may 23, 20071 alice offline tutorial markus oldenburg – cern [email protected] may 23, 2007...
TRANSCRIPT
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May 23, 2007 1
ALICE Offline Tutorial
Markus Oldenburg – [email protected]
May 23, 2007 – University of São Paulo
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May 23, 2007 2
ALICE Offline Tutorial
F.Carminati, P.Christakoglou, J.F.Grosse-Oetringhaus, P.Hristov, A.Peters, P.Saiz
April 13, 2007 – v1.3
based on:
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May 23, 2007 3
Part V: AliEn installation and Setup
available online at: http://cern.ch/Oldenburg -> Seminars
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May 23, 2007 4
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.
Outline
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May 23, 2007 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.
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May 23, 2007 6
Installation – Getting the installer
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May 23, 2007 7
Installation – Selecting the version
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May 23, 2007 8
Installation – Reuse of software
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May 23, 2007 9
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
Installation – Workspace directory
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May 23, 2007 10
Installation – Detecting the platftom
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May 23, 2007 11
Installation – Supported platforms
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May 23, 2007 12
Installation – Installation directory
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May 23, 2007 13
Installation – Selecting installation directory
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May 23, 2007 14
Installation – Overwriting files
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May 23, 2007 15
Installation – Selecting packages
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May 23, 2007 16
Installation – Progress bar
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Installation – Final window
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ROOT application
API client
Common libraries
Globus toolkit
Gcc compiler
Installation – Directory structure
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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
Installation – Try it out
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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 $ROOTSYS). This will take only a few minutes.
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Root Configuration: Example script Put the following lines in a file called cfg.sh. #!/bin/sh
ALIEN_ROOT=<prefix>/alien
./configure \ --with-pythia6-uscore=SINGLE \ --enable-cern --enable-rfio \ --enable-mathmore --enable-mathcore --enable-roofit \ --enable-asimage --enable-minuit2 \ --enable-alien \ --with-alien-incdir=${ALIEN_ROOT}/api/include \ --with-alien-libdir=${ALIEN_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.
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Certificates should be stored under $HOME/.globus
Globus enforces privacy on your private key!(chmod 400)
Authentication – Preparing the certificates
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Authentication – Changes in env. variables
This should be your user name!
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Authentication command – Username is optional (default is the local username)
Put certificate password
Happens every 24 hours
Authentication – Getting a GRID proxy
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Authentication – Getting an AliEn token
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Globus related:Permissions on $HOME/.globus/userkey.pem are not private to the user – chmod 400 userkey.pemYour 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.
Authentication – Authentication problems I
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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.
Authentication – Authentication problems II
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Upload your certificates to your machines:Store them under e.g: /afs/cern.ch/user/<u>/<user>/.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/<user>/
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?contribId=2&materialId=0&confId=14960
Authentication – Try it out
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Standard bash shell with grid comandsMain bash features are available.Not all shell helper programs are available.Some local commands (like ls, cat etc) are overwritten with the corresponding GRID commands.File/path tab completion in the virtual GRID directory.
Message of the day.
Shell (1) – Accessing the shell
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Tab completion working!!!
Shell (1) – Basic commands I
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Shell (1) – Basic commands II
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Shell (1) – Basic commands III
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Shell (1) – whereis command
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Shell (1) – Viewing the files I
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Shell (1) – Viewing the files II
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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!
Shell (1) – Editing files
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Shell (1) – Clear old versions
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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/AliAnalysisTaskPt.cxx
Shell (1) – Try it out
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GOLDEN RULEIf you want to access your local directory structure while you
are in the shell you should start by having the prefix “file:”
e.g: cp file:/home/pchrist/gshell.sh gshell.sh
Shell (2) – Copying files from/to the F.C.
