin:${PATH}
export LD_LIBRARY_PATH=${TestArea}/InstallArea/i686-slc3-gcc323-opt/lib:${LD_LIBRARY_PATH}
export CMTPATH=${TestArea}/:${CMTPATH}
export SEAL_PLUGINS=${TestArea}/InstallArea/i686-slc3-gcc323-opt/lib/modules:${SEAL_PLUGINS}
export PYTHONPATH=/${TestArea}/InstallArea/python:${PYTHONPATH}
export DATAPATH=${TestArea}/InstallArea/share:${DATAPATH}
export JOBOPTSEARCHPATH=${TestArea}/InstallArea/jobOptions,${JOBOPTSEARCHPATH}
export XMLPATH=${TestArea}/InstallArea/XML:${XMLPATH}

2 LXPLUS

2.1 Prolonging LXPLUS login ticket

When you login on LXPLUS you get a ticket valid for 25 hours, then you get disconnected. It can be prolonged by following command:

> kinit

It will ask for your AFS password.

2.2 How to make LXPLUS Startup Script

It is much more easier to setup your enviroment in a way, that all complicated commands are issued by calling one function. You can use the startup script for that. It is run just after you login to LXPLUS and needs to have a specific name according to your shell.

You can find out your shell type by issuing the following command:

> echo $SHELL

Startup Script File Name:

$SHELL	Startup script filename
/usr/local/bin/bash	.bash_login
/usr/local/bin/sh	.login
/usr/local/bin/zsh	.zlogin

More information here: https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasLogin

You can change your shell type here:
http://cra.cern.ch -> Login -> CRA (left menu) -> End-Users options -> User Info -> My Details -> Shell

Example of startup script content: Athena Load Function

# LOAD ATHENA by version, general function for the script
function Load.Athena {
    source ${CMT_HOME}/setup.sh -tag=$*
    shift
}

You run the setup by specifying your $CMT_HOME directory to where you want and then for instance do:

> Load.Athena 14.2.10,32

Download: You can download the whole startup ZSH script at the end of the page, however TWiki has intelligently modified the name of the script, so you will have to change to name to .zlogin:

• zlogin

2.3 LXBATCH

LXBATCH is batch system for LXPLUS users. It is also a part of the LHC Computing Grid (LCG).

Full Documentation: http://batch.web.cern.ch/batch/

Quick Introduction: http://batch.web.cern.ch/batch/doc/quick-intro.html
or try help for the bsub command: > bsub -h

Important note: athena vs. athena.py

Please note the following before you use LXBATCH:
For unknown magical reasons athena command alias is missing on LXBATCH. For this reason you have to use athena.py in all your batch scripts. It is suggested to use it everywhere.

athena.py <JobOptions>

3 GRID

3.1 Functions for startup script

Declares functions to load Grid, Ganga in a specified version of Athena

Note: Load.Grid and Load.Ganga requires Load.Athena function

LOAD GRID:

## ENVIROMENT VARIABLES
export LFC_HOST=lfc-atlas

## FUNCTIONS
# LOAD GRID function
function Load.Grid {
    cd ${HOME}/grid
   echo "Loading GRID Environment"   
   # Specify CMT_HOME Directory
    export CMT_HOME=${HOME}/cmt-grid
   echo "Your CMT home directory:" ${CMT_HOME}
   echo "Your LFC host:" ${LFC_HOST}
   # Initialize LXplus user interface
    source /afs/cern.ch/project/gd/LCG-share/sl4/etc/profile.d/grid-env.sh
   # DQ2 clients to be able to list and download files from the grid
   source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh
   echo "LXPLUS Interface Initialized"   
    # Show recommended TestArea
   echo ${TestArea} 
    # Login
   echo "Loging in to GRID"   
    voms-proxy-init --voms atlas
}

LOAD GANGA:

# LOAD GANGA function
function Load.Ganga {
    cd ${HOME}/grid
   echo "Loading Ganga Environment"
   echo "Your LFC host:" ${LFC_HOST}
   # automatic LXPLUS Ganga setup
    source /afs/cern.ch/sw/ganga/install/etc/setup-atlas.sh
}

Now just type Load.Grid and Load.Ganga into the shell and you are in.

-- MartinZeman - 23 Jul 2008

• zlogin: My startup script