Obtain your source code
The starting point for these exercises is the analysis template called AliAnalysisTaskMyTask. To obtain the source code of this analysis, choose one of the following two options:
- Clone the Git repository. Programmers use version control systems when developing their code. You will also use version control (in our case through Git) when you are contributing to the ALICE code base. So why not start with Git right now? You can clone the example task repository, which you can find it on here, by typing, in a terminal
git clone https://github.com/rbertens/ALICE_analysis_tutorial.git
This will clone the remote repository, so that you have access to a carbon copy of the full repository on your local computer.
- A more robust approach to working with Git, is creating a remote fork of a certain repository, and working on this fork. For this, you will need to open a GitHub [https://github.com/] account (which you will need in any case if you want to contribute to ALICE software). If you have a GitHub account, you create a fork of the example task repository by surfing here and clicking on fork at the top right of the screen. If you have forked the repository, you can proceed to cloning it on your laptop in the way as explained in option 1; this then allows you to develop the code, and push commits to your own fork
Whichever approach you chose, the end result should be that you have stored these files on your laptop. One word of caution: the path in which you store these files cannot contain spaces! E.g. /home/my task/ will not work, use /home/my_task/ .
A first look at your task
As a start, just take a look at code that makes up the task:
You will see that the code is extensively documented. Can you tell
which function is called for each event?
where are the output histogram defined?
where are the output histogram filled?
Remember, that for now, the name ‘AliAnalysisTaskMyTask’ doesn’t sound so bad, but when you develop a task ‘in real life’, make sure to give it a meaningful name, that explains what the task is aimed at.
Obtain input data
To run your own analysis task, you will also need to download a file that contains reconstructed collisions. This input file is called AliAOD.root, short for Analysis Object Data. In the following steps, will assume that we are looking at Pb-Pb data that was taken in 2015. You can also choose to run on data from a different period or collision system.
Source your environment
We will get the data form the ALICE file catalogue. To access the file catalogue, you will need to use xjalienfs or xalienfs packages and have a valid Grid certificate. This means that, at this point, we will assume that you have built all the ALICE software (see our build manual for that ).
Load your ALICE environment as explained here, e.g. by doing
alienv enter AliPhysics::latest
You should see which module files are currently loaded, e.g.
1) BASE/1.0 2) AliEn-Runtime/v2-19-le-49 3) OpenSSL/v1.0.2o-9 4) Python-modules/1.0-11 5) XRootD/v4.11.1-14 6) ROOT/v6-18-04-alice2-1 7) boost/v1.70.0-6 8) cgal/4.6.3-5 9) fastjet/v3.2.1_1.024-alice3-21 10) Vc/1.4.1-5 11) xjalienfs/1.0.6-2 12) JAliEn-ROOT/0.6.0-2 13) AliRoot/master-1 14) RooUnfold/V02-00-01-alice4-25 15) treelite/a7a0839-2 16) KFParticle/alice-v1.1-1-9 17) AliPhysics/latest 12) AliPhysics/latest Use alienv list to list loaded modules. Use exit to exit this environment.
The module xjalienfs is now available, which is what we will use to get our data.
Get a valid token (optional)
You can skip this step if you are using JAliEn. JAliEn clients create the token automatically, but you can still run alien-token-init to refresh it manually.
The ALICE file catalogue is only accessible if you are an ALICE member.
If you are using AliEn-ROOT-Legacy or ROOT5, then you first need to authenticate yourself and obtain a token
where username is your CERN username. You should be prompted to provide your PEM pass phrase, which is not the same as your CERN password unless you set them to be the same yourself.
If all goes well, you will see something like
[AliPhysics/latest] ~/sw $> alien-token-init rbertens --------------------------------------------------------------- Setting central config: =============================================================== export alien_API_SERVER_LIST="pcapiserv03.cern.ch:10000|pcapiserv08.cern.ch:10000|" export TERMINFO=/usr/share/terminfo =============================================================== --------------------------------------------------------------- Setting closest site to: CERN =============================================================== Using X509_CERT_DIR=/home/rbertens/sw/slc7_x86-64/AliEn-Runtime/v2-19-le-1/globus/share/certificates ********************************************************************************* Attention: You don't have a valid grid proxy ( or less than 1 hour left ) - doing xrdgsiproxy init for you ... ********************************************************************************* Enter PEM pass phrase: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ file : /tmp/x509up_u1000 issuer : /DC=ch/DC=cern/OU=Organic Units/OU=Users/CN=rbertens/CN=718303/CN=Redmer Alexander Bertens subject : /DC=ch/DC=cern/OU=Organic Units/OU=Users/CN=rbertens/CN=718303/CN=Redmer Alexander Bertens/CN=708532894 path length : 0 bits : 512 time left : 12h:0m:0s ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ => Trying to connect to Server  root://pcapiserv08.cern.ch:10000 as User rbertens /alice/cern.ch/user/a/alidaq/ /alice/cern.ch/user/r/rbertens/ Your identity: rbertens Creating token ..................................... Done Your token is valid until: Wed Nov 1 13:21:18 2017
For comparison, here is the output from the JAlien alien-token-init
[AliPhysics/latest] ~ > alien-token-init INFO: JAliEn client automatically creates tokens, alien-token-init is deprecated DN >>> /C=ch/O=AliEn2/CN=Users/CN=nhardi/OU=nhardi ISSUER >>> /C=ch/O=AliEn/CN=AliEn CA BEGIN >>> 2020-03-26 10:06:05 EXPIRE >>> 2020-04-26 08:16:48
Open the AliEn shell
You can now enter the alice environment shell by typing
Once you type this command, a the alice environment shell is loaded, and you should see
[AliPhysics/latest] ~ > alien.py Welcome to the ALICE GRID support mail: email@example.com AliEn[nhardi]:/alice/cern.ch/user/n/nhardi/ >
The AliEn legacy shell aliensh and JAliEn shell alien.py are very similar. The command prompt for aliensh shell looks like this:
[AliPhysics/latest] ~/sw $> aliensh [ aliensh 1.0.140x (C) ARDA/Alice: Andreas.Joachim.Peters@cern.ch/Derek.Feichtinger@cern.ch] aliensh:[alice]  /alice/cern.ch/user/r/rbertens/ >
This shell works a lot like a normal unix shell, but it is not - not all commands that you expect to find are defined.
Move to the directory where the data we are looking for is stored
and copy the AliAOD.root file that is inside this folder to your local hard drive by doing
cp AliAOD.root file:.
Note the syntax of the copy command, here we tell to copy the remote file AliAOD.root to our own laptop by specifying file:. .
JAliEn and AliEn shell documentation
You can find more information about the alien.py shell at jalien.docs.cern.ch. Reference documentation for the legacy AliEn shell is available at alien.web.cern.ch.
If for some reason this does not work for you - no fear. You can ask a colleague to provide a file for you, or send a mail to our mailing lists if you are having trouble with access.