ALICE Offline Tutorial

1
ALICE Offline Tutorial

• Markus Oldenburg CERN
• Markus.Oldenburg_at_cern.ch
• May 23, 2007 University of São Paulo

2
ALICE Offline Tutorial
based on

• F.Carminati, P.Christakoglou, J.F.Grosse-Oetringha
  us, P.Hristov, A.Peters, P.Saiz
• April 13, 2007 v1.3

3
Part V AliEn installation and Setup
available online at http//cern.ch/Oldenburg -gt
Seminars
4
Outline

• Installation of the AliEn software.
• Authentication Possible problems.
• General description of the shell
• Basic commands.
• Basic functionalities.
• Working with the file catalogue
• Copying files from/to the catalogue.
• File catalogue structure.
• Querying the file catalogue.
• ROOT API
• News on production.

5
Remarks

• Please follow through the tutorial by reading the
  pages, first.
• Only then, do the things described in the Try it
  out sections.
• Reason Only the Try it out sections have the
  correct commands/directories and right version
  numbers, while the explanatory slides might
  differ.

6
Installation Getting the installer
7
Installation Selecting the version
8
Installation Reuse of software
9
Installation Workspace directory
All the installation log files are stored in this
directory! In case of installation problems
please send the error message along with the
install.log file
10
Installation Detecting the platftom
11
Installation Supported platforms
12
Installation Installation directory
13
Installation Selecting installation directory
14
Installation Overwriting files
15
Installation Selecting packages
16
Installation Progress bar
17
Installation Final window
18
Installation Directory structure
19
Installation Try it out

• Download the alien installer from
  http//alien.cern.ch.
• Make the file executable.
• Run the installer.
• Select v2-13
• Platform should be i686.
• Select installation directory.
• Select the following packages
• Client
• gShell
• ROOT
• xrootd

20
ROOT compilation with AliEn support

• If not done already during your local ROOT
  installation, you have to enable the AliEn
  support in ROOT.
• Go to your ROOTSYS directory and modify the
  cfg.sh script (see next slide).
• Execute the cfg.sh script. This will reconfigure
  ROOT.
• Recompile ROOT (do make and make map in
  ROOTSYS). This will take only a few minutes.

21
Root Configuration Example script Put the
following lines in a file called cfg.sh.
!/bin/sh ALIEN_ROOTltprefixgt/alien ./configure
\ --with-pythia6-uscoreSINGLE \
--enable-cern --enable-rfio \
--enable-mathmore --enable-mathcore
--enable-roofit \ --enable-asimage
--enable-minuit2 \ --enable-alien \
--with-alien-incdirALIEN_ROOT/api/include \
--with-alien-libdirALIEN_ROOT/api/lib
The last three lines are the important ones,
which you might have ignored/commented out
during the ROOT installation! Change the second
line (ALIEN_ROOT) to point to your AliEn
installation directory.
22
Authentication Preparing the certificates
23
Authentication Changes in env. variables
This should be your user name!
24
Authentication Getting a GRID proxy
25
Authentication Getting an AliEn token
26
Authentication Authentication problems I

• Globus related
• Permissions on HOME/.globus/userkey.pem are not
  private to the user chmod 400 userkey.pem
• Your certificate authority is exotic and not
  known to the server.
• Your certificate has expired.
• Clock skew
• Your local computer time is in the future with
  respect to the server's time.
• Your local computer time is more in the past than
  the certificate life time.

27
Authentication Authentication problems II

• alien-token-init related
• You have not gone through all 5 steps of the
  AliEn user registration.
• You have not given the AliEn user name as an
  argument to the token-init command and your local
  user name is not identical to the AliEn user
  name.
• The script wants to bootstrap the installation
  but you don't have write permissions on the
  installation path Avoid bootstrapping by
  setting the GSHELL_ROOT environment variable.