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MARKUS OLDENBURG AN INTERNAL NOTE
IS ON THE WAY
Shell (2) – File catalogue structure
The path name will be:for ‘real’ data: /data/<Year>/<AcceleratorPeriod>/<RunNumber>/for simulated data: /sim/<Year>/<ProductionType>/<RunNumber>/
Subdirectories will be called:Raw/cond/ reco/<PassX>/ESD/reco/<PassX>/AOD/…
File names will look like this: <xxxx>.AliESD.root
For further information see:http://indico.cern.ch/conferenceDisplay.py?confId=3280http://cern.ch/Oldenburg/MetaData/MetaData.doc
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aliensh:[alice] [1] find -x pp
/alice/cern.ch/user/p/pchrista/production/pp/PDC06/*
AliESDs.root > pp.xml
Redirect the output
to
the xml collection.
Shell (2) – Querying the F.C. I
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aliensh:[alice] [1] find -x pp
/alice/data/2008/LHC08a/*/reco/Pass3/*
AliESDs.root
Run:collision_system=”pp” and
Run:stop<"2008-03-20 10:20:33" and
Run:start>"2008-03-19" > pp.xml
Shell (2) – Querying the F.C. II
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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
Shell (2) – Try it out I
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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
Shell (2) – Try it out II
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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/Tutorial/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.
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p+p min bias @ 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.
p+p min bias @ 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)
Production status (= available data)
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ROOT – ROOT API
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ROOT - Connecting
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ROOT – Accessing a GRID file
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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.gapicd $ALIEN/api/libCopy all the libgapiUI.so.2* files to the libgapiUI.so.3*
Or link your gcc to the version shipped with AliEn and compile everything with this.
ROOT – Problems with gcc versions
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Get the alienroot and alienaliroot executables from indico (= the agenda, see slide 28).
Store them under your /home/<username>/bin
Open the setenv.sh file, use it in your own .bashrc (or wherever you set your environment).You might want to modify the path definition:
export PATH=$PATH:$ALIEN/api/bin:$ALIEN/globus/bin:/home/<username>/bin
Once finished, get a token, type alienroot and then:
root [0] TGrid::Connect(“alien://”);
If it works without error messages you have installed everything successfully. If not then go back to the previous pages of this tutorial.
ROOT – Try it out
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BACKUP
AliEn Exercises
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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/AliEn).
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 $PATH. #!/bin/bashexport ALIEN=/home/trn2301/alienexport ROOTSYS=/home/trn2301/rootexport PATH=$ROOTSYS/bin:$PATHexport LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH:$ALIEN/api/lib
if [ -e /tmp/gclient_env_$UID ]; thensource /tmp/gclient_env_$UID;root.exe $*
fi
ROOT – Try it out I
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AliEn Tutorial
Solutions
Panos Christakoglou
University of Athens - CERN
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1. Download the installer from the web[bash]$ wget http://alien.cern.ch/alien-installer
2. Make the file executable[bash]$ chmod a+x alien-installer
3. Run the installer[bash]$ ./alien-installer
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/trn2301
change the names accordingly to match your case!!!
Installation – Try it out
[bash]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
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1. Upload your certificates to your machines[bash]$ scp -r <username>@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]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
Authentication – Try it out
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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/AliAnalysisTaskPt.cxx
[aliensh]$ whereis /alice/cern.ch/user/p/pchrist/Tutorial/LOCAL/ESD/AliAnalysisTaskPt.cxx
[bash]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
Shell (1) – Try it out
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[bash]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
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/Interactive/Kine $HOME/AliEn/Batch
2. Copy all the files under the AliEn directory /alice/cern.ch/user/p/pchrist/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/
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[bash]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
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/Tutorial/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/Tutorial/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/PDC06/002/ your local $HOME/AliEn/PDC06/001 and $HOME/AliEn/PDC06/002[aliensh]$ cp /alice/cern.ch/user/p/pchrist/Tutorial/PDC06/001/ file:/home/trn2301/AliEn/PDC06/[aliensh]$ cp /alice/cern.ch/user/p/pchrist/Tutorial/PDC06/002/ file:/home/trn2301/AliEn/PDC06/
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[bash]$ --> Your local bash shell[aliensh]$ --> Your alien bash shellNo notation --> inside a file
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 > 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 > 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/* *Merged*tag.root > 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 $HOME/AliEn/Interactive/ESD[bash]$ cp tag.xml $HOME/AliEn/Interactive/Kine