Howto aliroot at pdsf

Quick Start Guide

ALICE deploys software via cvmfs and uses modules to initialize the environment. In order to use modules, a module file needs to be prepared and put in a special location for modulefiles. Then one can include the modulefiles via

module use ...

and load a certain module via

module load ...

while

module avail 

gives you an overview of all modules available and

module list 

lists all modules currently loaded. cvmfs modules are available on all pdsf workers and the interactive nodes. In order to use them, include the path to the modulefiles of the cvmfs modules by

module use /cvmfs/alice.cern.ch/x86_64-2.6-gnu-4.1.2/Modules/modulefiles

Now the cvmfs modules are ready to be used. AliPhysics modules can be loaded for example by

module load AliPhysics/vAN-20150504

This will load by default also the corresponding ROOT and AliRoot tag. Other modules like fastjet need to be loaded extra, i.e.

module load fastjet/v3.0.6_1.012

cvmfs provides all ALICE software which is tagged and is always up to date.

Other modules

In order to compile aliroot (i.e. to test something in the master branch which is not yet tagged), other modules like cmake need to be loaded. They are provided by the pads admins, but in a different module path. For cmake do

module load cmake

For your own modules make sure that the module path contains your pdsf user name in order to avoid naming conflicts.

OS environment (via CHOS)

The ALICE environment was setup with Scientific Linux 6.4 Make sure that your $HOME/.chos file consists of a line with: sl64

[pdsf4:ploskon]~
> cat $HOME/.chos
sl64

Don't use anything older than this!

Working with own ALIROOT versions

The installed aliroot versions in cmvfs are read-only. Therefore if you have to make modifications beyond simple macros you have two options.

a) Install your own aliroot version in /project/projectdirs/alice/$USER

This is particularly useful if you have to modify a lot of libraries (modules), or if you need to stay closely with trunk.

b) Use https://twiki.cern.ch/twiki/bin/viewauth/ALICE/MyAliRootPage#Build_libraries_against_external

This package allows you to build libraries against an installed ALIROOT version. There is a readme that explains how to use it. If you have questions, suggestions or problems do not hesitate to contact Constantin.

OCDB

The full alice ocdb is provided via cvmfs. You can find it under

/cvmfs/alice-ocdb.cern.ch/calibration

Inside there are two folders: MC contains the three simulation OCDBs (full, residual, ideal) and data contains the raw OCDB.

Esd file location

All esd files are at /eliza17/alice/esdfiles The text file location that you can use in your analysis is still to be established. At the moment you can find them in /eliza6/alice/marr/fileCollection/

Email list

To be informed about changes on the alice pdsf setup subscribe to the alice-pdsf-users egroup at https://e-groups.cern.ch/e-groups/EgroupsSearch.do

Quick Summary

Note: CHOS is sl64

Include ALICE modules:

module use /cvmfs/alice.cern.ch/x86_64-2.6-gnu-4.1.2/Modules/modulefiles

Load environment:

module load AliPhysics/vAN-20150504 AliEn/v2-19-223 (fastjet/v3.0.6_1.012)

Outdated

The following entries contain outdated (historical) content and shall not be considered anymore:

Quick Start Guide

Please see the sections below for details and debugging information. This quick start guide describes only the basic steps to get access to installed software at NERSC, e.g. from pdsf.

In order to use the existing installations of aliroot and related software, just do:

module use /project/projectdirs/alice/software/modulefiles

This provides access to the modules. You can see a list of available modules using

module avail alice

aliroot modules come with root and geant3, so no need to load them separately. I (Tim) maintain three aliroot versions: train_dev is close to the trunk, updated at least once per week. train_new (approx. 2 weeks) and train_pro (approx. 4 weeks) will provide recent tagged versions of aliroot.

Load them using e.g.

module load alice/aliroot/train_dev

and you should see that aliroot, root and geant3 modules appear in your list of loaded module files. Call

module list

to see the list of loaded modules.

Then load additional modules according to your needs, e.g.

module load alice/fastjet/v2.4.4

or

module load alice/alien/default

Setup modules

Using custom module files

In order to enable usage of your own module files insert a line in .$HOME/.bashrc:

module load use.own

or execute the above statement whenever you need to.

The location of the custom module files is $HOME/privatemodules . Create the directory if necessary and put your modules there.

mkdir -v $HOME/privatemodules

Access to Alice's module files

Link the directory with the modules from Alice in your private modules directory.

cd $HOME/privatemodules
ln -s /project/projectdirs/alice/software/modulefiles/alice

Another, perhaps cleaner, way is to setup the modules via

module use /project/projectdirs/alice/software/modulefiles

The following assumes that this is what you have done.

Using the modules

Here we assume the modules are setup as above.

Try few commands.

module list

Lists modules currently loaded.

[pdsf4:ploskon]~
> module list
Currently Loaded Modulefiles:
  1) SGE/6.2            2) myquota/1.0        3) usg/1.0            4) subversion/1.6.9   5) use.own

module avail

This command will list available modules (both: system wide and your private modules).

[pdsf4:ploskon]~
> module avail

--------------------- /usr/local/pkg/Modules/modulefiles-arch ----------------------
...

---------------------------- /u/ploskon/privatemodules -----------------------------
...

The relevant ALICE specific modules (as of Aug 24, 2010) are:

--------------- /project/projectdirs/alice/software/modulefiles ----------------
alice/alien/v2-18.73        alice/aliroot/v4-20-05-AN
alice/aliroot/v4-18-Release alice/geant3/v1-11
alice/aliroot/v4-19-Release alice/root/v5.26.00c

Setting up alice environment

Setup Aliroot

After following p.1 above the list available modules should show all the ALICE's setup files: The relevant ALICE specific modules (as of Aug 24, 2010) are:

[pdsf4:ploskon]~
> module avail

--------------- /project/projectdirs/alice/software/modulefiles ----------------
alice/alien/v2-18.73        alice/aliroot/v4-20-05-AN
alice/aliroot/v4-18-Release alice/geant3/v1-11
alice/aliroot/v4-19-Release alice/root/v5.26.00c

One-by-one

Now, we can either load things individually (as needed):

module load alice/root/v5.26.00c  alice/geant3/v1-11
module load alice/alien/v2-18.73

and then setup the aliroot environment with your own script or location (you should set ALICE, ALICE_LEVEL, ALICE_ROOT, ALICE_TARGET and PATH, LD_LIBRARY_PATH manually)

or simply load an aliroot module (see below).

Simple setup

Run for example:

module load alice/aliroot/v4-18-Release

which loads appropriate root and geant3 versions along with setting up aliroot environment

subversion and cmake

In order to use svn and cmake (required for aliroot starting from Jan 2011) you can do

module load subversion/1.6.9
module load cmake/2.8.4

Setup alien

The alien module is NOT loaded automatically with aliroot modules. To use alien functionality execute:

module load alice/alien/v2-18.73

Location of OCDB mirror

For 2010 data:

/project/projectdirs/alice/software/OCDBmirror/OCDB/data/2010/OCDB

For simulation (v4-15-Release) - do not use if you do not know why you need it - NOT YET COMPLETE!:

/project/projectdirs/alice/software/OCDBmirror/OCDB/simulation/2008/v4-15-Release

Note: Updated daily from GRID via a cron job 
Dates and times of the updates: 
http://portal.nersc.gov/project/alice/ploskon/alice/OCDBsync/OCDBsync_run_at.log