28
Authentication Try it out

• Upload your certificates to your machines
• Store them under e.g /afs/cern.ch/user/ltugt/ltusergt
  /.globus/
• Check that the key file is read only.
• Get the setenv.sh file from the agenda (see
  below) and place it under e.g. /home/ltusergt/
• Modify it accordingly/
• Source it to set up your environment variables.
• Get a valid grid proxy.
• Get a valid alien token.
• Check the information of your proxy/token by
  typing
• grid-proxy-info
• alien-token-info
• Agenda http//indico.cern.ch/materialDisplay.py?c
  ontribId2ampmaterialId0ampconfId14960

29
Shell (1) Accessing the shell
30
Shell (1) Basic commands I
Tab completion working!!!
31
Shell (1) Basic commands II
32
Shell (1) Basic commands III
33
Shell (1) whereis command
34
Shell (1) Viewing the files I
35
Shell (1) Viewing the files II
36
Shell (1) Editing files
Define your preferred editor via the variable
EDITOR 'emacs' 'emacs -nw' 'xemacs' 'xemacs
-nw' 'pico' 'vi' (DEFAULT) 'vim' The file is
temporary in /tmp on your local disk and then is
uploaded once you exit the editor!
37
Shell (1) Clear old versions
38
Shell (1) Try it out

• Access the alien shell.
• Check your user name by typing whoami.
• List the contents of your home directory.
• Check the working directory.
• Create the following directory structure in your
  AliEn space
• HOME/bin (if it is not there)
• HOME/Tutorial/ESD and HOME/Tutorial/Kine
• HOME/Tutorial/ESD/output and HOME/Tutorial/Kine/
  output
• Get the information of the file (whereis)
  /alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/A
  liAnalysisTaskPt.cxx

39
Shell (2) Copying files from/to the F.C.
40
Shell (2) File catalogue structure

• The path name will be
• for real data /data/ltYeargt/ltAcceleratorPeriodgt/
  ltRunNumbergt/
• for simulated data /sim/ltYeargt/ltProductionTypegt/lt
  RunNumbergt/
• Subdirectories will be called
• Raw/
• cond/
• reco/ltPassXgt/ESD/
• reco/ltPassXgt/AOD/
• File names will look like this
  ltxxxxgt.AliESD.root
• For further information see
• http//indico.cern.ch/conferenceDisplay.py?confId
  3280
• http//cern.ch/Oldenburg/MetaData/MetaData.doc

MARKUS OLDENBURG AN INTERNAL NOTE IS ON THE WAY
41
Shell (2) Querying the F.C. I
alienshalice 1 find -x pp /alice/cern.ch/use
r/p/pchrista/production/pp/PDC06/ AliESDs.root
gt pp.xml
Redirect the output to the xml collection.
42
Shell (2) Querying the F.C. II
alienshalice 1 find -x pp /alice/data/2008/L
HC08a//reco/Pass3/ AliESDs.root
Runcollision_systempp and Runstoplt"2008-03-
20 102033" and Runstartgt"2008-03-19" gt pp.xml
43
Shell (2) Try it out I

• Create the following directory structure locally
• HOME/AliEn/PDC06/001 and HOME/AliEn/PDC06/002
• HOME/AliEn/Tags
• HOME/AliEn/Local/ESD and HOME/AliEn/Local/Kine
• HOME/AliEn/Interactive/ESD and
  HOME/AliEn/Interactive/Kine
• HOME/AliEn/Batch
• Copy all the files under the AliEn directory
  /alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/
  to your local HOME/AliEn/Local/ESD
• ESD.par - ANALYSIS.par - AliAnalysisTaskPt.h -
  AliAnalysisTaskPt.cxx - runESDAnalysis.C -
  demoLocal.C

44
Shell (2) Try it out II

• Copy all the AliEn files under /alice/cern.ch/user
  /p/pchrist/Tutorial/LOCAL/Kine/ to your local
  HOME/AliEn/Local/Kine
• AliAnalysisTaskRLPt.h - AliAnalysisTaskRLPt.cxx -
  runKineAnalysis.C - demoLocal.C
• Copy all the AliEn files under /alice/cern.ch/user
  /p/pchrist/Tutorial/TAGS/ to your local
  HOME/AliEn/Tags
• ESD.par - CreateTags.C - runTagCreator.C
• Copy all the root files under /alice/cern.ch/user/
  p/pchrist/Tutorial/PDC06/001/ and
  /alice/cern.ch/user/p/pchrist/Tutorial/PDC06/002/
  your local HOME/AliEn/PDC06/001 and
  HOME/AliEn/PDC06/002

45
Shell (2) Try it out III

• Query the f.c. and get all the tag files
  (.tag.root) under /alice/cern.ch/user/p/pchrist/
  Tutorial/PDC06/
• Get the output on your terminal.
• Redirect the results to the tag10.xml collection
  the output will not be stored in your AliEn
  working directory but rather in your local
  working directory.
• Repeat the previous exercise limiting the number
  of output files to 5 (find -l 5 ...).
• Query the f.c. for all the Merged.tag.root
  files under /alice/cern.ch/user/p/pchrist/Tutoria
  l/PDC06/ and redirect the result to the tag.xml
  file.
• Exit the shell and copy the xml to your local
  HOME/AliEn/Interactive/ESD and
  HOME/AliEn/Interactive/Kine.

