SetupAtlasAUThUI

Help to setup your account in hellasgrid.auth.gr user interface (ui).

How to connect

Connect to ui with:

ssh inomi@ui.afroditi.hellasgrid.gr

TIP: Useful alias to add in your ~/.bashrc:

alias ui2='ssh inomi@ui.afroditi.hellasgrid.gr' 

Setup bash

Create these wo files in your home area in the ui:

~/.profile:

# Source global definitions
if [ -f ~/.bashrc ]; then
    . ~/.bashrc
fi

~/.bashrc:

#!/bin/bash
# Source global definitions
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

TIP: Very useful things to add in .bashrc:

export PATH=$PATH:/groups/ATLAS/PUBLIC/scripts
export AFSHOME=/afs/cern.ch/user/i/inomidis
export SVNHOME='https://svn.hellasgrid.gr/svn/atlas.physics.auth.gr/'

### ROOT
. /groups/ATLAS/PUBLIC/root_v5.28.00c.Linux-slc4_amd64-gcc3.4/bin/thisroot.sh

### AtlasSetup for athena
alias asetup='source /groups/ATLAS/VO-Software/software/16.6.2/cmtsite/asetup.sh'

### gLite helpers for grid jobs
alias glsubmit='glite-wms-job-submit -o jobIDfile -a ' 
alias glstatus='glite-wms-job-status -i jobIDfile' 
alias gloutput='glite-wms-job-output -i jobIDfile --dir results'
alias glcancel='glite-wms-job-cancel -i jobIDfile'
alias glmatch='glite-wms-job-list-match -a '
alias glclean='rm -rf results jobIDfile'

Setup SVN

You need your grid certificate in .p12 format to be present in this location:

~/.globus/cert.p12 

If certificate doesn't exist in .p12 format, create it from usercert.pem and userkey.pem with this script:

/groups/ATLAS/PUBLIC/scripts/pem2pkcs12.sh 

You need your certificate (cern/hellasgrid) to be registered for SVN/TRAC, so contact support@gridNOSPAMPLEASE.auth.gr asking for it (give also your DN). Then follow this:

http://wiki.grid.auth.gr/wiki/bin/view/Groups/ATLAS/TracAndSvnServicesUsage

Code browser: https://trac.hellasgrid.gr/trac/atlas.physics.auth.gr

Basic commands: subversion-cheat-sheet-v1.pdf

TIP: You can also access the svn repository from your personal computer, just install the subversion client for your operating system and follow the same instructions.

Setup SVN to access the official ATLAS repositories

Create this file:

~/.ssh/config:

Host svn.cern.ch
  User inomidis
  GSSAPIAuthentication yes
  GSSAPIDelegateCredentials yes
  Protocol 2
  ForwardX11 no

That should do it. Before trying to access the repository, it really helps to setup AFS client.

Configure emacs editor

This is to enable syntax hi-lighting and to create a goto-line shortcut. Create this file:

~/.emacs:

(custom-set-variables
 '(global-font-lock-mode t nil (font-lock))
)
(global-set-key (kbd "M-g g") 'goto-line) ; Meta+g+g

Useful scripts

All scripts can be found here:

/groups/ATLAS/PUBLIC/scripts

I hope you added this address your $PATH, as recommended above.

AFS

 source afs.sh lxplus_username 

(if you omit lxplus_username, the ui username is picked-up by default)

DQ2

 source dq2.sh 

VOMS-proxy

Simple:

 voms-proxy-init -voms atlas 

For "ever"-lasting proxy:

 proxy-tools 

Where are the data/MC

All can be found under:

 /groups/ATLAS/

You can store your data/mc here, but respect the current structure.

TIP: Keep in mind that when you create a new folder, it's only you that's allowed to read its contents. If you want to make your new folder public to anyone, change permissions like this (works recursively for all included files/folders):

 chmod -R a+r MYFOLDER 

Setup SFRAME

1. Login on lxplus and switch to using the bash shell if you're not already doing so.

 bash

if you want to have a nice looking command prompt insert this in your .bashrc file:

 export PS1="\033[4;30;1m(\w)\033[0m\n\[\033[00;32m\]\u@\h\[\033[00;34m\]_\W$ \[\033[00m\]" 

2. Only first time! Create a working directory for SFRAME

 mkdir SFrame

 cd SFrame

3. Only first time! Download this script, put it under the SFrame directory and run it

 source SframeSetup.sh 

this will checkout and compile the necessary directories and setup the environment for SFrame

4. Only first time! Create your new analysis package

 smultiframe_new_package.sh AnalysisTest 

5a. Only first time! Create your analysis tool under the previous package e.g:

 smultiframe_create_tool.py -n HighEtaTool

5b. Only first time! Create your personal svn area to hold your package

 svn mkdir --parents $SVNUSR/$USER/AnalysisTest/trunk -m "First test import" 

5c. Only first time! Import your packge to your svn area

 cd AnalysisTest 

 svn import . svn+ssh://svn.cern.ch/reps/atlasusr/$USER/AnalysisTest/trunk -m "initial import"

 cd .. 

6. Checkout your code from your repository and compile:

 svn co svn+ssh://svn.cern.ch/reps/atlasusr/$USER/AnalysisTest/trunk/ AnalysisTest 

 cd AnalysisTest 

 make 

7. To run your package do:

 sframe_main config/HighEtaTool_config.xml 

NOTE: Every time you login to a new shell and start work you will only have to do under the SFrame/Analysis directory:

 source scripts/setup_lxplus_532.sh 

Some introduction to doing analysis with SFrame can be found here:

Install AFS client in Linux

Linux users only ! (up to Ubuntu 12.04)

It's very convenient to access AFS from your local machine. You can run lxplus' files locally on your own editor (emacs, vi..) or ROOT This can be done by doing the following:

Open a terminal, become root (with 'sudo -s') and enter:

  
apt-get install module-assistant
module-assistant -t auto-install openafs-modules
apt-get install openafs-client

and when asked, just set the domain to cern.ch and leave the rest as it is.

Then, install the following packages:

apt-get install heimdal-clients
apt-get install krb5-user openafs-krb5

A common troubleshooting action is to restart your client by doing:

sudo /etc/init.d/openafs-client restart

To login, open terminal and type:

kinit (yourusername)@CERN.CH 

aklog 

To access files:

 cd /afs/cern.ch/ (etc...)

-- IoannisNomidis - 16-Dec-2011