46
Production status ( available data)

• pp min bias _at_ 14TeV --- NEvents 50M
• /alice/cern.ch/user/a/aliprod/prod2006_2/output_pp
  / (5.4M)
• /alice/sim/2006/pp_minbias/ (45M)
• /alice/sim/2006/pp_x_vertex_1cm/ (1.1M)
• /alice/sim/2006/pp_x_vertex_05cm/ (1.1M)
• /alice/sim/2006/pp_minbias_full/ (1.1M)
• All RUNS have been tested and merged tag files
  have been produced at the RUN level for all
  RunIds.
• pp min bias _at_ 900GeV --- NEvents 200K
• /alice/sim/2006/pp_900GeV/
• All RUNS have been tested and merged tag files
  have been produced at the RUN level for all
  RunIds.
• Muon events --- NEvents 864K
• /alice/sim/2006/muon/ (64K)
• /alice/sim/2006/muon_signle/ (800K)

47
ROOT ROOT API
48
ROOT - Connecting
49
ROOT Accessing a GRID file
50
ROOT Problems with gcc versions

• AliEn software comes with a precompiled library
  with gcc 3.2.3 which is also shipped with AliEn.
• In the latest AliEn version 2.13 it will check
  automatically for the correct versions (and
  recompile if necessary). The following steps are
  not necessary in this case.
• Otherwise if you are using a different version
  of gcc (check it with gcc v) then do the
  following
• cd ALIEN/api/src
• ./recompile.gapi
• cd ALIEN/api/lib
• Copy all the libgapiUI.so.2 files to the
  libgapiUI.so.3
• Or link your gcc to the version shipped with
  AliEn and compile everything with this.

51
ROOT Try it out

• Get the alienroot and alienaliroot executables
  from indico ( the agenda, see slide 28).
• Store them under your /home/ltusernamegt/bin
• Open the setenv.sh file, use it in your own
  .bashrc (or wherever you set your environment).
• You might want to modify the path definition
• export PATHPATHALIEN/api/binALIEN/globus/bin
  /home/ltusernamegt/bin
• Once finished, get a token, type alienroot and
  then
• root 0 TGridConnect(alien//)
• If it works without error messages you have
  installed everything successfully. If not then go
  back to the previous pages of this tutorial.

52
BACKUP

• AliEn Exercises

53
ROOT Try it out I

• Go to your ROOTSYS and change the cfg.sh file
  change the location where you installed the grid
  software (it should be e.g. /home/trn2301/alice/Al
  iEn).
• Source the script and then type make and make
  map.
• Write the following script, name it alienroot,
  make it executable, place it in your HOME/bin
  directory and add it in your PATH.

!/bin/bash export ALIEN/home/trn2301/alien expor
t ROOTSYS/home/trn2301/root export
PATHROOTSYS/binPATH export LD_LIBRARY_PATHRO
OTSYS/libLD_LIBRARY_PATHALIEN/api/lib if
-e /tmp/gclient_env_UID then source
/tmp/gclient_env_UID root.exe fi
54

• AliEn Tutorial
• Solutions
• Panos Christakoglou
• University of Athens - CERN

55
Installation Try it out

• For the solutions, we assume that the user name
  is trn2301 with the following attributes
• Local home directory /home/trn2301
• Alien home directory /alice/cern.ch/user/t/trn23
  01
• change the names accordingly to match your case!!!

1. Download the installer from the web bash
wget http//alien.cern.ch/alien-installer 2.
Make the file executable bash chmod ax
alien-installer 3. Run the installer bash
./alien-installer
bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file
56
Authentication Try it out
1. Upload your certificates to your
machines bash scp -r ltusernamegt_at_lxplus.cern.ch
/.globus . 2. Get a valid token bash
alien-token-init trn2301 //the username is
optional and should be put if the local username
isn't the same as the alien one 3. Get your
proxy info bash grid-proxy-info 4. Get your
token info bash alien-token-info
bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file
57
Shell (1) Try it out
1. Access the shell bash aliensh 2. Check
your user name aliensh whoami 3. List the
contents of your alien directory aliensh
ls 4. Check the alien working direcory aliensh
pwd 5. Create the following directory structure
in your AliEn space HOME/bin (if it is not
there) - HOME/Tutorial/ESD and
HOME/Tutorial/Kine -HOME/Tutorial/ESD/output
and HOME/Tutorial/Kine/output aliensh mkdir
-p bin Tutorial/ESD/output Tutorial/Kine/output 6
. Get the information of the file
/alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/A
liAnalysisTaskPt.cxx aliensh whereis
/alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/A
liAnalysisTaskPt.cxx
bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file
58
Shell (2) Try it out I
1. Create the following directory structure
locally HOME/AliEn/PDC06/001 and
HOME/AliEn/PDC06/002 - HOME/AliEn/Tags -
HOME/AliEn/Local/ESD and HOME/AliEn/Local/Kine
- HOME/AliEn/Interactive/ESD and
HOME/AliEn/Interactive/Kine - HOME/AliEn/Batch
bash mkdir -p HOME/AliEn/PDC06/001
HOME/AliEn/PDC06/002 HOME/AliEn/Tags
HOME/AliEn/Local/ESD HOME/AliEn/Local/Kine
HOME/AliEn/Interactive/ESD HOME/AliEn/Interactiv
e/Kine HOME/AliEn/Batch 2. Copy all the files
under the AliEn directory /alice/cern.ch/user/p/pc
hrist/Tutorial/LOCAL/ESD/ to your local
HOME/AliEn/Local/ESD aliensh cp
/alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/
file/home/trn2301/AliEn/Local/
bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file
59
Shell (2) Try it out II

• 3. Copy all the AliEn files under
  /alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/Kine/
  to your local HOME/AliEn/Local/Kine
• aliensh cp /alice/cern.ch/user/p/pchrist/Tutori
  al/LOCAL/Kine/ file/home/trn2301/AliEn/Local/
• 4. Copy all the AliEn files under
  /alice/cern.ch/user/p/pchrist/Tutorial/TAGS/ to
  your local HOME/AliEn/Tags
• aliensh cp /alice/cern.ch/user/p/pchrist/Tutori
  al/TAGS/ file/home/trn2301/AliEn/
• 5. Copy all the root files under
  /alice/cern.ch/user/p/pchrist/Tutorial/PDC06/001/
  and /alice/cern.ch/user/p/pchrist/Tutorial/PDC06/0
  02/ your local HOME/AliEn/PDC06/001 and
  HOME/AliEn/PDC06/002
• aliensh cp /alice/cern.ch/user/p/pchrist/Tutori
  al/PDC06/001/ file/home/trn2301/AliEn/PDC06/
• aliensh cp /alice/cern.ch/user/p/pchrist/Tutori
  al/PDC06/002/ file/home/trn2301/AliEn/PDC06/

bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file
60
Shell (2) Try it out III
7. Query the f.c. and get all the tag files
(.tag.root) under /alice/cern.ch/user/p/pchrist/
Tutorial/PDC06/ aliensh find -x tag
/alice/cern.ch/user/p/pchrist/Tutorial/PDC06/
tag.root (Get the output on your
terminal) aliensh find -x tag
/alice/cern.ch/user/p/pchrist/Tutorial/PDC06/
tag.root gt tag10.xml (Redirect the results to
the tag10.xml collection) 8. Repeat the previous
exercise limiting the number of output files to 5
(find -l 5 ...). aliensh find -l 5 -x tag
/alice/cern.ch/user/p/pchrist/Tutorial/PDC06/
tag.root gt tag10.xml 9. Query the f.c. for all
the Merged.tag.root files under
/alice/cern.ch/user/p/pchrist/Tutorial/PDC06/ and
redirect the result to the tag.xml
file. aliensh find -x tag /alice/cern.ch/user/p
/pchrist/Tutorial/PDC06/ Mergedtag.root gt
tag.xml 10. Exit the shell and copy the xml to
your local HOME/AliEn/Interactive/ESD and
HOME/AliEn/Interactive/Kine. aliensh
exit bash cp tag.xml HOME/AliEn/Interactive/ES
D bash cp tag.xml HOME/AliEn/Interactive/Kine
bash --gt Your local bash shell aliensh --gt
Your alien bash shell No notation --gt inside a
file